Research workbench
Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine in complex with Ethylamine
Analyse Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D0U
- Type
- protein
- Length
- 908 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.68
- Source
- Bacillus megaterium
- Molecule
- Bifunctional cytochrome P450/NADPH--P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, D0L, NEH
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.68 · 1 distinct chain · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 454 | 55% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- D0L · (2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid · ligand · 2 copies · chains A, B
- NEH · Ethanamine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.86 | 0.87 | 112 | HEM, D0L, NEH, GOL |
| 2 | 1193 | 0.85 | 0.86 | 121 | HEM, D0L, NEH, GOL |
| 3 | 212 | 0.51 | 0.76 | 30 | GOL |
| 4 | 206 | 0.49 | 0.76 | 30 | empty |
| 5 | 153 | 0.49 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 933 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7D0U · Structure of the CYP102A1 haem domain with N-enanthyl-L-prolyl-L- phenylalanine in… · the same entry in another collection · chain A against A, TM-score 1.00
- P14779 · AlphaFold monomer V2.0 prediction for bifunctional cytochrome P450/NADPH--P450 reductase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P14779
- Elsewhere: RCSB PDB 7D0U · PDBe 7D0U · UniProt P14779
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