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Structure of quintuple mutant of the rat outer mitocondrial cytochrome B5.
Analyse Structure of quintuple mutant of the rat outer mitocondrial cytochrome B5. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LJ0
- Type
- protein
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B5 outer mitochondrial membrane isoform
- UniProt
- P04166
- Ligands
- HEM, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome B5 outer mitochondrial membrane isoform | protein | 89 | 34% helix, 22% strand | P04166 |
| C | Cytochrome B5 outer mitochondrial membrane isoform | protein | 88 | 41% helix, 23% strand | P04166 |
| D | Cytochrome B5 outer mitochondrial membrane isoform | protein | 86 | 37% helix, 23% strand | P04166 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.79 | 0.82 | 91 | HEM, MG |
| 2 | 331 | 0.73 | 0.85 | 42 | MG |
| 3 | 115 | 0.61 | 0.86 | 20 | HEM |
| 4 | 125 | 0.60 | 0.85 | 20 | HEM |
| 5 | 201 | 0.50 | 0.76 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 697 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 642 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 240 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 222 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1LJ0 · Structure of quintuple mutant of the rat outer mitocondrial cytochrome b5. · the same entry in another collection · chain D against D, TM-score 1.00
- P04166 · AlphaFold monomer V2.0 prediction for cytochrome B5 type B (P04166) · a predicted model of the same protein · chain D 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 P04166
- Elsewhere: RCSB PDB 1LJ0 · PDBe 1LJ0 · UniProt P04166
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