Research workbench
Crystal structure of high-molecular weight cytochrome C from desulfovibrio vulgaris (miyazaki F) in the presence of zinc ion
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
- 2E84
- Type
- protein
- Length
- 513 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High-molecular-weight cytochrome C
- UniProt
- Q8VUI3
- Ligands
- HEM, ZN, NA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High-molecular-weight cytochrome C | protein | 513 | 38% helix, 7% strand | Q8VUI3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 16 copies · chains A
- ZN · Zinc ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.83 | 0.89 | 81 | NA, HEM |
| 2 | 232 | 0.77 | 0.90 | 42 | HEM |
| 3 | 207 | 0.73 | 0.88 | 43 | HEM |
| 4 | 133 | 0.70 | 0.90 | 30 | HEM |
| 5 | 159 | 0.65 | 0.86 | 27 | HEM |
Modifications
Observed in the structure: 32 cofactor (heme attachment).
Compared structures
- 2E84 · 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
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 Q8VUI3
- Elsewhere: RCSB PDB 2E84 · PDBe 2E84 · UniProt Q8VUI3
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