Brand  (β version)

PDB ID: 4V7M

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Ligands
Code Name Style Show Link
MG Magnesium ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
Code Name Show
KBE Beta-lysine
DPP Diaminopropanoic acid
UAL (2z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
MYN (2s)-amino[(4r)-2-amino-1,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 4V7M   PDBj   RCSB PDB   PDBe
Header : RIBOSOME/ANTIBIOTIC
Title : The structures of Capreomycin bound to the 70S ribosome.
Release Data : 2014-07-09
Compound :
mol_id molecule chains
1 16S ribosomal RNA AA,CA
mol_id molecule chains
2 30S ribosomal protein S2 AB,CB
mol_id molecule chains
3 30S ribosomal protein S3 AC,CC
mol_id molecule chains
4 30S ribosomal protein S4 AD,CD
mol_id molecule chains
5 30S ribosomal protein S5 AE,CE
mol_id molecule chains synonym
6 30S ribosomal protein S6 AF,CF TS9
mol_id molecule chains
7 30S ribosomal protein S7 AG,CG
mol_id molecule chains
8 30S ribosomal protein S8 AH,CH
mol_id molecule chains
9 30S ribosomal protein S9 AI,CI
mol_id molecule chains
10 30S ribosomal protein S10 AJ,CJ
mol_id molecule chains
11 30S ribosomal protein S11 AK,CK
mol_id molecule chains
12 30S ribosomal protein S12 AL,CL
mol_id molecule chains
13 30S ribosomal protein S13 AM,CM
mol_id molecule chains
14 30S ribosomal protein S14 AN,CN
mol_id molecule chains
15 30S ribosomal protein S15 AO,CO
mol_id molecule chains
16 30S ribosomal protein S16 AP,CP
mol_id molecule chains
17 30S ribosomal protein S17 AQ,CQ
mol_id molecule chains
18 30S ribosomal protein S18 AR,CR
mol_id molecule chains
19 30S ribosomal protein S19 AS,CS
mol_id molecule chains
20 30S ribosomal protein S20 AT,CT
mol_id molecule chains synonym
21 30S ribosomal protein Thx AU,CU S31
mol_id molecule chains
22 RNA (5'-R(*AP*AP*AP*AP*AP*GP*GP*AP*AP*AP*UP*A*AP*AP*AP*AP*UP*GP*CP*AP*GP*UP*UP*CP*AP*AP*UP*CP*UP*A)-3') AV,CV
other_details: mRNA
mol_id molecule chains
23 tRNA-Gln AW,CW
other_details: A-site tRNA Gln
mol_id molecule chains
24 tRNA-Met AX
other_details: P-site tRNA fMet
mol_id molecule chains
25 tRNA-Gln AY,CY
other_details: E-site tRNA Gln
mol_id molecule chains
26 capreomycin IA AZ,CZ
mol_id molecule chains
27 23S ribosomal RNA BA,DA
mol_id molecule chains
28 5S ribosomal RNA BB,DB
mol_id molecule chains
29 50S ribosomal protein L1 BC,DC
mol_id molecule chains
30 50S ribosomal protein L2 BD,DD
mol_id molecule chains
31 50S ribosomal protein L3 BE,DE
mol_id molecule chains synonym
32 50S ribosomal protein L4 BF,DF L1e
mol_id molecule chains
33 50S ribosomal protein L5 BG,DG
mol_id molecule chains
34 50S ribosomal protein L6 BH,DH
mol_id molecule chains
35 50S ribosomal protein L9 BI,DI
mol_id molecule chains
36 50S ribosomal protein L13 BN,DN
mol_id molecule chains
37 50S ribosomal protein L14 BO,DO
mol_id molecule chains
38 50S ribosomal protein L15 BP,DP
mol_id molecule chains
39 50S ribosomal protein L16 BQ,DQ
mol_id molecule chains
40 50S ribosomal protein L17 BR,DR
mol_id molecule chains synonym
41 50S ribosomal protein L18 BS,DS TL24
mol_id molecule chains
42 50S ribosomal protein L19 BT,DT
mol_id molecule chains
43 50S ribosomal protein L20 BU,DU
mol_id molecule chains
44 50S ribosomal protein L21 BV,DV
mol_id molecule chains
45 50S ribosomal protein L22 BW,DW
mol_id molecule chains
46 50S ribosomal protein L23 BX,DX
mol_id molecule chains
47 50S ribosomal protein L24 BY,DY
mol_id molecule chains synonym
48 50S ribosomal protein L25 BZ,DZ TL5
mol_id molecule chains
49 50S ribosomal protein L27 B0,D0
mol_id molecule chains
50 50S ribosomal protein L28 B1,D1
mol_id molecule chains
51 50S ribosomal protein L29 B2,D2
mol_id molecule chains
52 50S ribosomal protein L30 B3,D3
mol_id molecule chains
53 50S ribosomal protein L31 B4,D4
mol_id molecule chains
54 50S ribosomal protein L32 B5,D5
mol_id molecule chains
55 50S ribosomal protein L33 B6,D6
mol_id molecule chains
56 50S ribosomal protein L34 B7,D7
mol_id molecule chains
57 50S ribosomal protein L35 B8,D8
mol_id molecule chains synonym
58 50S ribosomal protein L36 B9,D9 Ribosomal protein B
mol_id molecule chains
59 RNA (77-MER) CX
other_details: P-site tRNA fMet
Source :
mol_id organism_scientific
1 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
2 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
