MolNFT v1 · #110001 · protein

Dctp deaminase-dutpase from bacillus halodurans

4XJC · Deoxycytidine triphosphate deaminase: “Dctp deaminase-dutpase from bacillus halodurans”. X-ray diffraction, 2 ligands (TTP, MG), 6 pockets (best druggability 0.86). MolNFT v1 #110001 on GenesisL1: 3D structure, binding sites and…

PDB: 4XJC
Type: protein
Length: 1,054 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxycytidine triphosphate deaminase
EC: 3.5.4.13
UniProt: Q9KFV3
Ligands: TTP, MG
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, B, D	Deoxycytidine triphosphate deaminase (EC 3.5.4.13)	protein	177	11% helix, 42% strand	Q9KFV3
F	Deoxycytidine triphosphate deaminase (EC 3.5.4.13)	protein	169	9% helix, 43% strand	Q9KFV3

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 6 copies · chains A, E, C, B, F, D
MG · Magnesium ion · metal · 6 copies · chains A, C, E, B, D, F
PEG · Di(hydroxyethyl)ether · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	630	0.86	0.90	98	MG, TTP
2	607	0.84	0.89	97	TTP, MG
3	1197	0.81	0.82	116	empty
4	197	0.81	0.95	49	empty
5	269	0.78	0.91	45	MG, TTP

Interfaces

14 interfaces between chains.

A–C · 2010 Å² buried · 26 hydrogen bonds · protein-protein
A–E · 2002 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 1996 Å² buried · 24 hydrogen bonds · protein-protein
B–F · 1987 Å² buried · 26 hydrogen bonds · protein-protein
C–E · 1932 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

4XJC · dCTP deaminase-dUTPase from Bacillus halodurans · the same entry in another collection · chain B against B, TM-score 1.00
Q9KFV3 · AlphaFold monomer V2.0 prediction for dctp deaminase, dump-forming (Q9KFV3) · a predicted model of the same protein · chain F 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 Q9KFV3
Elsewhere: RCSB PDB 4XJC · PDBe 4XJC · UniProt Q9KFV3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.