MolNFT v1 · #94788 · protein
Crystal structure of the trypanosoma brucei inosine-adenosine- guanosine nucleoside hydrolase in complex with compound uamc-00312
4I73 · Inosine-adenosine-guanosine-nucleoside hydrolase: “Crystal structure of the trypanosoma brucei inosine-adenosine- guanosine nucleoside hydrolase in complex with…”. X-ray diffraction, 3 ligands (MBY, NI, CA), 9 pockets (best…
- PDB
- 4I73
- Type
- protein
- Length
- 1,296 residues
- Chains
- 4
- 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
- MBY, NI, CA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Inosine-adenosine-guanosine-nucleoside hydrolase (EC 3.2.2.1) | protein | 327 | 46% helix, 15% strand | Q57ZL6 |
| B | Inosine-adenosine-guanosine-nucleoside hydrolase (EC 3.2.2.1) | protein | 324 | 46% helix, 15% strand | Q57ZL6 |
| C | Inosine-adenosine-guanosine-nucleoside hydrolase (EC 3.2.2.1) | protein | 318 | 46% helix, 15% strand | Q57ZL6 |
Ligands and binding sites
- MBY · (2R,3R,4S)-2-(hydroxymethyl)-1-[(4-hydroxythieno[3,2-d]pyrimidin-7-yl)methyl]pyrrolidine-3,4-diol · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 17 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.80 | 0.85 | 71 | MBY, CA, NI |
| 2 | 874 | 0.77 | 0.80 | 93 | MBY, NI |
| 3 | 760 | 0.76 | 0.81 | 74 | NI |
| 4 | 88 | 0.62 | 0.89 | 16 | empty |
| 5 | 86 | 0.62 | 0.89 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1329 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1180 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 253 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 212 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 202 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4I73 · 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 4I73 · PDBe 4I73 · UniProt Q57ZL6
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