MolNFT v1 · #50335 · protein
Crystal structure of a cytochrome P450 from the thermoacidophilic archaeon picrophilus torridus
2RFB: “Crystal structure of a cytochrome P450 from the thermoacidophilic archaeon picrophilus torridus”. X-ray diffraction, 2 ligands (HEM, SO4), 9 pockets (best druggability 0.80). MolNFT v1 #50335 on GenesisL1: 3D structure, binding…
- PDB
- 2RFB
- Type
- protein
- Length
- 1,006 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- EC
- 1.14.14.1
- UniProt
- Q6KZ68
- Ligands
- HEM, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 (EC 1.14.14.1) | protein | 338 | 52% helix, 10% strand | Q6KZ68 |
| B | Cytochrome P450 (EC 1.14.14.1) | protein | 335 | 51% helix, 11% strand | Q6KZ68 |
| C | Cytochrome P450 (EC 1.14.14.1) | protein | 333 | 51% helix, 10% strand | Q6KZ68 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.80 | 0.86 | 52 | HEM |
| 2 | 581 | 0.80 | 0.85 | 55 | HEM |
| 3 | 472 | 0.79 | 0.87 | 51 | HEM |
| 4 | 53 | 0.66 | 0.95 | 17 | empty |
| 5 | 81 | 0.43 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 825 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 74 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2RFB · Crystal Structure of a Cytochrome P450 from the Thermoacidophilic Archaeon Picrophilus… · 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 Q6KZ68
- Elsewhere: RCSB PDB 2RFB · PDBe 2RFB · UniProt Q6KZ68
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