4YBB

High-resolution structure of the Escherichia coli ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6I7V


Literature

High-resolution structure of the Escherichia coli ribosome.

Noeske, J.Wasserman, M.R.Terry, D.S.Altman, R.B.Blanchard, S.C.Cate, J.H.

(2015) Nat Struct Mol Biol 22: 336-341

  • DOI: 10.1038/nsmb.2994
  • Primary Citation of Related Structures:  
    4YBB

  • PubMed Abstract: 
  • Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation have remained poorly understood. Moreover, the functions of modifications to ribosomal RNA and ribosomal proteins have also been unclear ...

    Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation have remained poorly understood. Moreover, the functions of modifications to ribosomal RNA and ribosomal proteins have also been unclear. Here we present the structure of the Escherichia coli 70S ribosome at 2.4-Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and it suggests how solvation contributes to ribosome integrity and function as well as how the conformation of ribosomal protein uS12 aids in mRNA decoding. This structure helps to explain the phylogenetic conservation of key elements of the ribosome, including post-transcriptional and post-translational modifications, and should serve as a basis for future antibiotic development.


    Organizational Affiliation

    1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA. [2] Department of Chemistry, University of California, Berkeley, Berkeley, California, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB], W [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], X [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], Y [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], Z [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], AA [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], BA [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], CA [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], DA [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], EA [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], FA [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], GA [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], HA [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], IA [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], JA [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], KA [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], LA [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], MA [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], NA [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], OA [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], PA [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: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2SA [auth CC], XB [auth DC]271Escherichia 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: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3TA [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: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4UA [auth CE], ZB [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: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5VA [auth CF], AC [auth DF]177Escherichia 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: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6WA [auth CG], BC [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: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9XA [auth CH], CC [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: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11YA [auth CJ], EC [auth DJ]134Escherichia 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: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13ZA [auth CK], FC [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: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14AB [auth CL], GC [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: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15BB [auth CM], HC [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: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16CB [auth CN], IC [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: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17DB [auth CO], JC [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: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18EB [auth CP], KC [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: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19FB [auth CQ], LC [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: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20GB [auth CR], MC [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: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21HB [auth CS], NC [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: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22IB [auth CT], OC [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: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23JB [auth CU], PC [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: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24KB [auth CV], QC [auth DV]102Escherichia 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: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25LB [auth CW], RC [auth DW]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27MB [auth CX], SC [auth DX]76Escherichia 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: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28NB [auth CY], TC [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: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29OB [auth CZ], UC [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: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30PB [auth C0], VC [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: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32QB [auth C1], WC [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: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33RB [auth C2], XC [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: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34SB [auth C3], YC [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: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35TB [auth C4], ZC [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: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36UB [auth C5], AD [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: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3YB [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: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10DC [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], V [auth BA]1534Escherichia coli K-12
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsLengthOrganismImage
23S rRNAQA [auth CA]2904Escherichia coli K-12
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsLengthOrganismImage
5S rRNARA [auth CB], WB [auth DB]120Escherichia coli K-12
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 53
MoleculeChainsLengthOrganismImage
23S rRNAVB [auth DA]2903Escherichia coli K-12
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

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

Download Ideal Coordinates CCD File 
EW [auth DA], GV [auth DA], LX [auth DQ], NX [auth DR], QX [auth DS], RH [auth BA], SF [auth AA]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GUN (Subject of Investigation/LOI)
Query on GUN

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

Download Ideal Coordinates CCD File 
CW [auth DA] , FW [auth DA] , NW [auth DA] , PX [auth DS] , RV [auth DA] , UX [auth DU] , XX [auth D1] , YX [auth D3] , 
CW [auth DA], FW [auth DA], NW [auth DA], PX [auth DS], RV [auth DA], UX [auth DU], XX [auth D1], YX [auth D3], ZU [auth DA]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

Download Ideal Coordinates CCD File 
AV [auth DA], MW [auth DA], UV [auth DA], WU [auth DA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
IW [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 
DV [auth DA] , DX [auth DE] , EX [auth DE] , FV [auth DA] , FX [auth DK] , IX [auth DN] , RX [auth DS] , SV [auth DA] , 
DV [auth DA], DX [auth DE], EX [auth DE], FV [auth DA], FX [auth DK], IX [auth DN], RX [auth DS], SV [auth DA], SX [auth DT], TF [auth AA], TX [auth DT], VV [auth DA], YF [auth AA], YV [auth DA]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BG [auth AL] , GW [auth DA] , GX [auth DL] , JX [auth DP] , KX [auth DQ] , MV [auth DA] , NV [auth DA] , OV [auth DA] , 
BG [auth AL], GW [auth DA], GX [auth DL], JX [auth DP], KX [auth DQ], MV [auth DA], NV [auth DA], OV [auth DA], OW [auth DA], PW [auth DA], ZX [auth D3]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

