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

Analyse Structure of trans-translation inhibitor bound to E. coli 70S ribosome with P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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
Molecule: 23S ribosomal RNA; 16S ribosomal RNA; 5S ribosomal RNA; mRNA; tRNA(gly); 50S ribosomal…
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
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.1 · 54 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	23S ribosomal RNA	rna	2903	—	—
2	16S ribosomal RNA	rna	1534	—	—
3	5S ribosomal RNA	rna	120	—	—
4	mRNA	rna	5	—	—
5	tRNA(gly)	rna	76	—	—
B	50S ribosomal protein L2	protein	271	4% helix, 30% strand	P60422
C	50S ribosomal protein L3	protein	209	11% helix, 37% strand	P60438
D	50S ribosomal protein L4	protein	201	35% helix, 10% strand	D7Z9F6
E	50S ribosomal protein L5	protein	177	36% helix, 20% strand	D7Z9G7
F	50S ribosomal protein L6	protein	175	22% helix, 37% strand	D7Z9H0
G	50S ribosomal protein L9	protein	149	33% helix, 23% strand	D7ZI15
J	50S ribosomal protein L13	protein	142	32% helix, 19% strand	D7ZET0
K	50S ribosomal protein L14	protein	123	5% helix, 37% strand	D7Z9G5
L	50S ribosomal protein L15	protein	144	17% helix, 10% strand	A0A037Y8L6
M	50S ribosomal protein L16	protein	136	20% helix, 28% strand	P0ADY7
N	50S ribosomal protein L17	protein	119	52% helix, 17% strand	A0A0A8UJP9
O	50S ribosomal protein L18	protein	116	46% helix, 20% strand	D7Z9H1
P	50S ribosomal protein L19	protein	114	13% helix, 45% strand	D7ZKU3
Q	50S ribosomal protein L20	protein	117	80% helix, 0% strand	B7MAS6
R	50S ribosomal protein L21	protein	103	0% helix, 61% strand	D7ZEN7
S	50S ribosomal protein L22	protein	110	38% helix, 35% strand	D7Z9G0
T	50S ribosomal protein L23	protein	94	30% helix, 37% strand	D7X2Z9
U	50S ribosomal protein L24	protein	103	6% helix, 51% strand	D7Z9G6
V	50S ribosomal protein L25	protein	94	22% helix, 46% strand	D7XH79
X	50S ribosomal protein L28	protein	77	27% helix, 36% strand	S0YB49
Y	50S ribosomal protein L29	protein	62	77% helix, 0% strand	D7Z9G3
Z	50S ribosomal protein L30	protein	58	33% helix, 26% strand	D7Z9H3
a	50S ribosomal protein L31	protein	66	20% helix, 24% strand	D7ZFP6
b	50S ribosomal protein L32	protein	56	18% helix, 14% strand	D7ZGG2
c	50S ribosomal protein L33	protein	52	0% helix, 52% strand	D7Z9P0
d	50S ribosomal protein L34	protein	46	59% helix, 0% strand	B7MGC4
e	50S ribosomal protein L35	protein	64	36% helix, 11% strand	D7Z814
f	50S ribosomal protein L36	protein	38	0% helix, 42% strand	A0A0E2L017
g	30S ribosomal protein S2	protein	225	48% helix, 15% strand	D7ZK99
h	30S ribosomal protein S3	protein	208	33% helix, 29% strand	B7MCS9
i	30S ribosomal protein S4	protein	205	43% helix, 10% strand	D7Z9H7
j	30S ribosomal protein S5	protein	156	31% helix, 37% strand	D7Z9H2
k	30S ribosomal protein S6	protein	104	29% helix, 43% strand	P02358
l	30S ribosomal protein S7	protein	151	58% helix, 7% strand	A0A2S5ZT99
m	30S ribosomal protein S8	protein	129	26% helix, 37% strand	D7Z9G9
n	30S ribosomal protein S9	protein	127	35% helix, 18% strand	D7ZES9
o	30S ribosomal protein S10	protein	99	27% helix, 43% strand	D7Z9F4
p	30S ribosomal protein S11	protein	117	22% helix, 29% strand	B7MCR3
q	30S ribosomal protein S12	protein	123	7% helix, 26% strand	L4V1L2
r	30S ribosomal protein S13	protein	116	52% helix, 5% strand	H4UQ02
s	30S ribosomal protein S14	protein	100	54% helix, 4% strand	D7Z9G8
t	30S ribosomal protein S15	protein	88	76% helix, 0% strand	D7ZEL4
u	30S ribosomal protein S16	protein	82	28% helix, 40% strand	B7MIU7
v	30S ribosomal protein S17	protein	80	0% helix, 54% strand	D7Z9G4
w	30S ribosomal protein S18	protein	66	47% helix, 3% strand	A0A0E2KXL3
x	30S ribosomal protein S19	protein	83	24% helix, 18% strand	D7Z9F9
y	30S ribosomal protein S20	protein	86	87% helix, 0% strand	D7ZAS2
z	30S ribosomal protein S21	protein	70	70% helix, 4% strand	A0A0E2L2J1
W	50S ribosomal protein L27	protein	84	0% helix, 36% strand	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.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	988	0.88	0.90	100	empty
2	728	0.86	0.91	79	empty
3	1173	0.86	0.87	101	empty
4	990	0.86	0.88	85	empty
5	784	0.86	0.89	92	empty

Interfaces

121 interfaces between chains.

1–B · 7185 Å² buried · 192 hydrogen bonds · protein-nucleic
1–C · 5137 Å² buried · 128 hydrogen bonds · protein-nucleic
1–L · 4509 Å² buried · 125 hydrogen bonds · protein-nucleic
1–D · 4188 Å² buried · 96 hydrogen bonds · protein-nucleic
1–Q · 4143 Å² buried · 118 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 34 modified (nucleotide modification, nonstandard).

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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