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Influenza a virus polymerase heterotrimer A/DUCK/FUJIAN/01/2002(H5N1)

Analyse Influenza a virus polymerase heterotrimer A/DUCK/FUJIAN/01/2002(H5N1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QPF
Type: protein
Length: 8,449 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
EC: 3.1.-.-, 2.7.7.48
UniProt: D3YNB8, D3YNB6, D3YNB5
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 10 distinct chains · 39% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G	Polymerase acidic protein (EC 3.1.-.-)	protein	716	38% helix, 13% strand	D3YNB8
B	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	685	44% helix, 9% strand	D3YNB6
C	Polymerase basic protein 2	protein	727	33% helix, 18% strand	D3YNB5
E	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	661	46% helix, 7% strand	D3YNB6
F	Polymerase basic protein 2	protein	731	34% helix, 18% strand	D3YNB5
H	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	673	45% helix, 9% strand	D3YNB6
I	Polymerase basic protein 2	protein	722	34% helix, 17% strand	D3YNB5
J	Polymerase acidic protein (EC 3.1.-.-)	protein	710	39% helix, 14% strand	D3YNB8
K	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	662	46% helix, 9% strand	D3YNB6
L	Polymerase basic protein 2	protein	730	34% helix, 17% strand	D3YNB5

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	1063	0.87	0.88	120	empty
2	959	0.86	0.87	113	empty
3	1025	0.85	0.85	126	empty
4	827	0.84	0.86	80	empty
5	772	0.83	0.87	105	empty

Interfaces

24 interfaces between chains.

H–I · 7725 Å² buried · 69 hydrogen bonds · protein-protein
A–B · 7589 Å² buried · 85 hydrogen bonds · protein-protein
J–K · 7561 Å² buried · 100 hydrogen bonds · protein-protein
G–H · 7474 Å² buried · 91 hydrogen bonds · protein-protein
D–E · 7473 Å² buried · 95 hydrogen bonds · protein-protein

Compared structures

6QPF · Influenza A virus Polymerase Heterotrimer A/duck/Fujian/01/2002(H5N1) · 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 D3YNB8
Every structure of UniProt D3YNB6
Every structure of UniProt D3YNB5
Elsewhere: RCSB PDB 6QPF · PDBe 6QPF · UniProt D3YNB8 · UniProt D3YNB6 · UniProt D3YNB5

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