Download Ideal Coordinates CCD File 
AW [auth DA] , BV [auth DA] , BW [auth DA] , CV [auth DA] , HW [auth DA] , HX [auth DM] , IV [auth DA] , JW [auth DA] , 
AW [auth DA], BV [auth DA], BW [auth DA], CV [auth DA], HW [auth DA], HX [auth DM], IV [auth DA], JW [auth DA], KW [auth DA], LW [auth DA], TV [auth DA], UF [auth AA], VF [auth AA], WF [auth AA], XF [auth AA], XU [auth DA]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
AX [auth DB] , BX [auth DB] , CX [auth DB] , DW [auth DA] , HV [auth DA] , KV [auth DA] , LV [auth DA] , OX [auth DR] , 
AX [auth DB], BX [auth DB], CX [auth DB], DW [auth DA], HV [auth DA], KV [auth DA], LV [auth DA], OX [auth DR], VX [auth D0], WV [auth DA], WX [auth D1], XV [auth DA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
EV [auth DA], JV [auth DA], PV [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] , AH [auth BA] , AI [auth CA] , AJ [auth CA] , AK [auth CA] , AL [auth CA] , AM [auth CA] , 
AE [auth AA], AF [auth AA], AH [auth BA], AI [auth CA], AJ [auth CA], AK [auth CA], AL [auth CA], AM [auth CA], AN [auth CA], AO [auth DA], AP [auth DA], AQ [auth DA], AR [auth DA], AS [auth DA], AT [auth DA], AU [auth DA], BD [auth AA], BE [auth AA], BF [auth AA], BH [auth BA], BI [auth CA], BJ [auth CA], BK [auth CA], BL [auth CA], BM [auth CA], BN [auth CA], BO [auth DA], BP [auth DA], BQ [auth DA], BR [auth DA], BS [auth DA], BT [auth DA], BU [auth DA], CD [auth AA], CE [auth AA], CF [auth AA], CG [auth BA], CH [auth BA], CI [auth CA], CJ [auth CA], CK [auth CA], CL [auth CA], CM [auth CA], CN [auth CA], CO [auth DA], CP [auth DA], CQ [auth DA], CR [auth DA], CS [auth DA], CT [auth DA], CU [auth DA], DD [auth AA], DE [auth AA], DF [auth AA], DG [auth BA], DH [auth BA], DI [auth CA], DJ [auth CA], DK [auth CA], DL [auth CA], DM [auth CA], DN [auth CA], DO [auth DA], DP [auth DA], DQ [auth DA], DR [auth DA], DS [auth DA], DT [auth DA], DU [auth DA], ED [auth AA], EE [auth AA], EF [auth AA], EG [auth BA], EH [auth BA], EI [auth CA], EJ [auth CA], EK [auth CA], EL [auth CA], EM [auth CA], EN [auth CA], EO [auth DA], EP [auth DA], EQ [auth DA], ER [auth DA], ES [auth DA], ET [auth DA], EU [auth DA], FD [auth AA], FE [auth AA], FF [auth AA], FG [auth BA], FH [auth BA], FI [auth CA], FJ [auth CA], FK [auth CA], FL [auth CA], FM [auth CA], FN [auth CA], FO [auth DA], FP [auth DA], FQ [auth DA], FR [auth DA], FS [auth DA], FT [auth DA], FU [auth DA], GD [auth AA], GE [auth AA], GF [auth AA], GG [auth BA], GH [auth BA], GI [auth CA], GJ [auth CA], GK [auth CA], GL [auth CA], GM [auth CA], GN [auth CA], GO [auth DA], GP [auth DA], GQ [auth DA], GR [auth DA], GS [auth DA], GT [auth DA], GU [auth DA], HD [auth AA], HE [auth AA], HF [auth AA], HG [auth BA], HH [auth BA], HI [auth CA], HJ [auth CA], HK [auth CA], HL [auth CA], HM [auth CA], HN [auth CA], HO [auth DA], HP [auth DA], HQ [auth DA], HR [auth DA], HS [auth DA], HT [auth DA], HU [auth DA], ID [auth AA], IE [auth AA], IF [auth AA], IG [auth BA], IH [auth BA], II [auth CA], IJ [auth CA], IK [auth CA], IL [auth CA], IM [auth CA], IN [auth CA], IO [auth DA], IP [auth DA], IQ [auth DA], IR [auth DA], IS [auth DA], IT [auth DA], IU [auth DA], JD [auth AA], JE [auth AA], JF [auth AA], JG [auth BA], JH [auth BA], JI [auth CA], JJ [auth CA], JK [auth CA], JL [auth CA], JM [auth CA], JN [auth CA], JO [auth DA], JP [auth DA], JQ [auth DA], JR [auth DA], JS [auth DA], JT [auth DA], JU [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 DA], KP [auth DA], KQ [auth DA], KR [auth DA], KS [auth