Research workbench
Inosine-guanosine nucleoside hydrolase (ig-nh)
Analyse Inosine-guanosine nucleoside hydrolase (ig-nh) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FZ0
- Type
- protein
- Length
- 1,319 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside hydrolase, putative
- EC
- 3.2.2.1
- UniProt
- Q57X73
- Ligands
- CA
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside hydrolase, putative (EC 3.2.2.1) | protein | 327 | 40% helix, 18% strand | Q57X73 |
| B | Nucleoside hydrolase, putative (EC 3.2.2.1) | protein | 338 | 38% helix, 18% strand | Q57X73 |
| C | Nucleoside hydrolase, putative (EC 3.2.2.1) | protein | 328 | 39% helix, 18% strand | Q57X73 |
| D | Nucleoside hydrolase, putative (EC 3.2.2.1) | protein | 326 | 40% helix, 17% strand | Q57X73 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.74 | 0.79 | 89 | CA, BTB |
| 2 | 335 | 0.67 | 0.81 | 47 | CA, BTB |
| 3 | 275 | 0.67 | 0.83 | 37 | CA, BTB |
| 4 | 371 | 0.67 | 0.80 | 51 | BTB |
| 5 | 387 | 0.62 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1085 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1082 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 841 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 804 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 143 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3FZ0 · Inosine-Guanosine Nucleoside Hydrolase (IG-NH) · 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 Q57X73
- Elsewhere: RCSB PDB 3FZ0 · PDBe 3FZ0 · UniProt Q57X73
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