Research workbench
Crystal structure of human microsomal P450 2A6 with methoxsalen bound
Analyse Crystal structure of human microsomal P450 2A6 with methoxsalen bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z11
- Type
- protein
- Length
- 1,859 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, 8MO
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450, family 2, subfamily a, polypeptide 6 (EC 1.14.14.1) | protein | 467 | 54% helix, 10% strand | P11509 |
| B | Cytochrome P450, family 2, subfamily a, polypeptide 6 (EC 1.14.14.1) | protein | 464 | 52% helix, 10% strand | P11509 |
| C, D | Cytochrome P450, family 2, subfamily a, polypeptide 6 (EC 1.14.14.1) | protein | 464 | 53% helix, 10% strand | P11509 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- 8MO · Methoxsalen · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.86 | 0.94 | 44 | HEM, 8MO |
| 2 | 415 | 0.86 | 0.94 | 41 | HEM, 8MO |
| 3 | 395 | 0.86 | 0.94 | 44 | HEM, 8MO |
| 4 | 388 | 0.85 | 0.93 | 44 | HEM, 8MO |
| 5 | 857 | 0.77 | 0.81 | 90 | empty |
Interfaces
5 interfaces between chains.
- A–B · 604 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 399 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 181 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 173 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Z11 · Crystal Structure of Human Microsomal P450 2A6 with Methoxsalen Bound · the same entry in another collection · chain D against D, TM-score 1.00
- P11509 · AlphaFold monomer V2.0 prediction for cytochrome P450 2A6 (P11509) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 1Z11 · PDBe 1Z11 · UniProt P11509
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