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Influenza a virus polymerase heterotrimer A/NT/60/1968(H3N2) in complex with nanobody NB8205

Analyse Influenza a virus polymerase heterotrimer A/NT/60/1968(H3N2) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QPG
Type: protein
Length: 8,803 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
EC: 2.7.7.48
UniProt: P03434, P03432, P03429
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 13 distinct chains · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polymerase acidic protein	protein	691	40% helix, 15% strand	P03434
B	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	656	45% helix, 9% strand	P03432
C	Polymerase basic protein 2	protein	717	34% helix, 18% strand	P03429
D	Polymerase acidic protein	protein	695	40% helix, 16% strand	P03434
E	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	666	45% helix, 11% strand	P03432
F	Polymerase basic protein 2	protein	726	34% helix, 19% strand	P03429
G	Polymerase acidic protein	protein	694	40% helix, 14% strand	P03434
H	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	667	45% helix, 10% strand	P03432
I	Polymerase basic protein 2	protein	728	34% helix, 18% strand	P03429
J	Polymerase acidic protein	protein	692	41% helix, 16% strand	P03434
K	RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48)	protein	664	45% helix, 9% strand	P03432
L	Polymerase basic protein 2	protein	723	35% helix, 18% strand	P03429
M, N, O, P	Nanobody NB8205	protein	121	5% helix, 41% 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	836	0.87	0.89	110	empty
2	897	0.85	0.87	89	empty
3	832	0.84	0.87	84	empty
4	650	0.84	0.88	100	empty
5	538	0.83	0.89	68	empty

Interfaces

35 interfaces between chains.

H–I · 7503 Å² buried · 65 hydrogen bonds · protein-protein
D–E · 7501 Å² buried · 92 hydrogen bonds · protein-protein
A–B · 7483 Å² buried · 100 hydrogen bonds · protein-protein
J–K · 7450 Å² buried · 94 hydrogen bonds · protein-protein
G–H · 7321 Å² buried · 87 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6QPG · Influenza A virus Polymerase Heterotrimer A/nt/60/1968(H3N2) in complex with Nanobody… · 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 P03434
Every structure of UniProt P03432
Every structure of UniProt P03429
Elsewhere: RCSB PDB 6QPG · PDBe 6QPG · UniProt P03434 · UniProt P03432 · UniProt P03429

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