Brand  (β version)

PDB ID: 4V7V

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Ligands
Code Name Style Show Link
MG Magnesium ion PoSSuM
CLY Clindamycin PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 4V7V   PDBj   RCSB PDB   PDBe
Header : RIBOSOME/ANTIBIOTIC
Title : Crystal structure of the E. coli ribosome bound to clindamycin.
Release Data : 2014-07-09
Compound :
mol_id molecule chains
1 16S rRNA AA
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
6 30S ribosomal protein S6 AF,CF
mol_id molecule chains
7 30S ribosomal protein S7 AG
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
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
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
21 30S ribosomal protein S21 AU,CU
mol_id molecule chains
22 23S rRNA BA,DA
mol_id molecule chains
23 5S rRNA BB
mol_id molecule chains
24 50S ribosomal protein L2 BC,DC
mol_id molecule chains
25 50S ribosomal protein L3 BD,DD
mol_id molecule chains
26 50S ribosomal protein L4 BE,DE
mol_id molecule chains
27 50S ribosomal protein L5 BF
mol_id molecule chains
28 50S ribosomal protein L6 BG,DG
mol_id molecule chains
29 50S ribosomal protein L9 BH,DH
mol_id molecule chains
30 50S ribosomal protein L11 BI,DI
mol_id molecule chains
31 50S ribosomal protein L13 BJ,DJ
mol_id molecule chains
32 50S ribosomal protein L14 BK,DK
mol_id molecule chains
33 50S ribosomal protein L15 BL,DL
mol_id molecule chains
34 50S ribosomal protein L16 BM,DM
mol_id molecule chains
35 50S ribosomal protein L17 BN,DN
mol_id molecule chains
36 50S ribosomal protein L18 BO,DO
mol_id molecule chains
37 50S ribosomal protein L19 BP,DP
mol_id molecule chains
38 50S ribosomal protein L20 BQ,DQ
mol_id molecule chains
39 50S ribosomal protein L21 BR,DR
mol_id molecule chains
40 50S ribosomal protein L22 BS,DS
mol_id molecule chains
41 50S ribosomal protein L23 BT,DT
mol_id molecule chains
42 50S ribosomal protein L24 BU,DU
mol_id molecule chains
43 50S ribosomal protein L25 BV,DV
mol_id molecule chains
44 50S ribosomal protein L27 BW,DW
mol_id molecule chains
45 50S ribosomal protein L28 BX,DX
mol_id molecule chains
46 50S ribosomal protein L29 BY,DY
mol_id molecule chains
47 50S ribosomal protein L30 BZ,DZ
mol_id molecule chains
48 50S ribosomal protein L32 B0,D0
mol_id molecule chains
49 50S ribosomal protein L33 B1,D1
mol_id molecule chains
50 50S ribosomal protein L34 B2,D2
mol_id molecule chains
51 50S ribosomal protein L35 B3,D3
mol_id molecule chains
52 50S ribosomal protein L36 B4,D4
mol_id molecule chains
53 16S rRNA CA
mol_id molecule chains
54 30S ribosomal protein S7 CG
mol_id molecule chains
55 30S ribosomal protein S13 CM
mol_id molecule chains
56 30S ribosomal protein S16 CP
mol_id molecule chains
57 5S rRNA DB
mol_id molecule chains
58 50S ribosomal protein L5 DF
Source :
mol_id organism_scientific
1 Escherichia coli  (taxid:562)
mol_id organism_scientific
2 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
3 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
4 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
5 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
6 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
7 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
8 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
9 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
10 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
11 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
12 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
13 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
14 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
15 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
16 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
17 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
18 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
19 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
20 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
21 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
22 Escherichia coli  (taxid:562)
mol_id organism_scientific
23 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
24 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
25 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
26 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
27 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
28 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
29 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
30 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
31 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
32 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
33 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
34 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
35 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
36 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
37 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
38 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
39 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
40 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
41 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
42 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
43 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
44 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
45 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
46 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
47 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
48 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
49 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
50 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
51 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
52 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
53 Escherichia coli  (taxid:562)
mol_id organism_scientific
54 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
55 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
56 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
57 Escherichia coli  (taxid:83333)
strain: K-12
mol_id organism_scientific
58 Escherichia coli  (taxid:83333)
strain: K-12
Authors : Dunkle, J.A., Xiong, L., Mankin, A.S., Cate, J.H.D.
Keywords : Protein biosynthesis, ribosomes, RNA, tRNA, transfer, clindamycin, antibiotic, exit, peptidyl, 30S, 70S, 16S, ribosomal subunit, small, RIBOSOME-ANTIBIOTIC complex
Exp. method : X-RAY DIFFRACTION ( 3.2891 Å )
Citation :

Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.

