MolNFT v2 · #151524 · protein + RNA

Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State III)

6GXN · 23S ribosomal RNA: “Cryo-EM structure of an E. coli 70S ribosome in complex with RF3-GDPCP, RF1(GAQ) and Pint-tRNA (State III)”. Electron microscopy at 3.9, 1 ligand (GCP), 20 pockets (best druggability 0.89). MolNFT v2 #151524 on…

PDB: 6GXN
Type: protein + RNA
Length: 11,379 residues
Chains: 58
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.9
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
UniProt: P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0A7J7, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7J3, P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P68679, P0A7I0, P0A7I4, Q8WSY8
Ligands: GCP
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.9 · 58 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	2895	—	—
B	5S ribosomal RNA	rna	120	—	—
C	50S ribosomal protein L2	protein	271	4% helix, 27% strand	P60422
D	50S ribosomal protein L3	protein	209	9% helix, 37% strand	P60438
E	50S ribosomal protein L4	protein	201	34% helix, 9% strand	P60723
F	50S ribosomal protein L5	protein	177	30% helix, 14% strand	P62399
G	50S ribosomal protein L6	protein	176	19% helix, 34% strand	P0AG55
H	50S ribosomal protein L9	protein	149	29% helix, 13% strand	P0A7R1
I	50S ribosomal protein L11	protein	141	28% helix, 4% strand	P0A7J7
J	50S ribosomal protein L13	protein	142	28% helix, 19% strand	P0AA10
K	50S ribosomal protein L14	protein	122	7% helix, 36% strand	P0ADY3
L	50S ribosomal protein L15	protein	143	10% helix, 8% strand	P02413
M	50S ribosomal protein L16	protein	136	19% helix, 28% strand	P0ADY7
N	50S ribosomal protein L17	protein	120	42% helix, 17% strand	P0AG44
O	50S ribosomal protein L18	protein	116	45% helix, 15% strand	P0C018
P	50S ribosomal protein L19	protein	114	16% helix, 39% strand	P0A7K6
Q	50S ribosomal protein L20	protein	117	79% helix, 0% strand	P0A7L3
R	50S ribosomal protein L21	protein	103	0% helix, 52% strand	P0AG48
S	50S ribosomal protein L22	protein	110	37% helix, 34% strand	P61175
T	50S ribosomal protein L23	protein	93	32% helix, 31% strand	P0ADZ0
U	50S ribosomal protein L24	protein	102	0% helix, 38% strand	P60624
V	50S ribosomal protein L25	protein	94	18% helix, 47% strand	P68919
W	50S ribosomal protein L27	protein	75	0% helix, 39% strand	P0A7L8
X	50S ribosomal protein L28	protein	77	25% helix, 31% strand	P0A7M2
Y	50S ribosomal protein L29	protein	63	75% helix, 0% strand	P0A7M6
Z	50S ribosomal protein L30	protein	58	33% helix, 26% strand	P0AG51
0	50S ribosomal protein L32	protein	56	20% helix, 14% strand	P0A7N4
1	50S ribosomal protein L33	protein	50	0% helix, 38% strand	P0A7N9
2	50S ribosomal protein L34	protein	46	57% helix, 0% strand	P0A7P5
3	50S ribosomal protein L35	protein	64	30% helix, 9% strand	P0A7Q1
4	50S ribosomal protein L36	protein	38	8% helix, 37% strand	P0A7Q6
5	50S ribosomal protein L10	protein	131	35% helix, 0% strand	P0A7J3
7	mRNA	rna	7	—	—
a	16S ribosomal RNA	rna	1539	—	—
b	30S ribosomal protein S2	protein	218	39% helix, 10% strand	P0A7V0
c	30S ribosomal protein S3	protein	206	33% helix, 29% strand	P0A7V3
d	30S ribosomal protein S4	protein	205	38% helix, 7% strand	P0A7V8
e	30S ribosomal protein S5	protein	157	26% helix, 21% strand	P0A7W1
f	30S ribosomal protein S6	protein	100	30% helix, 24% strand	P02358
g	30S ribosomal protein S7	protein	151	50% helix, 7% strand	P02359
h	30S ribosomal protein S8	protein	129	29% helix, 25% strand	P0A7W7
i	30S ribosomal protein S9	protein	127	23% helix, 19% strand	P0A7X3
j	30S ribosomal protein S10	protein	98	23% helix, 35% strand	P0A7R5
k	30S ribosomal protein S11	protein	116	20% helix, 28% strand	P0A7R9
l	30S ribosomal protein S12	protein	123	7% helix, 25% strand	P0A7S3
m	30S ribosomal protein S13	protein	114	48% helix, 2% strand	P0A7S9
n	30S ribosomal protein S14	protein	101	45% helix, 4% strand	P0AG59
o	30S ribosomal protein S15	protein	88	68% helix, 0% strand	P0ADZ4
p	30S ribosomal protein S16	protein	82	18% helix, 28% strand	P0A7T3
q	30S ribosomal protein S17	protein	80	0% helix, 49% strand	P0AG63
r	30S ribosomal protein S18	protein	65	35% helix, 3% strand	P0A7T7
s	30S ribosomal protein S19	protein	79	25% helix, 10% strand	P0A7U3
t	30S ribosomal protein S20	protein	85	82% helix, 0% strand	P0A7U7
u	30S ribosomal protein S21	protein	65	42% helix, 3% strand	P68679
v	Peptide chain release factor RF1	protein	348	46% helix, 19% strand	P0A7I0
w	Peptide chain release factor RF3	protein	496	23% helix, 14% strand	P0A7I4
x	fMet-tRNA	rna	77	—	—
z	Apidaecin	protein	14	0% helix, 0% strand	Q8WSY8

