Research workbench
A131Q mutant of cyt P460 of nitrosomonas sp. AL212 with bound NH2OH
Analyse A131Q mutant of cyt P460 of nitrosomonas sp. AL212 with bound NH2OH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E0Y
- Type
- protein
- Length
- 640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P460
- UniProt
- F9ZFJ0
- Ligands
- HEC, HOA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cytochrome P460 | protein | 161 | 22% helix, 35% strand | F9ZFJ0 |
| B, C | Cytochrome P460 | protein | 159 | 22% helix, 36% strand | F9ZFJ0 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- HOA · Hydroxyamine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.72 | 0.87 | 29 | HEC, HOA |
| 2 | 176 | 0.72 | 0.89 | 29 | HEC, HOA |
| 3 | 201 | 0.71 | 0.87 | 32 | HEC, HOA |
| 4 | 219 | 0.70 | 0.86 | 36 | HEC, HOA |
| 5 | 167 | 0.48 | 0.77 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1681 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1671 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 cofactor (heme c attachment).
Compared structures
- 6E0Y · A131Q mutant of cyt P460 of Nitrosomonas sp. AL212 with bound NH2OH · 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 F9ZFJ0
- Elsewhere: RCSB PDB 6E0Y · PDBe 6E0Y · UniProt F9ZFJ0
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