Research workbench
Crystal structure of purine nucleoside phosphorylase from trichomonas vaginalis with dadme-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
- 2ISC
- Type
- protein
- Length
- 1,394 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- A2E7Y6
- Ligands
- 223, PO4
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 227 | 34% helix, 31% strand | A2E7Y6 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 236 | 33% helix, 30% strand | A2E7Y6 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 231 | 33% helix, 30% strand | A2E7Y6 |
| D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 238 | 33% helix, 29% strand | A2E7Y6 |
| E | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 229 | 34% helix, 30% strand | A2E7Y6 |
| F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 233 | 33% helix, 30% strand | A2E7Y6 |
Ligands and binding sites
- 223 · (3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(hydroxymethyl)pyrrolidin-3-ol · ligand · 6 copies · chains A, B, C, E, D, F
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.76 | 0.78 | 98 | PO4 |
| 2 | 90 | 0.76 | 0.97 | 22 | empty |
| 3 | 81 | 0.74 | 0.97 | 20 | empty |
| 4 | 90 | 0.73 | 0.96 | 24 | empty |
| 5 | 434 | 0.70 | 0.81 | 53 | PO4, 223 |
Interfaces
12 interfaces between chains.
- E–F · 1726 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1726 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1718 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1570 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1568 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2ISC · Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with… · 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 2ISC · PDBe 2ISC · UniProt A2E7Y6
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