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Ligand bound (4-phenylimidazole) crystal structure of a cytochrome P450 from the thermoacidophilic archaeon picrophilus torridus
Analyse Ligand bound (4-phenylimidazole) crystal structure of a cytochrome P450 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RFC
- Type
- protein
- Length
- 1,352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- EC
- 1.14.14.1
- UniProt
- Q6KZ68
- Ligands
- HEM, PIM
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome P450 (EC 1.14.14.1) | protein | 338 | 49% helix, 9% strand | Q6KZ68 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- PIM · 4-phenyl-1H-imidazole · ligand · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.81 | 0.87 | 56 | HEM, PIM |
| 2 | 718 | 0.81 | 0.85 | 63 | HEM, PIM |
| 3 | 666 | 0.81 | 0.85 | 64 | HEM, PIM |
| 4 | 697 | 0.81 | 0.85 | 66 | HEM, PIM |
| 5 | 335 | 0.69 | 0.83 | 36 | empty |
Interfaces
5 interfaces between chains.
- B–D · 894 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 871 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 701 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 129 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2RFC · Ligand bound (4-phenylimidazole) Crystal Structure of a Cytochrome P450 from the… · the same entry in another collection · chain B against B, 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 Q6KZ68
- Elsewhere: RCSB PDB 2RFC · PDBe 2RFC · UniProt Q6KZ68
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