Research workbench
Dctp deaminase from escherichia COLI- E138A mutant enzyme in complex with dctp
Analyse Dctp deaminase from escherichia COLI- E138A mutant enzyme in complex with dctp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XS4
- 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
- DCP, MG
- Pockets
- 15 · 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
- DCP · 2'-deoxycytidine-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
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.87 | 0.88 | 113 | empty |
| 2 | 197 | 0.82 | 0.96 | 40 | DCP, MG |
| 3 | 207 | 0.81 | 0.95 | 41 | MG, DCP |
| 4 | 207 | 0.81 | 0.95 | 38 | DCP, MG |
| 5 | 217 | 0.81 | 0.94 | 43 | MG, DCP |
Interfaces
15 interfaces between chains.
- A–C · 2043 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2029 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2023 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2010 Ų buried · 38 hydrogen bonds · protein-protein
- D–F · 2004 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1XS4 · dCTP deaminase from Escherichia coli- E138A mutant enzyme in complex with dCTP · 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 D 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 1XS4 · PDBe 1XS4 · UniProt P28248
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