MolNFT v1 · #19464 · protein
Structure of the soluble domain of cytochrome C552 from paracoccus denitrificans in the oxidised state
1QL4: “Structure of the soluble domain of cytochrome C552 from paracoccus denitrificans in the oxidised state”. X-ray diffraction, 1 ligand (HEC), 6 pockets (best druggability 0.79). MolNFT v1 #19464 on GenesisL1: 3D structure, binding…
- 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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