Research workbench
Lysine-ligated yeast iso-1 cytochrome C
Analyse Lysine-ligated yeast iso-1 cytochrome C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q5P
- Type
- protein
- Length
- 314 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- HEM
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C iso-1 | protein | 106 | 38% helix, 9% strand | P00044 |
| B, C | Cytochrome C iso-1 | protein | 104 | 39% helix, 8% strand | P00044 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.80 | 0.84 | 70 | HEM |
| 2 | 241 | 0.75 | 0.89 | 38 | HEM |
| 3 | 350 | 0.74 | 0.85 | 43 | HEM |
| 4 | 98 | 0.40 | 0.77 | 16 | empty |
| 5 | 63 | 0.39 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 358 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme attachment).
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 P00044
- Elsewhere: RCSB PDB 4Q5P · PDBe 4Q5P · UniProt P00044
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