Dunkle, J.A.,Xiong, L.,Mankin, A.S.  et al.
(2010)  Proc.Natl.Acad.Sci.USA  107 : 17152 - 17157

PubMed: 20876128
DOI: 10.1073/pnas.1007988107

Reaction

Chain : AB, CB
UniProt : P0A7V0 (RS2_ECOLI)
Reaction : -
Chain : AC, CC
UniProt : P0A7V3 (RS3_ECOLI)
Reaction : -
Chain : AD, CD
UniProt : P0A7V8 (RS4_ECOLI)
Reaction : -
Chain : AE, CE
UniProt : P0A7W1 (RS5_ECOLI)
Reaction : -
Chain : AF, CF
UniProt : P02358 (RS6_ECOLI)
Reaction : -
Chain : CG
UniProt : P02359 (RS7_ECOLI)
Reaction : -
Chain : AH, CH
UniProt : P0A7W7 (RS8_ECOLI)
Reaction : -
Chain : AI, CI
UniProt : P0A7X3 (RS9_ECOLI)
Reaction : -
Chain : AJ, CJ
UniProt : P0A7R5 (RS10_ECOLI)
Reaction : -
Chain : AK, CK
UniProt : P0A7R9 (RS11_ECOLI)
Reaction : -
Chain : AL, CL
UniProt : P0A7S3 (RS12_ECOLI)
Reaction : -
Chain : CM
UniProt : P0A7S9 (RS13_ECOLI)
Reaction : -
Chain : AN, CN
UniProt : P0AG59 (RS14_ECOLI)
Reaction : -
Chain : AO, CO
UniProt : P0ADZ4 (RS15_ECOLI)
Reaction : -
Chain : CP
UniProt : P0A7T3 (RS16_ECOLI)
Reaction : -
Chain : AQ, CQ
UniProt : P0AG63 (RS17_ECOLI)
Reaction : -
Chain : AR, CR
UniProt : P0A7T7 (RS18_ECOLI)
Reaction : -
Chain : AS, CS
UniProt : P0A7U3 (RS19_ECOLI)
Reaction : -
Chain : AT, CT
UniProt : P0A7U7 (RS20_ECOLI)
Reaction : -
Chain : AU, CU
UniProt : P68679 (RS21_ECOLI)
Reaction : -
Chain : BC, DC
UniProt : P60422 (RL2_ECOLI)
Reaction : -
Chain : BD, DD
UniProt : P60438 (RL3_ECOLI)
Reaction : -
Chain : BE, DE
UniProt : P60723 (RL4_ECOLI)
Reaction : -
Chain : DF
UniProt : P62399 (RL5_ECOLI)
Reaction : -
Chain : BG, DG
UniProt : P0AG55 (RL6_ECOLI)
Reaction : -
Chain : BH, DH
UniProt : P0A7R1 (RL9_ECOLI)
Reaction : -
Chain : BI, DI
UniProt : P0A7J7 (RL11_ECOLI)
Reaction : -
Chain : BJ, DJ
UniProt : P0AA10 (RL13_ECOLI)
Reaction : -
Chain : BK, DK
UniProt : P0ADY3 (RL14_ECOLI)
Reaction : -
Chain : BL, DL
UniProt : P02413 (RL15_ECOLI)
Reaction : -
Chain : BM, DM
UniProt : P0ADY7 (RL16_ECOLI)
Reaction : -
Chain : BN, DN
UniProt : P0AG44 (RL17_ECOLI)
Reaction : -
Chain : BO, DO
UniProt : P0C018 (RL18_ECOLI)
Reaction : -
Chain : BP, DP
UniProt : P0A7K6 (RL19_ECOLI)
Reaction : -
Chain : BQ, DQ
UniProt : P0A7L3 (RL20_ECOLI)
Reaction : -
Chain : BR, DR
UniProt : P0AG48 (RL21_ECOLI)
Reaction : -
Chain : BS, DS
UniProt : P61175 (RL22_ECOLI)
Reaction : -
Chain : BT, DT
UniProt : P0ADZ0 (RL23_ECOLI)
Reaction : -
Chain : BU, DU
UniProt : P60624 (RL24_ECOLI)
Reaction : -
Chain : BV, DV
UniProt : P68919 (RL25_ECOLI)
Reaction : -
Chain : BW, DW
UniProt : P0A7L8 (RL27_ECOLI)
Reaction : -
Chain : BX, DX
UniProt : P0A7M2 (RL28_ECOLI)
Reaction : -
Chain : BY, DY
UniProt : P0A7M6 (RL29_ECOLI)
Reaction : -
Chain : BZ, DZ
UniProt : P0AG51 (RL30_ECOLI)
Reaction : -
Chain : B0, D0
UniProt : P0A7N4 (RL32_ECOLI)
Reaction : -
Chain : B1, D1
UniProt : P0A7N9 (RL33_ECOLI)
Reaction : -
Chain : B2, D2
UniProt : P0A7P5 (RL34_ECOLI)
Reaction : -
Chain : B3, D3
UniProt : P0A7Q1 (RL35_ECOLI)
Reaction : -
Chain : B4, D4
UniProt : P0A7Q6 (RL36_ECOLI)
Reaction : -