Research workbench
Purine nucleoside hydrolase with a transition state inhibitor
Analyse Purine nucleoside hydrolase with a transition state inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2MAS
- Type
- protein
- Length
- 1,252 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-uridine nucleoside N-ribohydrolase
- EC
- 3.2.2.1
- UniProt
- Q27546
- Ligands
- PIR, CA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Inosine-uridine nucleoside N-ribohydrolase (EC 3.2.2.1) | protein | 313 | 40% helix, 18% strand | Q27546 |
Ligands and binding sites
- PIR · 2-(4-amino-phenyl)-5-hydroxymethyl-pyrrolidine-3,4-diol · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.74 | 0.84 | 70 | PIR |
| 2 | 457 | 0.74 | 0.83 | 70 | PIR |
| 3 | 101 | 0.68 | 0.92 | 26 | CA, PIR |
| 4 | 106 | 0.67 | 0.90 | 24 | PIR |
| 5 | 549 | 0.66 | 0.77 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–D · 917 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 895 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 827 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 824 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2MAS · Purine nucleoside hydrolase with a transition state inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q27546 · AlphaFold monomer V2.0 prediction for inosine-uridine preferring nucleoside hydrolase… · 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 Q27546
- Elsewhere: RCSB PDB 2MAS · PDBe 2MAS · UniProt Q27546
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