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Dctp deaminase from escherichia COLI in complex with dutp

Analyse Dctp deaminase from escherichia COLI 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: 1XS1
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: 16 · best druggability 0.87

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 · 6 copies · chains A, B, C, D, E, F

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1096	0.87	0.88	110	empty
2	197	0.80	0.95	40	MG, DUT
3	161	0.80	0.96	36	MG, DUT
4	197	0.80	0.94	33	DUT, MG
5	195	0.79	0.94	37	DUT, MG

Interfaces

15 interfaces between chains.

E–F · 2058 Å² buried · 36 hydrogen bonds · protein-protein
D–E · 2027 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 2024 Å² buried · 35 hydrogen bonds · protein-protein
D–F · 2014 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 1995 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

1XS1 · dCTP deaminase from Escherichia coli in complex with dUTP · the same entry in another collection · chain F against F, TM-score 1.00
P28248 · AlphaFold monomer V2.0 prediction for dctp deaminase (P28248) · a predicted model of the same protein · chain E 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 1XS1 · PDBe 1XS1 · UniProt P28248

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