4WT8

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Bactobolin A Binds to a Site on the 70S Ribosome Distinct from Previously Seen Antibiotics.

Amunts, A.Fiedorczuk, K.Truong, T.T.Chandler, J.Peter Greenberg, E.Ramakrishnan, V.

(2015) J.Mol.Biol. 427: 753-755

  • DOI: 10.1016/j.jmb.2014.12.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ribosome is the target of a large number of antibiotics. Here, we report a 3.4-Å-resolution crystal structure of bactobolin A bound to 70S ribosome-tRNA complex. The antibiotic binds at a previously unseen site in the 50S subunit and displaces tR ...

    The ribosome is the target of a large number of antibiotics. Here, we report a 3.4-Å-resolution crystal structure of bactobolin A bound to 70S ribosome-tRNA complex. The antibiotic binds at a previously unseen site in the 50S subunit and displaces tRNA bound at the P-site. It thus likely has a similar mechanism of action as blasticidin S despite binding to a different site. The structure also rationalizes previously identified resistance mutations.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB20QH, UK.,MRC Laboratory of Molecular Biology, Cambridge CB20QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.,Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AA, BA
234Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
238Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, BD
208Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, BE
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, BF
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, BG
155Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, BH
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, BI
127Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, BJ
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, BK
119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, BL
124Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, BM
124Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
AN, BN
60Thermus aquaticusMutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, BO
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, BP
83Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AR, BR
99Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AS, BS
70Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AT, BT
78Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AU, BU
99Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
AW, BW
24Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
BC
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
CA
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
CB, DB
271Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
CC, DC
204Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
CD, DD
207Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
CE, DE
181Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
CF, DF
159Thermus aquaticusMutation(s): 0 
Gene Names: rplF
Find proteins for A0A0M9ADP1 (Thermus aquaticus)
Go to UniProtKB:  A0A0M9ADP1
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
CI, DI
145Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal L10 protein
CJ, DJ
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
CM, DM
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
CN, DN
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
CO, DO
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
CP, DP
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
CQ, DQ
117Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
CR, DR
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
CS, DS
137Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
CT, DT
117Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
CU, DU
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
CW
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
CX, DX
92Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
CY, DY
100Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
CZ, DZ
176Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
Ca, Da
84Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
CH, DH
93Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmB
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72G84
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
CK, DK
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP6
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
CL, DL
59Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
C5, D5
30Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
C6, D6
59Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
C7, D7
44Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
C8, D8
48Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
C9, D9
63Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
C0, D0
36Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR2
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
DA
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
DW
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 1
MoleculeChainsLengthOrganism
mRNAA29Thermus thermophilus HB8
Entity ID: 22
MoleculeChainsLengthOrganism
RNA (1504-MER)Ab,Bb1504Thermus thermophilus HB8
Entity ID: 23
MoleculeChainsLengthOrganism
mRNAB210Thermus thermophilus HB8
Entity ID: 25
MoleculeChainsLengthOrganism
A site tNA, E site tNAC2,C3,D376Thermus thermophilus HB8
Entity ID: 26
MoleculeChainsLengthOrganism
P site trNAC477Thermus thermophilus HB8
Entity ID: 58
MoleculeChainsLengthOrganism
23S rRNA (2899-MER)C1,D12899Thermus thermophilus HB8
Entity ID: 59
MoleculeChainsLengthOrganism
5S rRNA (119-MER)Cs,Ds119Thermus thermophilus HB8
Entity ID: 60
MoleculeChainsLengthOrganism
tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')D220Mitsuaria sp. 67
Entity ID: 61
MoleculeChainsLengthOrganism
tRNA (76-MER)D476Mitsuaria sp. 67
Entity ID: 64
MoleculeChainsLengthOrganism
DNA (55-MER)DV55Mitsuaria sp. 67
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download SDF File 
Download CCD File 
Ab, Bb
PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C1, D1
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3V6
Query on 3V6

Download SDF File 
Download CCD File 
C1, D1
Bactobolin A
C15 H22 Cl2 N2 O5
RREHSYIRMHYJHY-RQGKCFPDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
CA, CJ, DA, DJ
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 214.210α = 90.00
b = 457.450β = 90.00
c = 639.660γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Other
  • Version 1.3: 2018-07-18
    Type: Advisory, Data collection, Derived calculations