Research workbench
Structure of the CYP102A1 haem domain with N-dehydroabietoyl-L- tryptophan
Analyse Structure of the CYP102A1 haem domain with N-dehydroabietoyl-L- tryptophan in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JS8
- Type
- protein
- Length
- 909 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional cytochrome P450/NADPH--P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, C5R
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 455 | 54% helix, 11% strand | P14779 |
| B | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 454 | 54% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- C5R · (2S)-2-[[(1r,4as,10ar)-1,4A-dimethyl-7-propan-2-yl-2,3, 4,9,10,10A-hexahydrophenanthren-1-yl]carbonylamino]-3-(1H-indol-3-yl)propanoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 20 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.86 | 0.87 | 90 | HEM, DMS, C5R, GOL |
| 2 | 1161 | 0.85 | 0.86 | 109 | HEM, DMS, C5R, GOL |
| 3 | 240 | 0.59 | 0.80 | 30 | empty |
| 4 | 329 | 0.56 | 0.75 | 37 | GOL |
| 5 | 300 | 0.53 | 0.75 | 43 | GOL |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6JS8 · Structure of the CYP102A1 Haem Domain with N-Dehydroabietoyl-L-Tryptophan · 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 A 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 6JS8 · PDBe 6JS8 · UniProt P14779
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