5J8A

Structure of the E coli 70S ribosome with the U1052G mutation in 16S rRNA bound to tigecycline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors.

Cocozaki, A.I.Altman, R.B.Huang, J.Buurman, E.T.Kazmirski, S.L.Doig, P.Prince, D.B.Blanchard, S.C.Cate, J.H.Ferguson, A.D.

(2016) Proc Natl Acad Sci U S A 113: 8188-8193

  • DOI: 10.1073/pnas.1605127113
  • Primary Citation of Related Structures:  
    5IT8, 5J5B, 5J8A, 5J88, 5J7L, 5J91, 5JC9

  • PubMed Abstract: 
  • Mutations conferring resistance to translation inhibitors often alter the structure of rRNA. Reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly reduces the clinical utility of these agents ...

    Mutations conferring resistance to translation inhibitors often alter the structure of rRNA. Reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly reduces the clinical utility of these agents. The translation inhibitors negamycin and tetracycline interfere with tRNA binding to the aminoacyl-tRNA site on the small 30S ribosomal subunit. However, two negamycin resistance mutations display unexpected differential antibiotic susceptibility profiles. Mutant U1060A in 16S Escherichia coli rRNA is resistant to both antibiotics, whereas mutant U1052G is simultaneously resistant to negamycin and hypersusceptible to tetracycline. Using a combination of microbiological, biochemical, single-molecule fluorescence transfer experiments, and X-ray crystallography, we define the specific structural defects in the U1052G mutant 70S E. coli ribosome that explain its divergent negamycin and tetracycline susceptibility profiles. Unexpectedly, the U1052G mutant ribosome possesses a second tetracycline binding site that correlates with its hypersusceptibility. The creation of a previously unidentified antibiotic binding site raises the prospect of identifying similar phenomena in antibiotic-resistant pathogens in the future.


