MolNFT v1 · #39498 · protein

Crystal structure of dcmp deaminase from streptococcus mutans

2HVV · Deoxycytidylate deaminase: “Crystal structure of dcmp deaminase from streptococcus mutans”. X-ray diffraction, 2 ligands (ZN, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #39498 on GenesisL1: 3D structure, binding sites and…

PDB: 2HVV
Type: protein
Length: 286 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxycytidylate deaminase
EC: 3.5.4.12
UniProt: Q8DSE5
Ligands: ZN, SO4
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Deoxycytidylate deaminase (EC 3.5.4.12)	protein	143	34% helix, 22% strand	Q8DSE5

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

Pockets

3 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	536	0.69	0.78	56	SO4
2	105	0.39	0.76	19	SO4
3	112	0.39	0.76	26	SO4

Interfaces

1 interface between chains.

A–B · 1579 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2HVV · Crystal structure of dCMP deaminase from Streptococcus mutans · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8DSE5
Elsewhere: RCSB PDB 2HVV · PDBe 2HVV · UniProt Q8DSE5

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