Research workbench
Crystal structure of a purine nucleoside phosphorylase from entamoeba histolytica bound to adenosine
Analyse Crystal structure of a purine nucleoside phosphorylase from entamoeba… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U40
- Type
- protein
- Length
- 1,405 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- C4LXG4
- Ligands
- ADN, NO3, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 238 | 32% helix, 30% strand | C4LXG4 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 229 | 35% helix, 31% strand | C4LXG4 |
| D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 241 | 32% helix, 31% strand | C4LXG4 |
| E | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 232 | 31% helix, 31% strand | C4LXG4 |
| F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 227 | 33% helix, 31% strand | C4LXG4 |
Ligands and binding sites
- ADN · Adenosine · ligand · 6 copies · chains A, F, B, C, D, E
- NO3 · Nitrate ion · ion · 7 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.76 | 0.97 | 22 | empty |
| 2 | 635 | 0.76 | 0.82 | 66 | ADN |
| 3 | 93 | 0.75 | 0.96 | 22 | empty |
| 4 | 108 | 0.74 | 0.95 | 24 | empty |
| 5 | 474 | 0.70 | 0.80 | 47 | ADN |
Interfaces
12 interfaces between chains.
- E–F · 1705 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1670 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1655 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 1621 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1612 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3U40 · Crystal structure of a purine nucleoside phosphorylase from Entamoeba histolytica bound… · 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 C4LXG4
- Elsewhere: RCSB PDB 3U40 · PDBe 3U40 · UniProt C4LXG4
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