MolNFT v1 · #47761 · protein
Structure of human lung cytochrome P450 2A13 with indole bound in two alternate conformations
2P85: “Structure of human lung cytochrome P450 2A13 with indole bound in two alternate conformations”. X-ray diffraction, 2 ligands (IND, HEM), 20 pockets (best druggability 0.87). MolNFT v1 #47761 on GenesisL1: 3D structure, binding sites…
- 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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