Research workbench
Crystal structure of trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8- YLMETHYL)PYRROLIDIN-3,4-diol
Analyse Crystal structure of trypanosoma vivax nucleoside hydrolase in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EPX
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iag-nucleoside hydrolase
- EC
- 3.2.2.1
- UniProt
- Q9GPQ4
- Ligands
- IMQ, CA
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iag-nucleoside hydrolase (EC 3.2.2.1) | protein | 322 | 45% helix, 17% strand | Q9GPQ4 |
| B | Iag-nucleoside hydrolase (EC 3.2.2.1) | protein | 324 | 44% helix, 17% strand | Q9GPQ4 |
Ligands and binding sites
- IMQ · (2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8-ylmethyl)pyrrolidine-3,4-diol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.79 | 0.84 | 62 | CA, IMQ |
Interfaces
1 interface between chains.
- A–B · 1341 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3EPX · Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor… · 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 Q9GPQ4
- Elsewhere: RCSB PDB 3EPX · PDBe 3EPX · UniProt Q9GPQ4
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