Research workbench

Human deoxycytidine kinase damp, udp, mg ion product complex

Analyse Human deoxycytidine kinase damp, udp, mg ion product complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QRO
Type: protein
Length: 912 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxycytidine kinase
EC: 2.7.1.74
UniProt: P27707
Ligands: UDP, D5M, MG
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Deoxycytidine kinase (EC 2.7.1.74)	protein	228	57% helix, 12% strand	P27707

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
D5M · 2'-deoxyadenosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
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

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1150	0.77	0.79	98	UDP, D5M
2	107	0.75	0.95	26	D5M
3	152	0.69	0.89	33	UDP, D5M
4	173	0.67	0.86	33	UDP, D5M
5	61	0.33	0.77	15	UDP

Interfaces

3 interfaces between chains.

C–D · 1312 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1284 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 445 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2QRO · Human Deoxycytidine kinase dAMP, UDP, Mg ion product complex · the same entry in another collection · chain D against D, TM-score 1.00
P27707 · AlphaFold monomer V2.0 prediction for deoxycytidine kinase (P27707) · a predicted model of the same protein · chain C 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 P27707
Elsewhere: RCSB PDB 2QRO · PDBe 2QRO · UniProt P27707

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