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Structure of vaccinia-related kinase 2

Analyse Structure of vaccinia-related kinase 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V62
Type: protein
Length: 619 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase VRK2
EC: 2.7.11.1
UniProt: Q86Y07
Ligands: MG
Pockets: 8 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase VRK2 (EC 2.7.11.1)	protein	309	40% helix, 18% strand	Q86Y07
B	SERINE/THREONINE-protein kinase VRK2 (EC 2.7.11.1)	protein	310	38% helix, 18% strand	Q86Y07

Ligands and binding sites

MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
SIN · Succinic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	511	0.67	0.78	68	EDO
2	152	0.45	0.76	27	empty
3	99	0.38	0.75	14	empty
4	103	0.38	0.75	17	empty
5	75	0.38	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 714 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2V62 · Structure of vaccinia-related kinase 2 · the same entry in another collection · chain A against A, TM-score 1.00
Q86Y07 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase VRK2 (Q86Y07) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q86Y07
Elsewhere: RCSB PDB 2V62 · PDBe 2V62 · UniProt Q86Y07

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