MolNFT v1 · #113858 · protein
Hydrogenobacter thermophilus cytochrome C552 dimer formed by domain swapping at N-terminal region
5AUR · Cytochrome C-552: “Hydrogenobacter thermophilus cytochrome C552 dimer formed by domain swapping at N-terminal region”. X-ray diffraction, 2 ligands (HEC, IOD), 3 pockets (best druggability 0.85). MolNFT v1 #113858 on GenesisL1: 3D…
- PDB
- 5AUR
- Type
- protein
- Length
- 332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C-552
- UniProt
- P15452
- Ligands
- HEC, IOD
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Cytochrome C-552 | protein | 83 | 49% helix, 2% strand | P15452 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, C, E, G
- IOD · Iodide ion · ion · 11 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.85 | 0.85 | 126 | HEC |
| 2 | 456 | 0.78 | 0.85 | 52 | HEC |
| 3 | 266 | 0.76 | 0.89 | 40 | HEC |
Interfaces
6 interfaces between chains.
- A–C · 1737 Ų buried · 31 hydrogen bonds · protein-protein
- E–G · 1716 Ų buried · 32 hydrogen bonds · protein-protein
- A–G · 317 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 213 Ų buried · 0 hydrogen bonds · protein-protein
- C–G · 120 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 cofactor (heme c attachment).
Compared structures
- 5AUR · Hydrogenobacter thermophilus cytochrome c552 dimer formed by domain swapping at… · the same entry in another collection · chain G against G, TM-score 1.00
- P15452 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P15452) · a predicted model of the same protein · chain C against A, TM-score 0.72
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 P15452
- Elsewhere: RCSB PDB 5AUR · PDBe 5AUR · UniProt P15452
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