3 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
4 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
5 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
6 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
7 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
8 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
9 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
10 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
11 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
12 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
13 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
14 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
15 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
16 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
17 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
18 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
19 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
20 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
21 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
22
synthetic: yes
mol_id organism_scientific expression_system
23 Escherichia coli  (taxid:536056) Escherichia coli  (taxid:83333)
strain: DH1
gene: EcDH1_R0066, glnV glnX, Pecwa_R0066
expression_system_strain: K-12
expression_system_vector_type: lambda pL expression system
expression_system_plasmid: pRS3
mol_id organism_scientific expression_system
24 Escherichia coli  (taxid:536056) Escherichia coli  (taxid:634468)
strain: DH1
gene: EcDH1_R0011, metY, Pecwa_R0068
expression_system_strain: HB101
expression_system_plasmid: plppMet
mol_id organism_scientific expression_system
25 Pectobacterium wasabiae WPP163  (taxid:561231) Escherichia coli  (taxid:83333)
gene: EcDH1_R0066, glnV glnX, Pecwa_R0066
expression_system_strain: K-12
expression_system_vector_type: lambda pL expression system
expression_system_plasmid: pRS3
mol_id organism_scientific
26 Streptomyces puniceus  (taxid:67351)
mol_id organism_scientific
27 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
28 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
29 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
30 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
31 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
32 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
33 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
34 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
35 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
36 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
37 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
38 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
39 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
40 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
41 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
42 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
43 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
44 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
45 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
46 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
47 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
48 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
49 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
50 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
51 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
52 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
53 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
54 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
55 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
56 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
57 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific
58 Thermus thermophilus  (taxid:300852)
strain: HB8
mol_id organism_scientific expression_system
59 Escherichia coli  (taxid:536056) Escherichia coli  (taxid:634468)
strain: DH1
gene: EcDH1_R0011, metY, Pecwa_R0068
expression_system_strain: HB101
expression_system_plasmid: plppMet
Authors : Stanley, R.E., Blaha, G.
Keywords : Anti-tuberculosis antibiotic, 70S, ribosome, tRNA, mRNA, tuberactinomycin, capreomycin, RIBOSOME-ANTIBIOTIC complex
Exp. method : X-RAY DIFFRACTION ( 3.450 Å )
Citation :

