Research workbench
Human cytochrome P450 2A13 in complex with nicotine
Analyse Human cytochrome P450 2A13 in complex with nicotine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EJG
- Type
- protein
- Length
- 3,708 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2A13
- EC
- 1.14.14.1
- UniProt
- Q16696
- Ligands
- HEM, NCT
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cytochrome P450 2A13 (EC 1.14.14.1) | protein | 464 | 53% helix, 10% strand | Q16696 |
| D, E, F | Cytochrome P450 2A13 (EC 1.14.14.1) | protein | 465 | 52% helix, 10% strand | Q16696 |
| G | Cytochrome P450 2A13 (EC 1.14.14.1) | protein | 463 | 48% helix, 10% strand | Q16696 |
| H | Cytochrome P450 2A13 (EC 1.14.14.1) | protein | 458 | 47% helix, 10% strand | Q16696 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NCT · (S)-3-(1-methylpyrrolidin-2-yl)pyridine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.89 | 0.91 | 99 | HEM |
| 2 | 497 | 0.87 | 0.93 | 50 | HEM |
| 3 | 1006 | 0.86 | 0.87 | 99 | HEM, NCT |
| 4 | 417 | 0.86 | 0.94 | 48 | HEM |
| 5 | 482 | 0.86 | 0.92 | 58 | HEM, NCT |
Interfaces
8 interfaces between chains.
- C–D · 862 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 733 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 625 Ų buried · 1 hydrogen bond · protein-protein
- F–G · 560 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 557 Ų buried · 4 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 Q16696
- Elsewhere: RCSB PDB 4EJG · PDBe 4EJG · UniProt Q16696
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