MolNFT v1 · #151526 · protein
Cytochrome P450-153 from phenylobacterium zucineum
6HQG: “Cytochrome P450-153 from phenylobacterium zucineum”. X-ray diffraction, 1 ligand (HEM), 15 pockets (best druggability 0.78). MolNFT v1 #151526 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HQG
- Type
- protein
- Length
- 1,451 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- UniProt
- B4RGA3
- Ligands
- HEM
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 | protein | 363 | 50% helix, 12% strand | B4RGA3 |
| B | Cytochrome P450 | protein | 364 | 51% helix, 12% strand | B4RGA3 |
| C | Cytochrome P450 | protein | 362 | 51% helix, 12% strand | B4RGA3 |
| D | Cytochrome P450 | protein | 362 | 51% helix, 12% strand | B4RGA3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.78 | 0.85 | 60 | HEM |
| 2 | 671 | 0.78 | 0.83 | 78 | HEM |
| 3 | 692 | 0.78 | 0.82 | 79 | HEM |
| 4 | 659 | 0.77 | 0.82 | 77 | HEM |
| 5 | 1010 | 0.77 | 0.79 | 76 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1012 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 999 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 372 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 225 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HQG · Cytochrome P450-153 from Phenylobacterium zucineum · 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 B4RGA3
- Elsewhere: RCSB PDB 6HQG · PDBe 6HQG · UniProt B4RGA3
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