The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.

Stanley, R.E.,Blaha, G.,Grodzicki, R.L.  et al.
(2010)  Nat.Struct.Mol.Biol.  17 : 289 - 293

PubMed: 20154709
DOI: 10.1038/nsmb.1755

Reaction

Chain : AB, CB
UniProt : P80371 (RS2_THET8)
Reaction : -
Chain : AC, CC
UniProt : P80372 (RS3_THET8)
Reaction : -
Chain : AD, CD
UniProt : P80373 (RS4_THET8)
Reaction : -
Chain : AE, CE
UniProt : Q5SHQ5 (RS5_THET8)
Reaction : -
Chain : AF, CF
UniProt : Q5SLP8 (RS6_THET8)
Reaction : -
Chain : AG, CG
UniProt : P17291 (RS7_THET8)
Reaction : -
Chain : AH, CH
UniProt : Q5SHQ2 (RS8_THET8)
Reaction : -
Chain : AI, CI
UniProt : P80374 (RS9_THET8)
Reaction : -
Chain : AJ, CJ
UniProt : Q5SHN7 (RS10_THET8)
Reaction : -
Chain : AK, CK
UniProt : P80376 (RS11_THET8)
Reaction : -
Chain : AL, CL
UniProt : Q5SHN3 (RS12_THET8)
Reaction : -
Chain : AM, CM
UniProt : P80377 (RS13_THET8)
Reaction : -
Chain : AN, CN
UniProt : Q5SHQ1 (RS14Z_THET8)
Reaction : -
Chain : AO, CO
UniProt : Q5SJ76 (RS15_THET8)
Reaction : -
Chain : AP, CP
UniProt : Q5SJH3 (RS16_THET8)
Reaction : -
Chain : AQ, CQ
UniProt : Q5SHP7 (RS17_THET8)
Reaction : -
Chain : AR, CR
UniProt : Q5SLQ0 (RS18_THET8)
Reaction : -
Chain : AS, CS
UniProt : Q5SHP2 (RS19_THET8)
Reaction : -
Chain : AT, CT
UniProt : P80380 (RS20_THET8)
Reaction : -
Chain : AU, CU
UniProt : Q5SIH3 (RSHX_THET8)
Reaction : -
Chain : BC, DC
UniProt : Q5SLP7 (RL1_THET8)
Reaction : -
Chain : BD, DD
UniProt : P60405 (RL2_THET8)
Reaction : -
Chain : BE, DE
UniProt : Q5SHN8 (RL3_THET8)
Reaction : -
Chain : BF, DF
UniProt : Q5SHN9 (RL4_THET8)
Reaction : -
Chain : BG, DG
UniProt : Q5SHQ0 (RL5_THET8)
Reaction : -
Chain : BH, DH
UniProt : Q5SHQ3 (RL6_THET8)
Reaction : -
Chain : BI, DI
UniProt : Q5SLQ1 (RL9_THET8)
Reaction : -
Chain : BN, DN
UniProt : P60488 (RL13_THET8)
Reaction : -
Chain : BO, DO
UniProt : Q5SHP8 (RL14_THET8)
Reaction : -
Chain : BP, DP
UniProt : Q5SHQ7 (RL15_THET8)
Reaction : -
Chain : BQ, DQ
UniProt : P60489 (RL16_THET8)
Reaction : -
Chain : BR, DR
UniProt : Q9Z9H5 (RL17_THET8)
Reaction : -
Chain : BS, DS
UniProt : Q5SHQ4 (RL18_THET8)
Reaction : -
Chain : BT, DT
UniProt : P60490 (RL19_THET8)
Reaction : -
Chain : BU, DU
UniProt : P60491 (RL20_THET8)
Reaction : -
Chain : BV, DV
UniProt : P60492 (RL21_THET8)
Reaction : -
Chain : BW, DW
UniProt : Q5SHP3 (RL22_THET8)
Reaction : -
Chain : BX, DX
UniProt : Q5SHP0 (RL23_THET8)
Reaction : -
Chain : BY, DY
UniProt : Q5SHP9 (RL24_THET8)
Reaction : -
Chain : BZ, DZ
UniProt : Q5SHZ1 (RL25_THET8)
Reaction : -
Chain : B0, D0
UniProt : P60493 (RL27_THET8)
Reaction : -
Chain : B1, D1
UniProt : P60494 (RL28_THET8)
Reaction : -
Chain : B2, D2
UniProt : Q5SHP6 (RL29_THET8)
Reaction : -
Chain : B3, D3
UniProt : Q5SHQ6 (RL30_THET8)
Reaction : -
Chain : B4, D4
UniProt : Q5SJE1 (RL31_THET8)
Reaction : -
Chain : B5, D5
UniProt : P80339 (RL32_THET8)
Reaction : -
Chain : B6, D6
UniProt : P35871 (RL33_THET8)
Reaction : -
Chain : B7, D7
UniProt : P80340 (RL34_THET8)
Reaction : -
Chain : B8, D8
UniProt : Q5SKU1 (RL35_THET8)
Reaction : -
Chain : B9, D9
UniProt : Q5SHR2 (RL36_THET8)
Reaction : -