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5JVG

The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(X)
23S ribosomal RNApolymer2877932472.51GenBank (1026245073)Deinococcus radiodurans R1
2B
(Y)
5S ribosomal RNApolymer12439911.91GenBank (11612676)Deinococcus radiodurans R1
3C
(A)
50S ribosomal protein L2polymer27530107.81UniProt (Q9RXJ9)
Pfam (PF00181)
Pfam (PF03947)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
4D
(B)
50S ribosomal protein L3polymer21122477.21UniProt (Q9RXK2)
Pfam (PF00297)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
5E
(C)
50S ribosomal protein L4polymer20522308.21UniProt (Q9RXK1)
Pfam (PF00573)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
6F
(D)
50S ribosomal protein L5polymer18020379.91UniProt (Q9RXJ0)
Pfam (PF00281)
Pfam (PF00673)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
7G
(E)
50S ribosomal protein L6polymer18519613.61UniProt (Q9RSL3)
Pfam (PF00347)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
8H
(F)
50S ribosomal protein L11polymer14414889.21UniProt (Q9RSS7)
Pfam (PF03946)
Pfam (PF00298)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
9I
(G)
50S ribosomal protein L13polymer17419223.21UniProt (Q9RXY1)
Pfam (PF00572)
Deinococcus radiodurans
10J
(H)
50S ribosomal protein L14polymer13414256.51UniProt (Q9RXJ2)
Pfam (PF00238)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
11K
(I)
50S ribosomal protein L15polymer15616894.21UniProt (Q9RSK9)
Pfam (PF00828)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
12L
(J)
50S ribosomal protein L16polymer14116126.01UniProt (Q9RXJ5)
Pfam (PF00252)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
13M
(K)
50S ribosomal protein L17polymer11612926.11UniProt (Q9RSJ5)
Pfam (PF01196)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
14N
(L)
50S ribosomal protein L18polymer11412163.91UniProt (Q9RSL2)
Pfam (PF00861)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
15O
(M)
50S ribosomal protein L19polymer16618347.81UniProt (Q9RWB4)
Pfam (PF01245)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
16P
(N)
50S ribosomal protein L20polymer11813991.31UniProt (Q9RSW7)
Pfam (PF00453)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
17Q
(O)
50S ribosomal protein L21polymer10011165.71UniProt (Q9RY64)
Pfam (PF00829)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
18R
(P)
50S ribosomal protein L22polymer13415190.91UniProt (Q9RXJ7)
Pfam (PF00237)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
19S
(Q)
50S ribosomal protein L23polymer9510539.21UniProt (Q9RXK0)
Pfam (PF00276)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
20T
(R)
50S ribosomal protein L24polymer11512384.41UniProt (Q9RXJ1)
Pfam (PF00467)
Pfam (PF17136)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
21U
(S)
50S ribosomal protein L25polymer23725415.41UniProt (Q9RX88)
Pfam (PF01386)
Pfam (PF14693)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)General stress protein CTC
22V
(T)
50S ribosomal protein L27polymer919609.11UniProt (Q9RY65)
Pfam (PF01016)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
23W
(U)
50S ribosomal protein L28polymer818982.61UniProt (Q9RRG8)Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
24X
(V)
50S ribosomal protein L29polymer677775.01UniProt (Q9RXJ4)
Pfam (PF00831)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
25Y
(W)
50S ribosomal protein L30polymer556079.21UniProt (Q9RSL0)
Pfam (PF00327)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
26Z
(Z)
50S ribosomal protein L32polymer606810.01UniProt (P49228)
Pfam (PF01783)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
27AA
(1)
50S ribosomal protein L33polymer556374.51UniProt (Q9RSS4)
Pfam (PF00471)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
28BA
(2)
50S ribosomal protein L34polymer475626.61UniProt (Q9RSH2)
Pfam (PF00468)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
29CA
(3)
50S ribosomal protein L35polymer667448.11UniProt (Q9RSW6)
Pfam (PF01632)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
30DA
(X)
Avilamycinnon-polymer1404.21Chemie (6NO)
31AB, AC, AD, AE, AF...
(X, Y, A, J, K...)
MAGNESIUM IONnon-polymer24.3446Chemie (MG)
32BQ, CQ, DQ, EQ, FQ
(X)
(4S)-2-METHYL-2,4-PENTANEDIOLnon-polymer118.25Chemie (MPD)
33GQ, HQ, IQ
(X)
SPERMIDINEnon-polymer145.23Chemie (SPD)
Sequence modifications
X: 1 - 2877 (GenBank: 1026245073)
PDBExternal DatabaseDetails
U 1526C 140011conflict
A 1890G 140375conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains29
Total formula weight1359490.0
Non-Polymers*Number of molecules455
Total formula weight13270.9
All*Total formula weight1372760.8
*Water molecules are not included.

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PDB entries from 2026-01-14

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