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Crystal structure of the trypanosoma brucei inosine-adenosine- guanosine nucleoside hydrolase in complex with immucillin a
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
- 4I72
- Type
- protein
- Length
- 656 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
- UA2, NI, CA
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inosine-adenosine-guanosine-nucleoside hydrolase (EC 3.2.2.1) | protein | 328 | 45% helix, 15% strand | Q57ZL6 |
Ligands and binding sites
- UA2 · 3,4-pyrrolidinediol,2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-(hydroxymethyl)-2S,3S,4R,5R · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 7 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.81 | 0.88 | 63 | CA, UA2 |
| 2 | 73 | 0.62 | 0.90 | 15 | empty |
| 3 | 91 | 0.59 | 0.87 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1355 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4I72 · 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 4I72 · PDBe 4I72 · UniProt Q57ZL6
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