Research workbench
Crystal structure of pnp with dadmeimmh from yersinia pseudotuberculosis
Analyse Crystal structure of pnp with dadmeimmh from yersinia pseudotuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OCC
- Type
- protein
- Length
- 1,424 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- B1JL34
- Ligands
- DIH, PO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 36% helix, 28% strand | B1JL34 |
| C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 236 | 38% helix, 28% strand | B1JL34 |
| D, E, F | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 238 | 37% helix, 28% strand | B1JL34 |
Ligands and binding sites
- DIH · 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one · ligand · 6 copies · chains A, F, B, C, D, E
- PO4 · Phosphate ion · ion · 6 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.82 | 0.83 | 129 | DIH, PO4 |
| 2 | 243 | 0.70 | 0.86 | 44 | DIH, PO4 |
| 3 | 204 | 0.70 | 0.87 | 42 | DIH, PO4 |
| 4 | 209 | 0.69 | 0.86 | 44 | DIH, PO4 |
| 5 | 196 | 0.69 | 0.87 | 40 | DIH, PO4 |
Interfaces
12 interfaces between chains.
- A–F · 1882 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 1878 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 1850 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 1800 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1795 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3OCC · Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis · the same entry in another collection · chain F against F, TM-score 1.00
- B1JL34 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (B1JL34) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 B1JL34
- Elsewhere: RCSB PDB 3OCC · PDBe 3OCC · UniProt B1JL34
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