Research workbench
Crystal structure of high-molecular weight cytochrome C from desulfovibrio vulgaris (hildenborough)
Analyse Crystal structure of high-molecular weight cytochrome C from desulfovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CVC
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High-molecular-weight cytochrome C precursor
- UniProt
- P24092
- Ligands
- HEC
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High-molecular-weight cytochrome C precursor | protein | 500 | 36% helix, 8% strand | P24092 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.84 | 0.90 | 81 | HEC |
| 2 | 323 | 0.80 | 0.90 | 58 | HEC |
| 3 | 173 | 0.72 | 0.89 | 30 | HEC |
| 4 | 108 | 0.67 | 0.90 | 22 | HEC |
| 5 | 93 | 0.64 | 0.90 | 26 | HEC |
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 2CVC · Crystal structure of High-Molecular Weight Cytochrome c from Desulfovibrio vulgaris… · the same entry in another collection · chain A against A, TM-score 1.00
- P24092 · AlphaFold monomer V2.0 prediction for high-molecular-weight cytochrome C (P24092) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P24092
- Elsewhere: RCSB PDB 2CVC · PDBe 2CVC · UniProt P24092
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