Research workbench
Structure and dynamics of ferrocytochrome C553 from desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics
Analyse Structure and dynamics of ferrocytochrome C553 from desulfovibrio vulgaris… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DVH
- Type
- protein
- Length
- 79 residues
- Chains
- 1
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C553
- UniProt
- P04032
- Ligands
- HEC
- Pockets
- 1 · best druggability 0.69
Structure
solution nmr · 1 distinct chain · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C553 | protein | 79 | 54% helix, 0% strand | P04032 |
Ligands and binding sites
- HEC · Heme C · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.69 | 0.85 | 31 | HEC |
Modifications
Observed in the structure: 2 cofactor (heme c attachment).
Compared structures
- 1DVH · Structure and dynamics of ferrocytochrome C553 from desulfovibrio vulgaris studied by NMR… · the same entry in another collection · chain A against A, TM-score 1.00
- P04032 · AlphaFold monomer V2.0 prediction for cytochrome C-553 (P04032) · a predicted model of the same protein · chain A against A, TM-score 0.95
- 1DWL · The Ferredoxin-Cytochrome complex using heteronuclear NMR and docking simulation · a predicted model of the same protein · chain A against B, TM-score 0.70
- 1DWL · The ferredoxin-cytochrome complex using heteronuclear NMR and docking simulation · a predicted model of the same protein · chain A against B, TM-score 0.70
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 P04032
- Elsewhere: RCSB PDB 1DVH · PDBe 1DVH · UniProt P04032
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