DA], KT [auth DA], KU [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], LO [auth DA], LP [auth DA], LQ [auth DA], LR [auth DA], LS [auth DA], LT [auth DA], LU [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], MO [auth DA], MP [auth DA], MQ [auth DA], MR [auth DA], MS [auth DA], MT [auth DA], MU [auth DA], MX [auth DR], 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], NO [auth DA], NP [auth DA], NQ [auth DA], NR [auth DA], NS [auth DA], NT [auth DA], NU [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], OO [auth DA], OP [auth DA], OQ [auth DA], OR [auth DA], OS [auth DA], OT [auth DA], OU [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 DA], PP [auth DA], PQ [auth DA], PR [auth DA], PS [auth DA], PT [auth DA], PU [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], QO [auth DA], QP [auth DA], QQ [auth DA], QR [auth DA], QS [auth DA], QT [auth DA], QU [auth DA], QW [auth DA], RD [auth AA], RE [auth AA], RF [auth AA], RG [auth BA], RI [auth CA], RJ [auth CA], RK [auth CA], RL [auth CA], RM [auth CA], RN [auth CB], RO [auth DA], RP [auth DA], RQ [auth DA], RR [auth DA], RS [auth DA], RT [auth DA], RU [auth DA], RW [auth DB], SD [auth AA], SE [auth AA], SG [auth BA], SH [auth CA], SI [auth CA], SJ [auth CA], SK [auth CA], SL [auth CA], SM [auth CA], SN [auth CB], SO [auth DA], SP [auth DA], SQ [auth DA], SR [auth DA], SS [auth DA], ST [auth DA], SU [auth DA], SW [auth DB], TD [auth AA], TE [auth AA], TG [auth BA], TH [auth CA], TI [auth CA], TJ [auth CA], TK [auth CA], TL [auth CA], TM [auth CA], TN [auth CB], TO [auth DA], TP [auth DA], TQ [auth DA], TR [auth DA], TS [auth DA], TT [auth DA], TU [auth DA], TW [auth DB], UD [auth AA], UE [auth AA], UG [auth BA], UH [auth CA], UI [auth CA], UJ [auth CA], UK [auth CA], UL [auth CA], UM [auth CA], UN [auth C3], UO [auth DA], UP [auth DA], UQ [auth DA], UR [auth DA], US [auth DA], UT [auth DA], UU [auth DA], UW [auth DB], VD [auth AA], VE [auth AA], VG [auth BA], VH [auth CA], VI [auth CA], VJ [auth CA], VK [auth CA], VL [auth CA], VM [auth CA], VO [auth DA], VP [auth DA], VQ [auth DA], VR [auth DA], VS [auth DA], VT [auth DA], VU [auth DA], VW [auth DB], WD [auth AA], WE [auth AA], WG [auth BA], WH [auth CA], WI [auth CA], WJ [auth CA], WK [auth CA], WL [auth CA], WM [auth CA], WN [auth DA], WO [auth DA], WP [auth DA], WQ [auth DA], WR [auth DA], WS [auth DA], WT [auth DA], WW [auth DB], XD [auth AA], XE [auth AA], XG [auth BA], XH [auth CA], XI [auth CA], XJ [auth CA], XK [auth CA], XL [auth CA], XM [auth CA], XN [auth DA], XO [auth DA], XP [auth DA], XQ [auth DA], XR [auth DA], XS [auth DA], XT [auth DA], XW [auth DB], YD [auth AA], YE [auth AA], YG [auth BA], YH [auth CA], YI [auth CA], YJ [auth CA], YK [auth CA], YL [auth CA], YM [auth CA], YN [auth DA], YO [auth DA], YP [auth DA], YQ [auth DA], YR [auth DA], YS [auth DA], YT [auth DA], YW [auth DB], ZD [auth AA], ZE [auth AA], ZF [auth AA], ZG [auth BA], ZH [auth CA], ZI [auth CA], ZJ [auth CA], ZK [auth CA], ZL [auth CA], ZM [auth CA], ZN [auth DA], ZO [auth DA], ZP [auth DA], ZQ [auth DA], ZR [auth DA], ZS [auth DA], ZT [auth DA], ZW [auth DB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
D2T
Query on D2T
GA [auth BL], L [auth AL]L-PEPTIDE LINKINGC5 H9 N O4 SASP
4D4
Query on 4D4
CB [auth CN], IC [auth DN]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
MEQ
Query on MEQ
YB [auth DD]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.17α = 90
b = 433.89β = 90
c = 624.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references