MolNFT v1 · #18305 · protein
Structural basis for recognition and catalysis by the bifunctional dctp deaminase and dutpase from methanococcus jannaschii
1PKK · Bifunctional DEAMINASE/DIPHOSPHATASE: “Structural basis for recognition and catalysis by the bifunctional dctp deaminase and dutpase from…”. X-ray diffraction, 1 ligand (DCP), 2 pockets (best druggability 0.71). MolNFT v1 #18305 on…
- PDB
- 1PKK
- Type
- protein
- Length
- 359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional DEAMINASE/DIPHOSPHATASE
- EC
- 3.5.4.13, 3.6.1.23
- UniProt
- Q57872
- Ligands
- DCP
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional DEAMINASE/DIPHOSPHATASE (EC 3.5.4.13, 3.6.1.23) | protein | 182 | 15% helix, 42% strand | Q57872 |
| B | Bifunctional DEAMINASE/DIPHOSPHATASE (EC 3.5.4.13, 3.6.1.23) | protein | 177 | 15% helix, 43% strand | Q57872 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains B
- 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.71 | 0.78 | 60 | empty |
| 2 | 52 | 0.30 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 745 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1PKK · Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57872 · AlphaFold monomer V2.0 prediction for dctp deaminase, dump-forming (Q57872) · a predicted model of the same protein · chain B 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 Q57872
- Elsewhere: RCSB PDB 1PKK · PDBe 1PKK · UniProt Q57872
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