    Organizational Affiliation

    Structure and Biophysics, Discovery Sciences, AstraZeneca Pharmaceuticals, Waltham, MA 02451; Andrew.Ferguson@astrazeneca.com.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB], CA [auth BB]224Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Explore P0A7V0 
Go to UniProtKB:  P0A7V0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC], DA [auth BC]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Explore P0A7V3 
Go to UniProtKB:  P0A7V3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD], EA [auth BD]205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Explore P0A7V8 
Go to UniProtKB:  P0A7V8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE], FA [auth BE]155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Explore P0A7W1 
Go to UniProtKB:  P0A7W1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF], GA [auth BF]106Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
Explore P02358 
Go to UniProtKB:  P02358
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG], HA [auth BG]151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
UniProt
Find proteins for P02359 (Escherichia coli (strain K12))
Explore P02359 
Go to UniProtKB:  P02359
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH], IA [auth BH]129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Explore P0A7W7 
Go to UniProtKB:  P0A7W7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI], JA [auth BI]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Explore P0A7X3 
Go to UniProtKB:  P0A7X3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ], KA [auth BJ]99Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Explore P0A7R5 
Go to UniProtKB:  P0A7R5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK], LA [auth BK]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Explore P0A7R9 
Go to UniProtKB:  P0A7R9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL], MA [auth BL]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Explore P0A7S3 
Go to UniProtKB:  P0A7S3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM], NA [auth BM]114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Explore P0A7S9 
Go to UniProtKB:  P0A7S9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN], OA [auth BN]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12))
Explore P0AG59 
Go to UniProtKB:  P0AG59
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO], PA [auth BO]88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Explore P0ADZ4 
Go to UniProtKB:  P0ADZ4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP], QA [auth BP]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Explore P0A7T3 
Go to UniProtKB:  P0A7T3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ], RA [auth BQ]80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
Explore P0AG63 
Go to UniProtKB:  P0AG63
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR], SA [auth BR]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Explore P0A7T7 
Go to UniProtKB:  P0A7T7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS], TA [auth BS]79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Explore P0A7U3 
Go to UniProtKB:  P0A7U3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT], UA [auth BT]86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Explore P0A7U7 
Go to UniProtKB:  P0A7U7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth AU], VA [auth BU]56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
Explore P68679 
Go to UniProtKB:  P68679
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32V [auth C1], WA [auth D1]56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Explore P0A7N4 
Go to UniProtKB:  P0A7N4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33W [auth C2], XA [auth D2]51Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Explore P0A7N9 
Go to UniProtKB:  P0A7N9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34X [auth C3], YA [auth D3]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Explore P0A7P5 
Go to UniProtKB:  P0A7P5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35Y [auth C4], ZA [auth D4]64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Explore P0A7Q1 
Go to UniProtKB:  P0A7Q1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36Z [auth C5], AB [auth D5]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Explore P0A7Q6 
Go to UniProtKB:  P0A7Q6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth C0], BB [auth D0]58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
Explore P0AG51 
Go to UniProtKB:  P0AG51
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2DB [auth CC], GB [auth DC]272Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
Explore P60422 
Go to UniProtKB:  P60422
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3EB [auth CD]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
Explore P60438 
Go to UniProtKB:  P60438
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3HB [auth DD]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
Explore P60438 
Go to UniProtKB:  P60438
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4IB [auth CE], DC [auth DE]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
Explore P60723 
Go to UniProtKB:  P60723
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5JB [auth CF], EC [auth DF]178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
UniProt
Find proteins for P62399 (Escherichia coli (strain K12))
Explore P62399 
Go to UniProtKB:  P62399
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6KB [auth CG], FC [auth DG]176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12))
Explore P0AG55 
Go to UniProtKB:  P0AG55
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9LB [auth CH], GC [auth DH]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Explore P0A7R1 
Go to UniProtKB:  P0A7R1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11MB [auth CJ], HC [auth DJ]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Explore P0A7J7 
Go to UniProtKB:  P0A7J7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13NB [auth CK], IC [auth DK]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
Explore P0AA10 
Go to UniProtKB:  P0AA10
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14OB [auth CL], JC [auth DL]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Explore P0ADY3 
Go to UniProtKB:  P0ADY3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15PB [auth CM], KC [auth DM]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
Explore P02413 
Go to UniProtKB:  P02413
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16QB [auth CN], LC [auth DN]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Explore P0ADY7 
Go to UniProtKB:  P0ADY7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17RB [auth CO], MC [auth DO]125Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12))
Explore P0AG44 
Go to UniProtKB:  P0AG44
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18SB [auth CP], NC [auth DP]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12))
Explore P0C018 
Go to UniProtKB:  P0C018
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19TB [auth CQ], OC [auth DQ]114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Explore P0A7K6 
Go to UniProtKB:  P0A7K6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20UB [auth CR], PC [auth DR]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Explore P0A7L3 
Go to UniProtKB:  P0A7L3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21VB [auth CS], QC [auth DS]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
Explore P0AG48 
Go to UniProtKB:  P0AG48
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22WB [auth CT], RC [auth DT]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
Explore P61175 
Go to UniProtKB:  P61175
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23XB [auth CU], SC [auth DU]93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Explore P0ADZ0 
Go to UniProtKB:  P0ADZ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24YB [auth CV], TC [auth DV]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
Explore P60624 
Go to UniProtKB:  P60624
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25ZB [auth CW], UC [auth DW]94Escherichia coli O139:H28 str. E24377AMutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
Explore P68919 
Go to UniProtKB:  P68919
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27AC [auth CX], VC [auth DX]83Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Explore P0A7L8 
Go to UniProtKB:  P0A7L8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28BC [auth CY], WC [auth DY]77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Explore P0A7M2 
Go to UniProtKB:  P0A7M2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29CC [auth CZ], XC [auth DZ]62Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
Go to UniProtKB:  P0A7M6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10YC [auth DI]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
UniProt
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Explore P0A7J3 
Go to UniProtKB:  P0A7J3
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA [auth AA], BA1534Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsLengthOrganismImage
5S rRNACB, ZC [auth DB]120Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsLengthOrganismImage
23S rRNAFB [auth CA]2904Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 55
MoleculeChainsLengthOrganismImage
23S rRNAAD [auth DA]2904Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T1C
Query on T1C

Download Ideal Coordinates CCD File 
CG [auth AA], WH [auth BA]TIGECYCLINE
C29 H41 N5 O8
FPZLLRFZJZRHSY-HJYUBDRYSA-P
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
IX [auth DA], RW [auth DA]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
SF [auth AA], TO [auth DQ], VH [auth BA], VO [auth DR], WX [auth DA], XO [auth DS], ZW [auth DA]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GUN
Query on GUN

Download Ideal Coordinates CCD File 
RX [auth DA]GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
BP [auth DU] , CI [auth D1] , EI [auth D3] , FY [auth DA] , JX [auth DA] , SW [auth DA] , UX [auth DA] , WO [auth DS] , 
BP [auth DU],  CI [auth D1],  EI [auth D3],  FY [auth DA],  JX [auth DA],  SW [auth DA],  UX [auth DA],  WO [auth DS],  XX [auth DA]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

