Research workbench
Structure of the BM3 heme domain in complex with clotrimazole
Analyse Structure of the BM3 heme domain in complex with clotrimazole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H1T
- Type
- protein
- Length
- 1,824 residues
- Chains
- 4
- 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, CL6
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 456 | 54% helix, 11% strand | A0A1Q8UP87 |
| D | Bifunctional cytochrome P450/NADPH--P450 reductase (EC 1.14.14.1, 1.6.2.4) | protein | 456 | 53% helix, 11% strand | A0A1Q8UP87 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CL6 · 1-[(2-chlorophenyl)(diphenyl)methyl]-1H-imidazole · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 10 copies · chains A, B, C, D
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains B, D
- PGE · Triethylene glycol · additive · 2 copies · chains B, C
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.85 | 0.86 | 90 | HEM, CL6, MPD, EDO |
| 2 | 1155 | 0.85 | 0.85 | 103 | HEM, CL6, MPD, EDO |
| 3 | 1180 | 0.85 | 0.85 | 104 | HEM, CL6, MPD, EDO |
| 4 | 1115 | 0.85 | 0.85 | 101 | HEM, CL6, MPD |
| 5 | 767 | 0.71 | 0.77 | 67 | MPO, MPD |
Interfaces
4 interfaces between chains.
- C–D · 974 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 289 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 192 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6H1T · Structure of the BM3 heme domain in complex with clotrimazole · 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 6H1T · PDBe 6H1T · UniProt A0A1Q8UP87
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