Research workbench
Heterodimer constructed from M61A pa cyt C551-ht cyt C552 and ht cyt C552-pa cyt C551 chimeric proteins
Analyse Heterodimer constructed from M61A pa cyt C551-ht cyt C552 and ht cyt C552-pa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XED
- Type
- protein
- Length
- 162 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C-551,CYTOCHROME C-552; Cytochrome C-552,CYTOCHROME C-551
- UniProt
- P00099, P15452
- Ligands
- HEC
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C-551,CYTOCHROME C-552 | protein | 82 | 51% helix, 2% strand | P00099, P15452 |
| C | Cytochrome C-552,CYTOCHROME C-551 | protein | 80 | 50% helix, 3% strand | P00099, P15452 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, C
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 | 308 | 0.77 | 0.88 | 35 | HEC |
| 2 | 201 | 0.70 | 0.87 | 32 | HEC |
| 3 | 74 | 0.37 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 1565 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 5XED · Heterodimer constructed from M61A PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551… · the same entry in another collection · chain A against A, TM-score 1.00
- P00099 · AlphaFold monomer V2.0 prediction for cytochrome C-551 (P00099) · a predicted model of the same protein · chain C against A, TM-score 0.76
- P15452 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P15452) · a predicted model of the same protein · chain C against A, TM-score 0.75
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 P00099
- Every structure of UniProt P15452
- Elsewhere: RCSB PDB 5XED · PDBe 5XED · UniProt P00099 · UniProt P15452
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