Research workbench
Crystal structure of loop deletion mutant of trypanosoma vivax nucleoside hydrolase (3GTVNH) in complex with immh
Analyse Crystal structure of loop deletion mutant of trypanosoma vivax nucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B9G
- Type
- protein
- Length
- 633 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, NA
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iag-nucleoside hydrolase (EC 3.2.2.1) | protein | 317 | 46% 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
- NA · Sodium ion · metal · 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 | 410 | 0.69 | 0.81 | 55 | CA, IMH |
Interfaces
1 interface between chains.
- A–B · 945 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3B9G · Crystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase… · 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 3B9G · PDBe 3B9G · UniProt Q9GPQ4
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