MolNFT v1 · #147053 · protein
A131E mutant of cyt P460 of nitrosomonas sp. AL212
6E0X · Cytochrome P460: “A131E mutant of cyt P460 of nitrosomonas sp. AL212”. X-ray diffraction, 1 ligand (HEC), 10 pockets (best druggability 0.69). MolNFT v1 #147053 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6E0X
- Type
- protein
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P460
- UniProt
- F9ZFJ0
- Ligands
- HEC
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P460 | protein | 160 | 24% helix, 36% strand | F9ZFJ0 |
| B | Cytochrome P460 | protein | 161 | 22% helix, 36% strand | F9ZFJ0 |
| C, D | Cytochrome P460 | protein | 159 | 24% helix, 36% strand | F9ZFJ0 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.69 | 0.87 | 31 | HEC |
| 2 | 196 | 0.69 | 0.86 | 31 | HEC |
| 3 | 183 | 0.68 | 0.86 | 31 | HEC |
| 4 | 178 | 0.67 | 0.86 | 30 | HEC |
| 5 | 153 | 0.47 | 0.77 | 27 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1674 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1664 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 274 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor (heme c attachment).
Compared structures
- 6E0X · A131E mutant of cyt P460 of Nitrosomonas sp. AL212 · the same entry in another collection · chain C against C, 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 6E0X · PDBe 6E0X · UniProt F9ZFJ0
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