Research workbench
Crystal structure of pnp with an inhibitor DADME_IMMH from vibrio cholerae
Analyse Crystal structure of pnp with an inhibitor DADME_IMMH from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OF3
- Type
- protein
- Length
- 2,878 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type 1
- EC
- 2.4.2.1
- UniProt
- Q9KPM0
- Ligands
- DIH, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, I, J, K, L | Purine nucleoside phosphorylase deod-type 1 (EC 2.4.2.1) | protein | 240 | 36% helix, 28% strand | Q9KPM0 |
| D | Purine nucleoside phosphorylase deod-type 1 (EC 2.4.2.1) | protein | 238 | 37% helix, 29% strand | Q9KPM0 |
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 · 12 copies · chains A, C, B, E, D, L, F, J, G, I, H, K
- PO4 · Phosphate ion · ion · 12 copies · chains A, C, B, E, D, L, F, J, G, I, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.80 | 0.85 | 76 | DIH, PO4 |
| 2 | 929 | 0.75 | 0.78 | 67 | empty |
| 3 | 181 | 0.74 | 0.91 | 42 | DIH, PO4 |
| 4 | 216 | 0.73 | 0.89 | 49 | DIH, PO4 |
| 5 | 744 | 0.72 | 0.78 | 67 | empty |
Interfaces
26 interfaces between chains.
- A–C · 1981 Ų buried · 6 hydrogen bonds · protein-protein
- G–I · 1978 Ų buried · 5 hydrogen bonds · protein-protein
- F–J · 1972 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 1971 Ų buried · 7 hydrogen bonds · protein-protein
- D–L · 1966 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3OF3 · Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae · the same entry in another collection · chain L against L, 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 Q9KPM0
- Elsewhere: RCSB PDB 3OF3 · PDBe 3OF3 · UniProt Q9KPM0
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