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Crystal structure of purine nucleoside phosphorylase from leptotrichia buccalis C-1013-B, nysgrc target 029767.
Analyse Crystal structure of purine nucleoside phosphorylase from leptotrichia buccalis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M7W
- Type
- protein
- Length
- 706 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- C7N9Q9
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 236 | 36% helix, 28% strand | C7N9Q9 |
| B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 234 | 35% helix, 28% strand | C7N9Q9 |
Ligands and binding sites
- 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.72 | 0.79 | 69 | PO4 |
| 2 | 483 | 0.70 | 0.80 | 61 | PO4 |
| 3 | 305 | 0.56 | 0.76 | 43 | empty |
| 4 | 236 | 0.53 | 0.76 | 34 | PO4 |
| 5 | 122 | 0.41 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1590 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 4M7W · Crystal structure of purine nucleoside phosphorylase from Leptotrichia buccalis C-1013-b… · 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 C7N9Q9
- Elsewhere: RCSB PDB 4M7W · PDBe 4M7W · UniProt C7N9Q9
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