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Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme domain of cytochrome P450-BM3
Analyse Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BEN
- Type
- protein
- Length
- 911 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 102
- EC
- 1.14.14.1
- UniProt
- P14779
- Ligands
- HEM, LEH, MG
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 102 (EC 1.14.14.1) | protein | 454 | 54% helix, 11% strand | P14779 |
| B | Cytochrome P450 102 (EC 1.14.14.1) | protein | 457 | 54% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- LEH · N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.88 | 0.89 | 103 | HEM, LEH |
| 2 | 1168 | 0.85 | 0.85 | 110 | HEM, LEH |
| 3 | 348 | 0.64 | 0.79 | 49 | empty |
| 4 | 140 | 0.59 | 0.84 | 27 | empty |
| 5 | 52 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 614 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3BEN · Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- P14779 · AlphaFold monomer V2.0 prediction for bifunctional cytochrome P450/NADPH--P450 reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P14779
- Elsewhere: RCSB PDB 3BEN · PDBe 3BEN · UniProt P14779
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