MolNFT v1 · #124667 · protein
Crystal structure of a domain-swapped dimer of yeast iso-1-cytochrome C with omega-undecylenyl-beta-D-maltopyranoside
5KLU · Cytochrome C iso-1: “Crystal structure of a domain-swapped dimer of yeast iso-1-cytochrome C with…”. X-ray diffraction, 3 ligands (HEC, 6UZ, SO4), 3 pockets (best druggability 0.76). MolNFT v1 #124667 on GenesisL1: 3D structure…
- PDB
- 5KLU
- Type
- protein
- Length
- 209 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- HEC, 6UZ, SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C iso-1 | protein | 103 | 45% helix, 2% strand | P00044 |
| B | Cytochrome C iso-1 | protein | 106 | 35% helix, 0% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- 6UZ · omega-undecylenyl-beta-D-maltopyranoside · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.76 | 0.84 | 52 | HEC |
| 2 | 362 | 0.76 | 0.86 | 40 | HEC |
| 3 | 72 | 0.33 | 0.75 | 17 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2416 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 5KLU · Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · chain A against A, TM-score 0.70
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 P00044
- Elsewhere: RCSB PDB 5KLU · PDBe 5KLU · UniProt P00044
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