Research workbench
Crystal structure of bacillus megaterium BM3 heme domain mutant F261E
Analyse Crystal structure of bacillus megaterium BM3 heme domain mutant F261E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KX5
- Type
- protein
- Length
- 910 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
- UniProt
- P14779
- Ligands
- HEM, SO4
- Pockets
- 8 · best druggability 0.88
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) | protein | 455 | 55% helix, 11% strand | P14779 |
| B | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1) | protein | 455 | 54% helix, 11% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.88 | 0.89 | 105 | HEM |
| 2 | 979 | 0.83 | 0.84 | 88 | HEM |
| 3 | 255 | 0.57 | 0.78 | 30 | empty |
| 4 | 91 | 0.56 | 0.86 | 28 | empty |
| 5 | 197 | 0.55 | 0.79 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3KX5 · Crystal structure of Bacillus megaterium BM3 heme domain mutant F261E · 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 3KX5 · PDBe 3KX5 · UniProt P14779
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