MolNFT v1 · #102636 · protein

Structure of influenza B PB2 cap-binding domain complex with GDP

4ORO · Polymerase PB2: “Structure of influenza B PB2 cap-binding domain complex with GDP”. X-ray diffraction, 1 ligand (GDP), 5 pockets (best druggability 0.76). MolNFT v1 #102636 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4ORO
Type: protein
Length: 676 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase PB2
Ligands: GDP
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Polymerase PB2	protein	169	22% helix, 41% strand	—

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	517	0.76	0.84	55	GDP
2	173	0.52	0.78	25	GDP
3	142	0.50	0.78	22	GDP
4	126	0.48	0.79	22	GDP
5	79	0.37	0.77	12	empty

Interfaces

2 interfaces between chains.

C–D · 732 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 407 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4ORO · Structure of Influenza B PB2 cap-binding domain complex with GDP · 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
Elsewhere: RCSB PDB 4ORO · PDBe 4ORO

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