Research workbench
Crystal structure of the trypanosoma brucei inosine-adenosine- guanosine nucleoside hydrolase in complex with the nitris metalorganic complex
Analyse Crystal structure of the trypanosoma brucei inosine-adenosine- guanosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I75
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-adenosine-guanosine-nucleoside hydrolase
- EC
- 3.2.2.1
- UniProt
- Q57ZL6
- Ligands
- NI, CA
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-adenosine-guanosine-nucleoside hydrolase (EC 3.2.2.1) | protein | 325 | 46% helix, 16% strand | Q57ZL6 |
| B | Inosine-adenosine-guanosine-nucleoside hydrolase (EC 3.2.2.1) | protein | 322 | 46% helix, 16% strand | Q57ZL6 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 9 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.69 | 0.87 | 30 | CA, NI, TRS |
| 2 | 199 | 0.67 | 0.85 | 32 | NI, TRS |
| 3 | 147 | 0.66 | 0.87 | 20 | empty |
| 4 | 52 | 0.35 | 0.79 | 16 | empty |
| 5 | 51 | 0.29 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1306 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4I75 · Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside… · 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 Q57ZL6
- Elsewhere: RCSB PDB 4I75 · PDBe 4I75 · UniProt Q57ZL6
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