Research workbench
Crystal structure of human ADP-ribose pyrophosphatase NUDT5
Analyse Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DSB
- Type
- protein
- Length
- 824 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-sugar pyrophosphatase
- EC
- 3.6.1.13, 3.6.1.-
- UniProt
- Q9UKK9
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.-) | protein | 206 | 23% helix, 39% strand | Q9UKK9 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.79 | 0.82 | 95 | empty |
| 2 | 481 | 0.74 | 0.83 | 43 | empty |
| 3 | 403 | 0.72 | 0.83 | 45 | empty |
| 4 | 411 | 0.70 | 0.82 | 45 | empty |
| 5 | 388 | 0.68 | 0.81 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3658 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 3192 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 822 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 278 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 174 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2DSB · Crystal structure of human ADP-ribose pyrophosphatase NUDT5 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9UKK9
- Elsewhere: RCSB PDB 2DSB · PDBe 2DSB · UniProt Q9UKK9
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