MolNFT v1 · #167794 · protein

Structure of the cydia pomonella granulovirus kinase, pk-1

6VVG · Arginine kinase: “Structure of the cydia pomonella granulovirus kinase, pk-1”. X-ray diffraction, 1 ligand (AMP), 8 pockets (best druggability 0.65). MolNFT v1 #167794 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VVG
Type: protein
Length: 531 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginine kinase
UniProt: A0A097P1P8
Ligands: AMP
Pockets: 8 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arginine kinase	protein	267	37% helix, 16% strand	A0A097P1P8
B	Arginine kinase	protein	264	41% helix, 18% strand	A0A097P1P8

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B

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

Pockets

8 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	346	0.65	0.80	36	AMP
2	286	0.60	0.78	33	AMP
3	115	0.45	0.78	18	empty
4	134	0.44	0.76	21	empty
5	91	0.40	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 1732 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6VVG · Structure of the Cydia pomonella Granulovirus kinase, PK-1 · 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 A0A097P1P8
Elsewhere: RCSB PDB 6VVG · PDBe 6VVG · UniProt A0A097P1P8

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