MolNFT v1 · #27722 · protein
Dctp deaminase from escherichia COLI. E138A mutant enzyme in complex with dutp
1XS6 · Deoxycytidine triphosphate deaminase: “Dctp deaminase from escherichia COLI. E138A mutant enzyme in complex with dutp”. X-ray diffraction, 2 ligands (DUT, MG), 12 pockets (best druggability 0.81). MolNFT v1 #27722 on GenesisL1: 3D…
- 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.
| Volume (ų) | 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 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2007 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2003 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 1997 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 1992 Ų 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
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