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Human dcmp deaminase

Analyse Human dcmp deaminase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2W4L
Type: protein
Length: 930 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxycytidylate deaminase
EC: 3.5.4.12
UniProt: P32321
Ligands: ZN, CL
Pockets: 11 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxycytidylate deaminase (EC 3.5.4.12)	protein	160	30% helix, 21% strand	P32321
B	Deoxycytidylate deaminase (EC 3.5.4.12)	protein	157	32% helix, 22% strand	P32321
C	Deoxycytidylate deaminase (EC 3.5.4.12)	protein	142	32% helix, 24% strand	P32321
D	Deoxycytidylate deaminase (EC 3.5.4.12)	protein	150	35% helix, 23% strand	P32321
E	Deoxycytidylate deaminase (EC 3.5.4.12)	protein	162	30% helix, 21% strand	P32321
F	Deoxycytidylate deaminase (EC 3.5.4.12)	protein	159	31% helix, 21% strand	P32321

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 4 copies · chains A, B, E, F

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

Pockets

11 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	1065	0.76	0.78	107	empty
2	892	0.75	0.79	105	CL
3	821	0.74	0.78	96	CL
4	497	0.68	0.79	68	empty
5	237	0.62	0.81	40	empty

Interfaces

10 interfaces between chains.

A–F · 2415 Å² buried · 28 hydrogen bonds · protein-protein
B–C · 2039 Å² buried · 26 hydrogen bonds · protein-protein
D–E · 1989 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1434 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1390 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

2W4L · Human dCMP deaminase · the same entry in another collection · chain F against F, TM-score 1.00
P32321 · AlphaFold monomer V2.0 prediction for deoxycytidylate deaminase (P32321) · 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 P32321
Elsewhere: RCSB PDB 2W4L · PDBe 2W4L · UniProt P32321

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