Research workbench
Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ampcpr
Analyse Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BM4
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- 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
- Ligands
- ADV, MG
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.-) | protein | 197 | 24% helix, 44% strand | Q9UKK9 |
Ligands and binding sites
- ADV · Alpha-beta methylene adp-ribose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.72 | 0.84 | 46 | MG, ADV |
| 2 | 375 | 0.72 | 0.83 | 47 | MG, ADV |
| 3 | 64 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3180 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3BM4 · Crystal Structure of Human ADP-ribose Pyrophosphatase NUDT5 In complex with magnesium and… · 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 3BM4 · PDBe 3BM4 · UniProt Q9UKK9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.