MolNFT v1 · #62302 · protein

Crystal structure of an avian influenza virus protein

3EBJ · Polymerase acidic protein: “Crystal structure of an avian influenza virus protein”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.71). MolNFT v1 #62302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EBJ
Type: protein
Length: 701 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polymerase acidic protein
UniProt: Q9Q0U9
Ligands: MG
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Polymerase acidic protein	protein	175	50% helix, 13% strand	Q9Q0U9
B	Polymerase acidic protein	protein	175	51% helix, 13% strand	Q9Q0U9
C	Polymerase acidic protein	protein	176	52% helix, 13% strand	Q9Q0U9

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	529	0.71	0.80	39	MG
2	444	0.68	0.80	39	MG
3	597	0.68	0.77	48	MG
4	461	0.63	0.76	38	MG
5	467	0.57	0.73	37	empty

Interfaces

4 interfaces between chains.

A–B · 606 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 596 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 156 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 25 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3EBJ · Crystal structure of an avian influenza virus protein · 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 Q9Q0U9
Elsewhere: RCSB PDB 3EBJ · PDBe 3EBJ · UniProt Q9Q0U9

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