MolNFT v1 · #4683 · protein
Structure and dynamics of ferrocytochrome C553 from desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics
1DVH: “Structure and dynamics of ferrocytochrome C553 from desulfovibrio vulgaris studied by NMR spectroscopy and…”. Solution nmr, 1 ligand (HEC), 1 pocket (best druggability 0.69). MolNFT v1 #4683 on GenesisL1: 3D structure, binding sites…
- 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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