MolNFT v1 · #69661 · protein
Crystal structure of bacillus megaterium BM3 heme domain mutant L86E
3KX3 · Bifunctional P-450/NADPH-P450 reductase: “Crystal structure of bacillus megaterium BM3 heme domain mutant L86E”. X-ray diffraction, 2 ligands (HEM, 140), 7 pockets (best druggability 0.88). MolNFT v1 #69661 on GenesisL1: 3D…
- PDB
- 3KX3
- 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, 140
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1) | protein | 454 | 54% helix, 12% strand | P14779 |
| B | Bifunctional P-450/NADPH-P450 reductase (EC 1.14.14.1) | protein | 456 | 54% helix, 12% strand | P14779 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 140 · N-palmitoylglycine · 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 | 567 | 0.88 | 0.94 | 77 | HEM, 140 |
| 2 | 604 | 0.88 | 0.93 | 85 | HEM, 140 |
| 3 | 1108 | 0.82 | 0.83 | 84 | empty |
| 4 | 163 | 0.57 | 0.82 | 25 | empty |
| 5 | 162 | 0.55 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 752 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3KX3 · Crystal structure of Bacillus megaterium BM3 heme domain mutant L86E · 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 0.98
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 3KX3 · PDBe 3KX3 · UniProt P14779
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