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Structure of the midlink and cap-binding domains of influenza a polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor

Analyse Structure of the midlink and cap-binding domains of influenza a polymerase PB2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EUY
Type: protein
Length: 821 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase basic protein 2
UniProt: P31345
Ligands: BYB, SO4
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polymerase basic protein 2	protein	277	31% helix, 31% strand	P31345
B	Polymerase basic protein 2	protein	267	33% helix, 30% strand	P31345
C	Polymerase basic protein 2	protein	277	31% helix, 30% strand	P31345

Ligands and binding sites

BYB · (2~{S},3~{S})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrazolo[3,4-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1091	0.84	0.85	103	BYB, SO4
2	355	0.73	0.84	39	BYB
3	433	0.69	0.80	42	empty
4	436	0.61	0.76	61	empty
5	272	0.55	0.77	47	empty

Interfaces

3 interfaces between chains.

A–C · 976 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 442 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 15 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6EUY · Structure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit… · 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 P31345
Elsewhere: RCSB PDB 6EUY · PDBe 6EUY · UniProt P31345

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