MolNFT v1 · #157820 · protein
Cytochrome P450CAM-putidaredoxin complex bound to camphor and cyanide
6NBL · Camphor 5-monooxygenase: “Cytochrome P450CAM-putidaredoxin complex bound to camphor and cyanide”. X-ray diffraction, 6 ligands (HEM, CAM, FES), 10 pockets (best druggability 0.85). MolNFT v1 #157820 on GenesisL1: 3D structure…
- PDB
- 6NBL
- Type
- protein
- Length
- 1,021 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camphor 5-monooxygenase; Putidaredoxin
- EC
- 1.14.15.1
- UniProt
- P00183, P00259
- Ligands
- HEM, CAM, FES, 1N0, CA, CYN
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camphor 5-monooxygenase (EC 1.14.15.1) | protein | 405 | 51% helix, 11% strand | P00183 |
| B | Camphor 5-monooxygenase (EC 1.14.15.1) | protein | 403 | 52% helix, 10% strand | P00183 |
| C | Putidaredoxin | protein | 106 | 16% helix, 22% strand | P00259 |
| D | Putidaredoxin | protein | 107 | 18% helix, 23% strand | P00259 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CAM · Camphor · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, D
- 1N0 · 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione · ligand · 2 copies · chains A, C, B, D
- CA · Calcium ion · metal · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.85 | 0.86 | 88 | HEM, CYN, CAM |
| 2 | 1159 | 0.85 | 0.85 | 87 | HEM, CYN, CAM |
| 3 | 878 | 0.76 | 0.79 | 83 | empty |
| 4 | 375 | 0.58 | 0.75 | 37 | empty |
| 5 | 290 | 0.57 | 0.77 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 649 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 649 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 567 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6NBL · Cytochrome P450cam-putidaredoxin complex bound to camphor and cyanide · the same entry in another collection · chain D against D, TM-score 1.00
- P00259 · AlphaFold monomer V2.0 prediction for putidaredoxin (P00259) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P00183 · AlphaFold monomer V2.0 prediction for camphor 5-monooxygenase (P00183) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P00183
- Every structure of UniProt P00259
- Elsewhere: RCSB PDB 6NBL · PDBe 6NBL · UniProt P00183 · UniProt P00259
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.