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Crystal structure of purine nucleoside phosphorylase from trichomonas vaginalis with imm-a
Analyse Crystal structure of purine nucleoside phosphorylase from trichomonas vaginalis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I4T
- Type
- protein
- Length
- 689 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trichomonas vaginalis purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- A2E7Y6
- Ligands
- UA2, PO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trichomonas vaginalis purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 230 | 35% helix, 30% strand | A2E7Y6 |
| B | Trichomonas vaginalis purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 235 | 34% helix, 29% strand | A2E7Y6 |
| C | Trichomonas vaginalis purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 224 | 32% helix, 26% strand | A2E7Y6 |
Ligands and binding sites
- UA2 · 3,4-pyrrolidinediol,2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-(hydroxymethyl)-2S,3S,4R,5R · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 5 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.74 | 0.97 | 22 | PO4 |
| 2 | 253 | 0.69 | 0.85 | 39 | PO4, UA2 |
| 3 | 333 | 0.63 | 0.79 | 42 | PO4, UA2 |
| 4 | 200 | 0.52 | 0.77 | 31 | PO4, UA2 |
| 5 | 162 | 0.51 | 0.79 | 19 | PO4 |
Interfaces
3 interfaces between chains.
- A–C · 1708 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1670 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 98 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2I4T · Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with Imm-A · 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 A2E7Y6
- Elsewhere: RCSB PDB 2I4T · PDBe 2I4T · UniProt A2E7Y6
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