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Crystal structure of human microsomal P450 2A6 with coumarin bound
Analyse Crystal structure of human microsomal P450 2A6 with coumarin bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z10
- Type
- protein
- Length
- 1,858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450, family 2, subfamily a, polypeptide 6
- EC
- 1.14.14.1
- UniProt
- P11509
- Ligands
- HEM, COU
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450, family 2, subfamily a, polypeptide 6 (EC 1.14.14.1) | protein | 465 | 54% helix, 10% strand | P11509 |
| B | Cytochrome P450, family 2, subfamily a, polypeptide 6 (EC 1.14.14.1) | protein | 465 | 54% helix, 10% strand | P11509 |
| C, D | Cytochrome P450, family 2, subfamily a, polypeptide 6 (EC 1.14.14.1) | protein | 464 | 54% helix, 11% strand | P11509 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- COU · Coumarin · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.86 | 0.94 | 44 | HEM, COU |
| 2 | 384 | 0.86 | 0.94 | 44 | HEM, COU |
| 3 | 417 | 0.85 | 0.93 | 46 | HEM, COU |
| 4 | 445 | 0.85 | 0.92 | 50 | HEM, COU |
| 5 | 1018 | 0.79 | 0.80 | 101 | empty |
Interfaces
5 interfaces between chains.
- A–B · 656 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 418 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 404 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 194 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 161 Ų buried · 0 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 P11509
- Elsewhere: RCSB PDB 1Z10 · PDBe 1Z10 · UniProt P11509
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