Ligands and binding sites

GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains w

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	1200	0.89	0.91	92	empty
2	1011	0.89	0.91	116	empty
3	704	0.88	0.93	72	empty
4	911	0.87	0.90	81	empty
5	639	0.87	0.93	82	empty

Interfaces

133 interfaces between chains.

A–C · 7572 Å² buried · 161 hydrogen bonds · protein-nucleic
A–D · 5112 Å² buried · 104 hydrogen bonds · protein-nucleic
A–L · 4633 Å² buried · 82 hydrogen bonds · protein-nucleic
A–E · 4307 Å² buried · 85 hydrogen bonds · protein-nucleic
A–Q · 4249 Å² buried · 96 hydrogen bonds · protein-nucleic

Compared structures

P60422 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60422) · a predicted model of the same protein · chain C against A, TM-score 0.99
P0AA10 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (P0AA10) · a predicted model of the same protein · chain J against A, TM-score 0.98
P0ADY7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (P0ADY7) · a predicted model of the same protein · chain M against A, TM-score 0.98
P60723 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L4 (P60723) · a predicted model of the same protein · chain E against A, TM-score 0.96
P0AG51 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L30 (P0AG51) · a predicted model of the same protein · chain Z against A, TM-score 0.96
P0ADZ0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L23 (P0ADZ0) · a predicted model of the same protein · chain T against A, TM-score 0.94
P61175 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (P61175) · a predicted model of the same protein · chain S against A, TM-score 0.94
P0A7I4 · AlphaFold monomer V2.0 prediction for peptide chain release factor RF3 (P0A7I4) · a predicted model of the same protein · chain w against A, TM-score 0.93
P0AG48 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (P0AG48) · a predicted model of the same protein · chain R against A, TM-score 0.93
P0A7X3 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S9 (P0A7X3) · a predicted model of the same protein · chain i against A, TM-score 0.93
P0A7P5 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L34 (P0A7P5) · a predicted model of the same protein · chain 2 against A, TM-score 0.89
P0A7N4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L32 (P0A7N4) · a predicted model of the same protein · chain 0 against A, TM-score 0.83

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