Research workbench
Crystal structure of trypanosoma vivax nucleoside hydrolase soaked with immucillinh
Analyse Crystal structure of trypanosoma vivax nucleoside hydrolase soaked with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FF1
- Type
- protein
- Length
- 630 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
- IMH, CA
- Pockets
- 3 · best druggability 0.59
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 | 314 | 45% helix, 17% strand | Q9GPQ4 |
| B | Iag-nucleoside hydrolase (EC 3.2.2.1) | protein | 316 | 45% helix, 17% strand | Q9GPQ4 |
Ligands and binding sites
- IMH · 1,4-dideoxy-4-aza-1-(S)-(9-deazahypoxanthin-9-yl)-D-ribitol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.59 | 0.86 | 22 | IMH |
| 2 | 197 | 0.53 | 0.78 | 27 | CA, IMH |
| 3 | 101 | 0.38 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2FF1 · Crystal structure of Trypanosoma vivax nucleoside hydrolase soaked with ImmucillinH · 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 2FF1 · PDBe 2FF1 · UniProt Q9GPQ4
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