Research workbench
Cytochrome P450 107G1 (rapn) with everolimus
Analyse Cytochrome P450 107G1 (rapn) with everolimus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L3A
- Type
- protein
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450
- UniProt
- A0A0A0NSZ7
- Ligands
- HEM, E53
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 | protein | 390 | 47% helix, 9% strand | A0A0A0NSZ7 |
| B | Cytochrome P450 | protein | 393 | 48% helix, 9% strand | A0A0A0NSZ7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- E53 · Everolimus · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.80 | 0.82 | 68 | HEM |
| 2 | 922 | 0.80 | 0.82 | 67 | HEM, E53 |
| 3 | 1074 | 0.77 | 0.79 | 86 | empty |
| 4 | 347 | 0.69 | 0.82 | 36 | empty |
| 5 | 92 | 0.44 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 709 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme attachment).
Compared structures
- 6L3A · Cytochrome P450 107G1 (RapN) with everolimus · the same entry in another collection · chain A 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 A0A0A0NSZ7
- Elsewhere: RCSB PDB 6L3A · PDBe 6L3A · UniProt A0A0A0NSZ7
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