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Structural insight into the interaction between RNA polymerase and vpg for norovirus replication

Analyse Structural insight into the interaction between RNA polymerase and vpg for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y3D
Type: protein
Length: 2,946 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-dependent RNA polymerase; Viral protein genome-linked (vpg)
UniProt: Q80J95
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-dependent RNA polymerase	protein	479	42% helix, 17% strand	Q80J95
B	RNA-dependent RNA polymerase	protein	479	41% helix, 17% strand	Q80J95
C	RNA-dependent RNA polymerase	protein	480	41% helix, 17% strand	Q80J95
D	RNA-dependent RNA polymerase	protein	479	41% helix, 17% strand	Q80J95
E	RNA-dependent RNA polymerase	protein	483	41% helix, 17% strand	Q80J95
F	RNA-dependent RNA polymerase	protein	481	41% helix, 17% strand	Q80J95
G	Viral protein genome-linked (vpg)	protein	33	76% helix, 0% strand	—
H	Viral protein genome-linked (vpg)	protein	32	75% helix, 0% strand	—

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	841	0.83	0.85	96	empty
2	714	0.77	0.82	82	empty
3	304	0.75	0.87	48	empty
4	975	0.70	0.75	98	empty
5	831	0.68	0.75	85	empty

Interfaces

12 interfaces between chains.

C–E · 1313 Å² buried · 18 hydrogen bonds · protein-protein
D–F · 1308 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1257 Å² buried · 19 hydrogen bonds · protein-protein
B–E · 645 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 627 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5Y3D · Structural insight into the interaction between RNA polymerase and VPg for norovirus… · 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 Q80J95
Elsewhere: RCSB PDB 5Y3D · PDBe 5Y3D · UniProt Q80J95

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