Research workbench
Structure of double mutant of human inos oxygenase domain with bound immidazole
Analyse Structure of double mutant of human inos oxygenase domain with bound immidazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EJ8
- Type
- protein
- Length
- 1,684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide synthase, inducible
- EC
- 1.14.13.39
- UniProt
- P35228
- Ligands
- HEC, H4B, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nitric oxide synthase, inducible (EC 1.14.13.39) | protein | 421 | 40% helix, 16% strand | P35228 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- H4B · 5,6,7,8-tetrahydrobiopterin · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.85 | 0.85 | 84 | HEC, H4B, IMD |
| 2 | 1069 | 0.84 | 0.85 | 78 | HEC, H4B, IMD |
| 3 | 1074 | 0.84 | 0.85 | 81 | HEC, H4B, IMD |
| 4 | 1148 | 0.84 | 0.85 | 88 | HEC, H4B, IMD |
| 5 | 58 | 0.71 | 0.98 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2729 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2725 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 378 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3EJ8 · Structure of double mutant of human iNOS oxygenase domain with bound immidazole · the same entry in another collection · chain A against A, TM-score 1.00
- P35228 · AlphaFold monomer V2.0 prediction for nitric oxide synthase, inducible (P35228) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P35228
- Elsewhere: RCSB PDB 3EJ8 · PDBe 3EJ8 · UniProt P35228
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