MolNFT v1 · #9958 · protein
Rat outer mitochondrial membrane cytochrome B5
1ICC · Cytochrome B5 outer mitochondrial membrane isoform: “Rat outer mitochondrial membrane cytochrome B5”. X-ray diffraction, 2 ligands (HEM, MG), 7 pockets (best druggability 0.72). MolNFT v1 #9958 on GenesisL1: 3D structure, binding…
- PDB
- 1ICC
- Type
- protein
- Length
- 344 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
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Cytochrome B5 outer mitochondrial membrane isoform | protein | 87 | 36% helix, 23% strand | P04166 |
| C | Cytochrome B5 outer mitochondrial membrane isoform | protein | 83 | 42% helix, 22% 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.72 | 0.84 | 42 | MG |
| 2 | 506 | 0.71 | 0.80 | 54 | HEM |
| 3 | 335 | 0.71 | 0.84 | 42 | MG |
| 4 | 110 | 0.61 | 0.86 | 18 | HEM |
| 5 | 112 | 0.59 | 0.85 | 19 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 624 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 607 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 228 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 1ICC · PDBe 1ICC · UniProt P04166
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