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Structure of RNA polymerase complex and genome within a dsrna virus provides insights into the mechanisms of transcription and assembly

Analyse Structure of RNA polymerase complex and genome within a dsrna virus provides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZVS
Type: protein
Length: 12,872 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP3; VP2; Putative core protein NTPASE/VP5
UniProt: Q9E3V8, Q9E3V9, Q8JU68
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 8 distinct chains · 30% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	VP3	protein	1060	28% helix, 12% strand	Q9E3V8
B, D, F, J	VP3	protein	1154	27% helix, 12% strand	Q9E3V8
E	VP3	protein	1032	30% helix, 13% strand	Q9E3V8
G	VP3	protein	1062	31% helix, 12% strand	Q9E3V8
H	VP3	protein	1155	28% helix, 12% strand	Q9E3V8
I	VP3	protein	1059	32% helix, 12% strand	Q9E3V8
2	VP2	protein	1245	38% helix, 8% strand	Q9E3V9
4	Putative core protein NTPASE/VP5	protein	583	25% helix, 19% strand	Q8JU68

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	1109	0.88	0.89	115	empty
2	1047	0.88	0.89	135	empty
3	959	0.87	0.89	112	empty
4	869	0.84	0.86	76	empty
5	524	0.80	0.86	58	empty

Interfaces

24 interfaces between chains.

A–B · 3879 Å² buried · 51 hydrogen bonds · protein-protein
D–C · 3725 Å² buried · 48 hydrogen bonds · protein-protein
I–J · 3722 Å² buried · 50 hydrogen bonds · protein-protein
G–H · 3631 Å² buried · 50 hydrogen bonds · protein-protein
E–F · 3584 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

5ZVS · Structure of RNA polymerase complex and genome within a dsRNA virus provides insights… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9E3V8
Every structure of UniProt Q9E3V9
Every structure of UniProt Q8JU68
Elsewhere: RCSB PDB 5ZVS · PDBe 5ZVS · UniProt Q9E3V8 · UniProt Q9E3V9 · UniProt Q8JU68

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