MolNFT v1 · #47647 · protein
Structure of purine nucleoside phosphorylase from anopheles gambiae in complex with dadme-immh
2P4S: “Structure of purine nucleoside phosphorylase from anopheles gambiae in complex with dadme-immh”. X-ray diffraction, 2 ligands (DIH, PO4), 10 pockets (best druggability 0.79). MolNFT v1 #47647 on GenesisL1: 3D structure, binding…
- PDB
- 2P4S
- Type
- protein
- Length
- 846 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- A4Q998
- Ligands
- DIH, PO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 282 | 37% helix, 24% strand | A4Q998 |
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 · 3 copies · chains A, C, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.79 | 0.98 | 28 | PO4, DIH |
| 2 | 100 | 0.78 | 0.98 | 23 | PO4, DIH |
| 3 | 97 | 0.78 | 0.98 | 23 | PO4, DIH |
| 4 | 52 | 0.74 | 0.99 | 16 | PO4 |
| 5 | 299 | 0.56 | 0.76 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1217 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1205 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1202 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2P4S · Structure of Purine Nucleoside Phosphorylase from Anopheles gambiae in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- A4Q998 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (A4Q998) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A4Q998
- Elsewhere: RCSB PDB 2P4S · PDBe 2P4S · UniProt A4Q998
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