Research workbench
Structure of BM3 heme domain in complex with troglitazone
Analyse Structure of BM3 heme domain in complex with troglitazone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HN8
- Type
- protein
- Length
- 905 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional cytochrome P450/NADPH--P450 reductase
- EC
- 1.14.14.1, 1.6.2.4
- UniProt
- A0A1Q8UP87
- Ligands
- HEM, TDZ
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 453 | 54% helix, 11% strand | A0A1Q8UP87 |
| B | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 452 | 54% helix, 11% strand | A0A1Q8UP87 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- TDZ · (5R)-5-(4-{[(2R)-6-hydroxy-2,5,7,8-tetramethyl-3,4-dihydro-2H-chromen-2-yl]methoxy}benzyl)-1,3-thiazolidine-2,4-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.88 | 0.91 | 77 | HEM, TDZ |
| 2 | 718 | 0.87 | 0.91 | 76 | HEM, TDZ |
| 3 | 1024 | 0.80 | 0.81 | 74 | empty |
| 4 | 247 | 0.60 | 0.80 | 31 | empty |
| 5 | 147 | 0.56 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 789 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HN8 · Structure of BM3 heme domain in complex with troglitazone · 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 A0A1Q8UP87
- Elsewhere: RCSB PDB 6HN8 · PDBe 6HN8 · UniProt A0A1Q8UP87
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