Research workbench
Purine nucleoside phosphorylase from cellulomonas sp. in complex with 8-iodo-guanine
Analyse Purine nucleoside phosphorylase from cellulomonas sp. 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
- 1C3X
- Type
- protein
- Length
- 798 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentosyltransferase
- UniProt
- P81989
- Ligands
- 8IG, CA, PO4
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pentosyltransferase | protein | 266 | 33% helix, 25% strand | P81989 |
Ligands and binding sites
- 8IG · 8-iodo-guanine · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.84 | 0.95 | 43 | empty |
| 2 | 598 | 0.67 | 0.77 | 64 | empty |
| 3 | 324 | 0.64 | 0.80 | 45 | PO4, 8IG |
| 4 | 311 | 0.62 | 0.79 | 45 | PO4, 8IG |
| 5 | 297 | 0.62 | 0.80 | 44 | PO4, 8IG |
Interfaces
3 interfaces between chains.
- B–C · 832 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 796 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1C3X · Purine nucleoside phosphorylase from cellulomonas sp. in complex with 8-iodo-guanine · 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 1C3X · PDBe 1C3X · UniProt P81989
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