MolNFT v1 · #96978 · protein
Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph (E68A mutant) bound to GTP
4JZT · Dgtp pyrophosphohydrolase: “Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph (E68A mutant) bound to GTP”. X-ray diffraction, 1 ligand (GTP), 4 pockets (best druggability 0.70). MolNFT v1 #96978 on GenesisL1: 3D…
- PDB
- 4JZT
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dgtp pyrophosphohydrolase
- EC
- 3.6.1.55
- UniProt
- O35013
- Ligands
- GTP
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dgtp pyrophosphohydrolase (EC 3.6.1.55) | protein | 158 | 16% helix, 42% strand | O35013 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.70 | 0.81 | 40 | empty |
| 2 | 223 | 0.55 | 0.78 | 34 | empty |
| 3 | 179 | 0.48 | 0.76 | 33 | GTP |
| 4 | 113 | 0.37 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–D · 690 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4JZT · Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH (E68A mutant)… · the same entry in another collection · chain A against A, TM-score 1.00
- O35013 · AlphaFold monomer V2.0 prediction for putative 8-oxo-dgtp diphosphatase ytkd (O35013) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O35013
- Elsewhere: RCSB PDB 4JZT · PDBe 4JZT · UniProt O35013
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