Research workbench
Structure of the A82F BM3 heme domain in complex with omeprazole
Analyse Structure of the A82F BM3 heme domain in complex with omeprazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KEW
- Type
- protein
- Length
- 893 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional P-450/NADPH-P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- P14779
- Ligands
- HEM, 1C6
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 450 | 55% helix, 11% strand | P14779 |
| B | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 443 | 54% helix, 12% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 1C6 · 6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.89 | 0.90 | 117 | HEM, 1C6 |
| 2 | 711 | 0.87 | 0.91 | 95 | HEM, 1C6 |
| 3 | 174 | 0.56 | 0.81 | 33 | empty |
| 4 | 166 | 0.56 | 0.81 | 26 | empty |
| 5 | 180 | 0.55 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 820 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4KEW · structure of the A82F BM3 heme domain in complex with omeprazole · 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 B against A, TM-score 0.98
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 4KEW · PDBe 4KEW · UniProt P14779
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