Research workbench
Structural basis for recognition and catalysis by the bifunctional dctp deaminase and dutpase from methanococcus jannaschii
Analyse Structural basis for recognition and catalysis by the bifunctional dctp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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