MolNFT v2 · #160461 · protein + RNA

Structure of trans-translation inhibitor bound to E. coli 70S ribosome with P site tRNA

6OM6: “Structure of trans-translation inhibitor bound to E. coli 70S ribosome with P site tRNA”. Electron microscopy at 3.1, 1 ligand (KKL). MolNFT v2 #160461 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6OM6
Type: protein + RNA
Length: 10,353 residues
Chains: 54
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.1
Source: Escherichia coli
UniProt: P60422, P60438, D7Z9F6, D7Z9G7, D7Z9H0, D7ZI15, D7ZET0, D7Z9G5, A0A037Y8L6, P0ADY7, A0A0A8UJP9, D7Z9H1, D7ZKU3, B7MAS6, D7ZEN7, D7Z9G0, D7X2Z9, D7Z9G6, D7XH79, S0YB49, D7Z9G3, D7Z9H3, D7ZFP6, D7ZGG2, D7Z9P0, B7MGC4, D7Z814, A0A0E2L017, D7ZK99, B7MCS9, D7Z9H7, D7Z9H2, P02358, A0A2S5ZT99, D7Z9G9, D7ZES9, D7Z9F4, B7MCR3, L4V1L2, H4UQ02, D7Z9G8, D7ZEL4, B7MIU7, D7Z9G4, A0A0E2KXL3, D7Z9F9, D7ZAS2, A0A0E2L2J1, P0A7L8
Ligands: KKL

Structure

electron microscopy · resolution 3.1 · 54 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	—	rna	2903	—	—
2	—	rna	1534	—	—
3	—	rna	120	—	—
4	—	rna	5	—	—
5	—	rna	76	—	—
B	—	protein	271	—	P60422
C	—	protein	209	—	P60438
D	—	protein	201	—	D7Z9F6
E	—	protein	177	—	D7Z9G7
F	—	protein	175	—	D7Z9H0
G	—	protein	149	—	D7ZI15
J	—	protein	142	—	D7ZET0
K	—	protein	123	—	D7Z9G5
L	—	protein	144	—	A0A037Y8L6
M	—	protein	136	—	P0ADY7
N	—	protein	119	—	A0A0A8UJP9
O	—	protein	116	—	D7Z9H1
P	—	protein	114	—	D7ZKU3
Q	—	protein	117	—	B7MAS6
R	—	protein	103	—	D7ZEN7
S	—	protein	110	—	D7Z9G0
T	—	protein	94	—	D7X2Z9
U	—	protein	103	—	D7Z9G6
V	—	protein	94	—	D7XH79
X	—	protein	77	—	S0YB49
Y	—	protein	62	—	D7Z9G3
Z	—	protein	58	—	D7Z9H3
a	—	protein	66	—	D7ZFP6
b	—	protein	56	—	D7ZGG2
c	—	protein	52	—	D7Z9P0
d	—	protein	46	—	B7MGC4
e	—	protein	64	—	D7Z814
f	—	protein	38	—	A0A0E2L017
g	—	protein	225	—	D7ZK99
h	—	protein	208	—	B7MCS9
i	—	protein	205	—	D7Z9H7
j	—	protein	156	—	D7Z9H2
k	—	protein	104	—	P02358
l	—	protein	151	—	A0A2S5ZT99
m	—	protein	129	—	D7Z9G9
n	—	protein	127	—	D7ZES9
o	—	protein	99	—	D7Z9F4
p	—	protein	117	—	B7MCR3
q	—	protein	123	—	L4V1L2
r	—	protein	116	—	H4UQ02
s	—	protein	100	—	D7Z9G8
t	—	protein	88	—	D7ZEL4
u	—	protein	82	—	B7MIU7
v	—	protein	80	—	D7Z9G4
w	—	protein	66	—	A0A0E2KXL3
x	—	protein	83	—	D7Z9F9
y	—	protein	86	—	D7ZAS2
z	—	protein	70	—	A0A0E2L2J1
W	—	protein	84	—	P0A7L8

Ligands and binding sites

KKL · 4-amino-N-[5-(4-ethynylphenyl)-1,3,4-oxadiazol-2-yl]benzamide · ligand · chains 1, 5

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Compared structures

B7MCR3 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S11 (B7MCR3) · a predicted model of the same protein · chain p against A, TM-score 0.98
B7MCS9 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (B7MCS9) · a predicted model of the same protein · chain h against A, TM-score 0.98
B7MAS6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (B7MAS6) · a predicted model of the same protein · chain Q against A, TM-score 0.98
B7MIU7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (B7MIU7) · a predicted model of the same protein · chain u against A, TM-score 0.97
B7MGC4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L34 (B7MGC4) · a predicted model of the same protein · chain d against A, TM-score 0.92

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