Research workbench

Dctp deaminase from escherichia COLI. E138A mutant enzyme in complex with dutp

Analyse Dctp deaminase from escherichia COLI. E138A mutant enzyme in complex with dutp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XS6
Type: protein
Length: 1,158 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: P28248
Ligands: DUT, MG
Pockets: 12 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Deoxycytidine triphosphate deaminase (EC 3.5.4.13)	protein	193	19% helix, 35% strand	P28248

Ligands and binding sites

DUT · Deoxyuridine-5'-triphosphate · ligand · 6 copies · chains A, C, B, D, F, E
MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	184	0.81	0.96	38	MG, DUT
2	210	0.81	0.95	41	MG, DUT
3	199	0.81	0.95	38	MG, DUT
4	198	0.80	0.95	39	DUT, MG
5	176	0.80	0.96	35	MG, DUT

Interfaces

8 interfaces between chains.

B–C · 2029 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 2007 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2003 Å² buried · 35 hydrogen bonds · protein-protein
D–E · 1997 Å² buried · 36 hydrogen bonds · protein-protein
D–F · 1992 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

1XS6 · dCTP deaminase from Escherichia coli. E138A mutant enzyme in complex with dUTP · the same entry in another collection · chain D against D, TM-score 1.00
P28248 · AlphaFold monomer V2.0 prediction for dctp deaminase (P28248) · a predicted model of the same protein · chain F 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 P28248
Elsewhere: RCSB PDB 1XS6 · PDBe 1XS6 · UniProt P28248

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