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Crystal structure of a deoxycytidine triphosphate deaminase (dctp deaminase) from burkholderia thailandensis
Analyse Crystal structure of a deoxycytidine triphosphate deaminase (dctp deaminase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DHK
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxycytidine triphosphate deaminase
- EC
- 3.5.4.13
- UniProt
- Q2T083
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxycytidine triphosphate deaminase (EC 3.5.4.13) | protein | 171 | 11% helix, 47% strand | Q2T083 |
| B | Deoxycytidine triphosphate deaminase (EC 3.5.4.13) | protein | 159 | 11% helix, 48% strand | Q2T083 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.47 | 0.75 | 23 | empty |
| 2 | 76 | 0.34 | 0.75 | 17 | EDO |
| 3 | 53 | 0.34 | 0.78 | 14 | EDO |
| 4 | 55 | 0.30 | 0.75 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 281 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4DHK · Crystal structure of a deoxycytidine triphosphate deaminase (dCTP deaminase) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2T083 · AlphaFold monomer V2.0 prediction for dctp deaminase (Q2T083) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q2T083
- Elsewhere: RCSB PDB 4DHK · PDBe 4DHK · UniProt Q2T083
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