MolNFT v1 · #69160 · protein
Crystal structure of grouper iridovirus purine nucleoside phosphorylase
3KHS: “Crystal structure of grouper iridovirus purine nucleoside phosphorylase”. X-ray diffraction, 1 ligand (PO4), 17 pockets (best druggability 0.80). MolNFT v1 #69160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KHS
- Type
- protein
- Length
- 1,066 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q5YBA4
- Ligands
- PO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 264 | 36% helix, 26% strand | Q5YBA4 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 270 | 37% helix, 25% strand | Q5YBA4 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 270 | 35% helix, 25% strand | Q5YBA4 |
| D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 262 | 37% helix, 26% strand | Q5YBA4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.80 | 0.98 | 20 | empty |
| 2 | 89 | 0.61 | 0.88 | 24 | empty |
| 3 | 93 | 0.59 | 0.87 | 24 | empty |
| 4 | 93 | 0.59 | 0.87 | 22 | empty |
| 5 | 94 | 0.57 | 0.86 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1022 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1000 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 994 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 336 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3KHS · Crystal structure of grouper iridovirus purine nucleoside phosphorylase · 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 Q5YBA4
- Elsewhere: RCSB PDB 3KHS · PDBe 3KHS · UniProt Q5YBA4
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