MolNFT v1 · #119513 · protein
Structure of CYP153A from marinobacter aquaeolei in complex with hydroxydodecanoic acid
5FYG · Cytochrome P450: “Structure of CYP153A from marinobacter aquaeolei in complex with hydroxydodecanoic acid”. X-ray diffraction, 2 ligands (HEM, 12H), 10 pockets (best druggability 0.86). MolNFT v1 #119513 on GenesisL1: 3D structure…
- PDB
- 5FYG
- Type
- protein
- Length
- 841 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- UniProt
- A1TY82
- Ligands
- HEM, 12H
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 | protein | 422 | 51% helix, 11% strand | A1TY82 |
| B | Cytochrome P450 | protein | 419 | 51% helix, 11% strand | A1TY82 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 12H · 12-hydroxydodecanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.86 | 0.93 | 73 | HEM, 12H |
| 2 | 515 | 0.85 | 0.91 | 76 | HEM, 12H |
| 3 | 690 | 0.80 | 0.85 | 77 | empty |
| 4 | 160 | 0.64 | 0.86 | 32 | empty |
| 5 | 129 | 0.58 | 0.84 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 583 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5FYG · Structure of CYP153A from Marinobacter aquaeolei in complex with hydroxydodecanoic acid · 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 A1TY82
- Elsewhere: RCSB PDB 5FYG · PDBe 5FYG · UniProt A1TY82
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