Research workbench
Crystal structure of nudix hydrolase DR1025 in complexed with gnp and MG+2
Analyse Crystal structure of nudix hydrolase DR1025 in complexed with gnp and MG+2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SZ3
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MUTT/NUDIX family protein
- EC
- 3.6.1.-
- UniProt
- Q9RVK2
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MUTT/NUDIX family protein (EC 3.6.1.-) | protein | 155 | 23% helix, 33% strand | Q9RVK2 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.51 | 0.77 | 28 | empty |
| 2 | 187 | 0.49 | 0.76 | 26 | empty |
| 3 | 116 | 0.45 | 0.78 | 23 | GNP |
| 4 | 72 | 0.39 | 0.79 | 20 | empty |
| 5 | 58 | 0.35 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1755 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1SZ3 · Crystal structure of nudix hydrolase DR1025 in complexed with gnp and MG+2 · 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 Q9RVK2
- Elsewhere: RCSB PDB 1SZ3 · PDBe 1SZ3 · UniProt Q9RVK2
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