MolNFT v1 · #104339 · protein

Complex structure of viral RNA polymerase

4Q7J · Elongation factor ts: “Complex structure of viral RNA polymerase”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.73). MolNFT v1 #104339 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q7J
Type: protein
Length: 2,730 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Elongation factor ts; Elongation factor tu 1; Q beta replicase; 30S ribosomal protein S1
UniProt: P0A6P1, P0CE47, Q8LTE0, P0AG67
Ligands: SO4
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 8 distinct chains · 37% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Elongation factor ts	protein	278	51% helix, 19% strand	P0A6P1
B	Elongation factor tu 1	protein	362	21% helix, 38% strand	P0CE47
C	Q beta replicase	protein	547	44% helix, 16% strand	Q8LTE0
D	30S ribosomal protein S1	protein	177	25% helix, 32% strand	P0AG67
E	Elongation factor ts	protein	280	51% helix, 19% strand	P0A6P1
F	Elongation factor tu 1	protein	364	23% helix, 39% strand	P0CE47
G	Q beta replicase	protein	545	45% helix, 15% strand	Q8LTE0
H	30S ribosomal protein S1	protein	177	18% helix, 27% strand	P0AG67

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains B, C, F, G

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1096	0.73	0.76	111	SO4
2	637	0.73	0.80	75	empty
3	571	0.69	0.78	55	empty
4	274	0.68	0.83	35	SO4
5	210	0.66	0.84	45	empty

Interfaces

14 interfaces between chains.

G–H · 2352 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 2309 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1853 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1835 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1793 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4Q7J · Complex structure of viral RNA polymerase · the same entry in another collection · chain H against H, TM-score 1.00
P0A6P1 · AlphaFold monomer V2.0 prediction for elongation factor ts (P0A6P1) · a predicted model of the same protein · chain E against A, TM-score 0.96
P0CE47 · AlphaFold monomer V2.0 prediction for elongation factor tu 1 (P0CE47) · a predicted model of the same protein · chain B against A, TM-score 0.54

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0A6P1
Every structure of UniProt P0CE47
Every structure of UniProt Q8LTE0
Every structure of UniProt P0AG67
Elsewhere: RCSB PDB 4Q7J · PDBe 4Q7J · UniProt P0A6P1 · UniProt P0CE47 · UniProt Q8LTE0 · UniProt P0AG67

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