Research workbench
Structure of human cytochrome P450 1A1 with bergamottin
Analyse Structure of human cytochrome P450 1A1 with bergamottin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DWM
- Type
- protein
- Length
- 1,874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 1A1
- EC
- 1.14.14.1
- UniProt
- P04798
- Ligands
- HEM, HJJ, CPS
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 470 | 53% helix, 10% strand | P04798 |
| B | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 476 | 53% helix, 10% strand | P04798 |
| C | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 464 | 53% helix, 10% strand | P04798 |
| D | Cytochrome P450 1A1 (EC 1.14.14.1) | protein | 464 | 53% helix, 10% strand | P04798 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- HJJ · 4-{[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-7H-furo[3, 2-g][1]benzopyran-7-one · ligand · 4 copies · chains A, B, C, D
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 2 copies · chains A, D
- GOL · Glycerol · additive · 2 copies · chains B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.87 | 0.93 | 62 | HEM, HJJ |
| 2 | 554 | 0.87 | 0.92 | 56 | HEM, HJJ |
| 3 | 534 | 0.87 | 0.92 | 60 | HEM, HJJ |
| 4 | 664 | 0.86 | 0.90 | 78 | HEM, HJJ |
| 5 | 775 | 0.70 | 0.76 | 78 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 678 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 518 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P04798
- Elsewhere: RCSB PDB 6DWM · PDBe 6DWM · UniProt P04798
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