Research workbench
Structure of human lung cytochrome P450 2A13 with indole bound in two alternate conformations
Analyse Structure of human lung cytochrome P450 2A13 with indole bound in two alternate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P85
- Type
- protein
- Length
- 2,784 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2A13
- EC
- 1.14.14.1
- UniProt
- Q16696
- Ligands
- IND, HEM
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Cytochrome P450 2A13 (EC 1.14.14.1) | protein | 464 | 53% helix, 10% strand | Q16696 |
Ligands and binding sites
- IND · Indole · ligand · 12 copies · chains A, B, C, D, E, F
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.87 | 0.94 | 57 | HEM, IND |
| 2 | 485 | 0.87 | 0.93 | 62 | HEM, IND |
| 3 | 474 | 0.87 | 0.93 | 50 | HEM, IND |
| 4 | 459 | 0.86 | 0.93 | 52 | HEM, IND |
| 5 | 454 | 0.86 | 0.93 | 56 | HEM, IND |
Interfaces
10 interfaces between chains.
- A–B · 479 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 408 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 319 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 281 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 271 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2P85 · Structure of Human Lung Cytochrome P450 2A13 with indole bound in two alternate… · the same entry in another collection · chain F against F, TM-score 1.00
- Q16696 · AlphaFold monomer V2.0 prediction for cytochrome P450 2A13 (Q16696) · a predicted model of the same protein · chain E 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 Q16696
- Elsewhere: RCSB PDB 2P85 · PDBe 2P85 · UniProt Q16696
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