MolNFT v1 · #19240 · protein
Purine nucleoside phosphorylase from cellulomonas sp. in complex with phosphate
1QE5 · Pentosyltransferase: “Purine nucleoside phosphorylase from cellulomonas sp. in complex with phosphate”. X-ray diffraction, 2 ligands (CA, PO4), 7 pockets (best druggability 0.82). MolNFT v1 #19240 on GenesisL1: 3D structure, binding…
- PDB
- 1QE5
- Type
- protein
- Length
- 798 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentosyltransferase
- EC
- 2.4.2.1
- UniProt
- P81989
- Ligands
- CA, PO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pentosyltransferase (EC 2.4.2.1) | protein | 266 | 32% helix, 24% strand | P81989 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.82 | 0.95 | 41 | empty |
| 2 | 714 | 0.71 | 0.78 | 82 | empty |
| 3 | 433 | 0.66 | 0.79 | 50 | PO4 |
| 4 | 307 | 0.62 | 0.79 | 45 | PO4 |
| 5 | 290 | 0.61 | 0.79 | 41 | PO4 |
Interfaces
3 interfaces between chains.
- A–B · 806 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 798 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 789 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1QE5 · Purine nucleoside phosphorylase from cellulomonas sp. in complex with phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P81989 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P81989) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P81989
- Elsewhere: RCSB PDB 1QE5 · PDBe 1QE5 · UniProt P81989
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