Download Ideal Coordinates CCD File 
EY [auth DA], MX [auth DA], PW [auth DA], TW [auth DA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
AY [auth DA]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
AP [auth DT] , KX [auth DA] , LO [auth DE] , MO [auth DE] , NO [auth DK] , NX [auth DA] , QO [auth DN] , QX [auth DA] , 
AP [auth DT],  KX [auth DA],  LO [auth DE],  MO [auth DE],  NO [auth DK],  NX [auth DA],  QO [auth DN],  QX [auth DA],  TF [auth AA],  WW [auth DA],  YF [auth AA],  YO [auth DS],  YW [auth DA],  ZO [auth DT]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
DI [auth D1] , EG [auth AL] , FI [auth D3] , FX [auth DA] , GX [auth DA] , GY [auth DA] , HY [auth DA] , OO [auth DL] , 
DI [auth D1],  EG [auth AL],  FI [auth D3],  FX [auth DA],  GX [auth DA],  GY [auth DA],  HY [auth DA],  OO [auth DL],  RO [auth DP],  SO [auth DQ],  YX [auth DA]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

Download Ideal Coordinates CCD File 
BX [auth DA] , BY [auth DA] , CY [auth DA] , DY [auth DA] , LX [auth DA] , PP [auth DA] , QW [auth DA] , SX [auth DA] , 
BX [auth DA],  BY [auth DA],  CY [auth DA],  DY [auth DA],  LX [auth DA],  PP [auth DA],  QW [auth DA],  SX [auth DA],  TX [auth DA],  UF [auth AA],  UW [auth DA],  VF [auth AA],  VW [auth DA],  WF [auth AA],  XF [auth AA],  ZX [auth DA]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DG [auth AB], FG [auth C5], GI [auth D5]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AX [auth DA] , BI [auth D1] , CP [auth DB] , DX [auth DA] , EX [auth DA] , MP [auth DB] , NP [auth DB] , OP [auth DB] , 
AX [auth DA],  BI [auth D1],  CP [auth DB],  DX [auth DA],  EX [auth DA],  MP [auth DB],  NP [auth DB],  OP [auth DB],  OX [auth DA],  PX [auth DA],  QP [auth DA],  VX [auth DA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
CX [auth DA], HX [auth DA], XW [auth DA]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth AA] , AF [auth AA] , AG [auth AA] , AH [auth BA] , AI [auth BA] , AJ [auth CA] , AK [auth CA] , AL [auth CA] , 
AE [auth AA],  AF [auth AA],  AG [auth AA],  AH [auth BA],  AI [auth BA],  AJ [auth CA],  AK [auth CA],  AL [auth CA],  AM [auth CA],  AN [auth CA],  AO [auth CA],  AQ [auth DA],  AR [auth DA],  AS [auth DA],  AT [auth DA],  AU [auth DA],  AV [auth DA],  AW [auth DA],  BD [auth AA],  BE [auth AA],  BF [auth AA],  BG [auth AA],  BH [auth BA],  BJ [auth CA],  BK [auth CA],  BL [auth CA],  BM [auth CA],  BN [auth CA],  BO [auth CA],  BQ [auth DA],  BR [auth DA],  BS [auth DA],  BT [auth DA],  BU [auth DA],  BV [auth DA],  BW [auth DA],  CD [auth AA],  CE [auth AA],  CF [auth AA],  CH [auth BA],  CJ [auth CA],  CK [auth CA],  CL [auth CA],  CM [auth CA],  CN [auth CA],  CO [auth CA],  CQ [auth DA],  CR [auth DA],  CS [auth DA],  CT [auth DA],  CU [auth DA],  CV [auth DA],  CW [auth DA],  DD [auth AA],  DE [auth AA],  DF [auth AA],  DH [auth BA],  DJ [auth CA],  DK [auth CA],  DL [auth CA],  DM [auth CA],  DN [auth CA],  DO [auth CA],  DP [auth DB],  DQ [auth DA],  DR [auth DA],  DS [auth DA],  DT [auth DA],  DU [auth DA],  DV [auth DA],  DW [auth DA],  ED [auth AA],  EE [auth AA],  EF [auth AA],  EH [auth BA],  EJ [auth CA],  EK [auth CA],  EL [auth CA],  EM [auth CA],  EN [auth CA],  EO [auth CA],  EP [auth DB],  EQ [auth DA],  ER [auth DA],  ES [auth DA],  ET [auth DA],  EU [auth DA],  EV [auth DA],  EW [auth DA],  FD [auth AA],  FE [auth AA],  FF [auth AA],  FH [auth BA],  FJ [auth CA],  FK [auth CA],  FL [auth CA],  FM [auth CA],  FN [auth CA],  FO [auth CA],  FP [auth DB],  FQ [auth DA],  FR [auth DA],  FS [auth DA],  FT [auth DA],  FU [auth DA],  FV [auth DA],  FW [auth DA],  GD [auth AA],  GE [auth AA],  GF [auth AA],  GG [auth BA],  GH [auth BA],  GJ [auth CA],  GK [auth CA],  GL [auth CA],  GM [auth CA],  GN [auth CA],  GO [auth CA],  GP [auth DB],  GQ [auth DA],  GR [auth DA],  GS [auth DA],  GT [auth DA],  GU [auth DA],  GV [auth DA],  GW [auth DA],  HD [auth AA],  HE [auth AA],  HF [auth AA],  HG [auth BA],  HH [auth BA],  HI [auth CB],  HJ [auth CA],  HK [auth CA],  HL [auth CA],  HM [auth CA],  HN [auth CA],  HO [auth CA],  HP [auth DB],  HQ [auth DA],  HR [auth DA],  HS [auth DA],  HT [auth DA],  HU [auth DA],  HV [auth DA],  HW [auth DA],  ID [auth AA],  IE [auth AA],  IF [auth AA],  IG [auth BA],  IH [auth BA],  II [auth CB],  IJ [auth CA],  IK [auth CA],  IL [auth CA],  IM [auth CA],  IN [auth CA],  IO [auth CA],  IP [auth DB],  IQ [auth DA],  IR [auth DA],  IS [auth DA],  IT [auth DA],  IU [auth DA],  IV [auth DA],  IW [auth DA],  IY [auth DA],  JD [auth AA],  JE [auth AA],  JF [auth AA],  JG [auth BA],  JH [auth BA],  JI [auth CB],  JJ [auth CA],  JK [auth CA],  JL [auth CA],  JM [auth CA],  JN [auth CA],  JO [auth CA],  JP [auth DB],  JQ [auth DA],  JR [auth DA],  JS [auth DA],  JT [auth DA],  JU [auth DA],  JV [auth DA],  JW [auth DA],  JY [auth DA],  KD [auth AA],  KE [auth AA],  KF [auth AA],  KG [auth BA],  KH [auth BA],  KI [auth CA],  KJ [auth CA],  KK [auth CA],  KL [auth CA],  KM [auth CA],  KN [auth CA],  KO [auth DD],  KP [auth DB],  KQ [auth DA],  KR [auth DA],  KS [auth DA],  KT [auth DA],  KU [auth DA],  KV [auth DA],  KW [auth DA],  KY [auth DA],  LD [auth AA],  LE [auth AA],  LF [auth AA],  LG [auth BA],  LH [auth BA],  LI [auth CA],  LJ [auth CA],  LK [auth CA],  LL [auth CA],  LM [auth CA],  LN [auth CA],  LP [auth DB],  LQ [auth DA],  LR [auth DA],  LS [auth DA],  LT [auth DA],  LU [auth DA],  LV [auth DA],  LW [auth DA],  LY [auth DA],  MD [auth AA],  ME [auth AA],  MF [auth AA],  MG [auth BA],  MH [auth BA],  MI [auth CA],  MJ [auth CA],  MK [auth CA],  ML [auth CA],  MM [auth CA],  MN [auth CA],  MQ [auth DA],  MR [auth DA],  MS [auth DA],  MT [auth DA],  MU [auth DA],  MV [auth DA],  MW [auth DA],  ND [auth AA],  NE [auth AA],  NF [auth AA],  NG [auth BA],  NH [auth BA],  NI [auth CA],  NJ [auth CA],  NK [auth CA],  NL [auth CA],  NM [auth CA],  NN [auth CA],  NQ [auth DA],  NR [auth DA],  NS [auth DA],  NT [auth DA],  NU [auth DA],  NV [auth DA],  NW [auth DA],  OD [auth AA],  OE [auth AA],  OF [auth AA],  OG [auth BA],  OH [auth BA],  OI [auth CA],  OJ [auth CA],  OK [auth CA],  OL [auth CA],  OM [auth CA],  ON [auth CA],  OQ [auth DA],  OR [auth DA],  OS [auth DA],  OT [auth DA],  OU [auth DA],  OV [auth DA],  OW [auth DA],  PD [auth AA],  PE [auth AA],  PF [auth AA],  PG [auth BA],  PH [auth BA],  PI [auth CA],  PJ [auth