Research workbench
Structure of the soluble domain of cytochrome C552 from paracoccus denitrificans in the oxidised state
Analyse Structure of the soluble domain of cytochrome C552 from paracoccus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QL4
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C552
- UniProt
- P54820
- Ligands
- HEC
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C552 | protein | 99 | 42% helix, 2% strand | P54820 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.79 | 0.92 | 42 | HEC |
| 2 | 192 | 0.76 | 0.90 | 32 | HEC |
| 3 | 644 | 0.74 | 0.81 | 77 | HEC |
| 4 | 200 | 0.74 | 0.89 | 31 | HEC |
| 5 | 103 | 0.37 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–D · 387 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 350 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 135 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 1QL4 · Structure of the soluble domain of cytochrome c552 from Paracoccus denitrificans in the… · the same entry in another collection · chain B against B, TM-score 1.00
- P54820 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P54820) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P54820
- Elsewhere: RCSB PDB 1QL4 · PDBe 1QL4 · UniProt P54820
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