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In situ structure of btv RNA-dependent RNA polymerase in btv virion

Analyse In situ structure of btv RNA-dependent RNA polymerase in btv virion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PNS
Type: protein
Length: 10,064 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA polymerase; Inner core structural protein VP3
EC: 2.7.7.48
UniProt: W0G557, Q1AE73
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 7 distinct chains · 36% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-directed RNA polymerase (EC 2.7.7.48)	protein	1291	41% helix, 11% strand	W0G557
B	Inner core structural protein VP3	protein	873	34% helix, 17% strand	Q1AE73
C, E, G, I, K	Inner core structural protein VP3	protein	885	34% helix, 13% strand	Q1AE73
D	Inner core structural protein VP3	protein	865	35% helix, 16% strand	Q1AE73
F	Inner core structural protein VP3	protein	867	36% helix, 16% strand	Q1AE73
H	Inner core structural protein VP3	protein	874	35% helix, 16% strand	Q1AE73
J	Inner core structural protein VP3	protein	869	33% helix, 17% strand	Q1AE73

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	681	0.85	0.89	67	empty
2	1097	0.85	0.86	112	empty
3	973	0.85	0.86	98	empty
4	767	0.85	0.88	98	empty
5	389	0.85	0.93	53	empty

Interfaces

22 interfaces between chains.

G–H · 2917 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 2907 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 2906 Å² buried · 30 hydrogen bonds · protein-protein
H–I · 2853 Å² buried · 27 hydrogen bonds · protein-protein
B–K · 2850 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6PNS · In situ structure of BTV RNA-dependent RNA polymerase in BTV virion · the same entry in another collection · chain G against G, 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 W0G557
Every structure of UniProt Q1AE73
Elsewhere: RCSB PDB 6PNS · PDBe 6PNS · UniProt W0G557 · UniProt Q1AE73

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