Research workbench

Human deoxycytidine kinase dcmp, udp, mg ion product complex

Analyse Human deoxycytidine kinase dcmp, 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: 2QRN
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, DCM, MG
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Deoxycytidine kinase (EC 2.7.1.74)	protein	228	56% helix, 12% strand	P27707

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
DCM · 2'-deoxycytidine-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

8 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	862	0.80	0.82	77	MG, UDP, DCM
2	183	0.70	0.88	34	MG, UDP, DCM
3	190	0.70	0.87	34	UDP, DCM
4	187	0.68	0.87	31	UDP, DCM
5	55	0.31	0.76	11	empty

Interfaces

3 interfaces between chains.

C–D · 1301 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1231 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 425 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2QRN · Human Deoxycytidine kinase dCMP, 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 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 P27707
Elsewhere: RCSB PDB 2QRN · PDBe 2QRN · UniProt P27707

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