CA],  PK [auth CA],  PL [auth CA],  PM [auth CA],  PN [auth CA],  PO [auth DM],  PQ [auth DA],  PR [auth DA],  PS [auth DA],  PT [auth DA],  PU [auth DA],  PV [auth DA],  QD [auth AA],  QE [auth AA],  QF [auth AA],  QG [auth BA],  QH [auth BA],  QI [auth CA],  QJ [auth CA],  QK [auth CA],  QL [auth CA],  QM [auth CA],  QN [auth CA],  QQ [auth DA],  QR [auth DA],  QS [auth DA],  QT [auth DA],  QU [auth DA],  QV [auth DA],  RD [auth AA],  RE [auth AA],  RF [auth AA],  RG [auth BA],  RH [auth BA],  RI [auth CA],  RJ [auth CA],  RK [auth CA],  RL [auth CA],  RM [auth CA],  RN [auth CA],  RP [auth DA],  RQ [auth DA],  RR [auth DA],  RS [auth DA],  RT [auth DA],  RU [auth DA],  RV [auth DA],  SD [auth AA],  SE [auth AA],  SG [auth BA],  SH [auth BA],  SI [auth CA],  SJ [auth CA],  SK [auth CA],  SL [auth CA],  SM [auth CA],  SN [auth CA],  SP [auth DA],  SQ [auth DA],  SR [auth DA],  SS [auth DA],  ST [auth DA],  SU [auth DA],  SV [auth DA],  TD [auth AA],  TE [auth AA],  TG [auth BA],  TH [auth BA],  TI [auth CA],  TJ [auth CA],  TK [auth CA],  TL [auth CA],  TM [auth CA],  TN [auth CA],  TP [auth DA],  TQ [auth DA],  TR [auth DA],  TS [auth DA],  TT [auth DA],  TU [auth DA],  TV [auth DA],  UD [auth AA],  UE [auth AA],  UG [auth BA],  UH [auth BA],  UI [auth CA],  UJ [auth CA],  UK [auth CA],  UL [auth CA],  UM [auth CA],  UN [auth CA],  UO [auth DR],  UP [auth DA],  UQ [auth DA],  UR [auth DA],  US [auth DA],  UT [auth DA],  UU [auth DA],  UV [auth DA],  VD [auth AA],  VE [auth AA],  VG [auth BA],  VI [auth CA],  VJ [auth CA],  VK [auth CA],  VL [auth CA],  VM [auth CA],  VN [auth CA],  VP [auth DA],  VQ [auth DA],  VR [auth DA],  VS [auth DA],  VT [auth DA],  VU [auth DA],  VV [auth DA],  WD [auth AA],  WE [auth AA],  WG [auth BA],  WI [auth CA],  WJ [auth CA],  WK [auth CA],  WL [auth CA],  WM [auth CA],  WN [auth CA],  WP [auth DA],  WQ [auth DA],  WR [auth DA],  WS [auth DA],  WT [auth DA],  WU [auth DA],  WV [auth DA],  XD [auth AA],  XE [auth AA],  XG [auth BA],  XH [auth BA],  XI [auth CA],  XJ [auth CA],  XK [auth CA],  XL [auth CA],  XM [auth CA],  XN [auth CA],  XP [auth DA],  XQ [auth DA],  XR [auth DA],  XS [auth DA],  XT [auth DA],  XU [auth DA],  XV [auth DA],  YD [auth AA],  YE [auth AA],  YG [auth BA],  YH [auth BA],  YI [auth CA],  YJ [auth CA],  YK [auth CA],  YL [auth CA],  YM [auth CA],  YN [auth CA],  YP [auth DA],  YQ [auth DA],  YR [auth DA],  YS [auth DA],  YT [auth DA],  YU [auth DA],  YV [auth DA],  ZD [auth AA],  ZE [auth AA],  ZF [auth AA],  ZG [auth BA],  ZH [auth BA],  ZI [auth CA],  ZJ [auth CA],  ZK [auth CA],  ZL [auth CA],  ZM [auth CA],  ZN [auth CA],  ZP [auth DA],  ZQ [auth DA],  ZR [auth DA],  ZS [auth DA],  ZT [auth DA],  ZU [auth DA],  ZV [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
D2T
Query on D2T
L [auth AL], MA [auth BL]L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
HB [auth DD]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
LC [auth DN], QB [auth CN]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.72α = 90
b = 435.19β = 90
c = 622.83γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Structure summary
  • Version 1.2: 2016-08-03
    Changes: Database references