MolNFT v1 · #25211 · protein
Crystal structure of putative ADP ribose pyrophosphatase
1VIU · ADP-ribose pyrophosphatase: “Crystal structure of putative ADP ribose pyrophosphatase”. X-ray diffraction, 5 pockets (best druggability 0.67). MolNFT v1 #25211 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VIU
- Type
- protein
- Length
- 715 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribose pyrophosphatase
- UniProt
- P37128
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribose pyrophosphatase | protein | 180 | 21% helix, 42% strand | P37128 |
| B | ADP-ribose pyrophosphatase | protein | 181 | 22% helix, 44% strand | P37128 |
| C | ADP-ribose pyrophosphatase | protein | 175 | 23% helix, 43% strand | P37128 |
| D | ADP-ribose pyrophosphatase | protein | 179 | 22% helix, 45% strand | P37128 |
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.67 | 0.75 | 71 | empty |
| 2 | 347 | 0.66 | 0.81 | 48 | empty |
| 3 | 332 | 0.64 | 0.80 | 48 | empty |
| 4 | 310 | 0.63 | 0.80 | 50 | empty |
| 5 | 265 | 0.60 | 0.79 | 40 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2545 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2523 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
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 P37128
- Elsewhere: RCSB PDB 1VIU · PDBe 1VIU · UniProt P37128
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