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Human vaccinia-related kinase 1

Analyse Human vaccinia-related kinase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OP5
Type: protein
Length: 1,249 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase VRK1
EC: 2.7.11.1
UniProt: Q99986
Ligands: REB
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1)	protein	320	39% helix, 18% strand	Q99986
B	SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1)	protein	319	39% helix, 18% strand	Q99986
C	SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1)	protein	308	40% helix, 19% strand	Q99986
D	SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1)	protein	302	42% helix, 18% strand	Q99986

Ligands and binding sites

REB · [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1057	0.80	0.82	106	empty
2	751	0.73	0.78	69	GOL
3	324	0.64	0.80	32	REB
4	273	0.60	0.79	30	REB
5	52	0.60	0.92	19	EDO

Interfaces

4 interfaces between chains.

A–B · 799 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 625 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 570 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 287 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3OP5 · Human vaccinia-related kinase 1 · the same entry in another collection · chain D against D, TM-score 1.00
Q99986 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase VRK1 (Q99986) · a predicted model of the same protein · chain D 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 Q99986
Elsewhere: RCSB PDB 3OP5 · PDBe 3OP5 · UniProt Q99986

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