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Structure of septuple mutant of rat outer mitochondrial membrane cytochrome B5
Analyse Structure of septuple mutant of rat outer mitochondrial membrane cytochrome B5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I89
- Type
- protein
- Length
- 350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B5 type B
- UniProt
- P04166
- Ligands
- HEM, MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome B5 type B | protein | 90 | 38% helix, 22% strand | P04166 |
| C | Cytochrome B5 type B | protein | 85 | 41% helix, 24% strand | P04166 |
| D | Cytochrome B5 type B | protein | 85 | 35% helix, 24% 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
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 | 368 | 0.71 | 0.83 | 44 | MG |
| 2 | 499 | 0.71 | 0.80 | 56 | HEM |
| 3 | 98 | 0.68 | 0.92 | 20 | empty |
| 4 | 116 | 0.61 | 0.86 | 20 | HEM |
| 5 | 117 | 0.60 | 0.85 | 22 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 679 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 650 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 260 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 250 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 223 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2I89 · Structure of septuple mutant of Rat Outer Mitochondrial Membrane 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 2I89 · PDBe 2I89 · UniProt P04166
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