Research workbench
Crystal structure of flavocytochrome C from thermochromatium tepidum
Analyse Crystal structure of flavocytochrome C from thermochromatium tepidum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VRD
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavocytochrome C heme subunit; Flavocytochrome C flavin subunit
- UniProt
- D0G7Q3, D0G7Q4
- Ligands
- HEC, FAD, NO3
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavocytochrome C heme subunit | protein | 174 | 60% helix, 0% strand | D0G7Q3 |
| B | Flavocytochrome C flavin subunit | protein | 400 | 31% helix, 27% strand | D0G7Q4 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.84 | 0.89 | 70 | HEC, GOL |
| 2 | 516 | 0.76 | 0.84 | 63 | FAD |
| 3 | 251 | 0.52 | 0.76 | 50 | empty |
| 4 | 113 | 0.40 | 0.75 | 27 | empty |
| 5 | 67 | 0.33 | 0.76 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 1554 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor, 2 modified (heme c attachment, oxidation, flavinylation).
Compared structures
- 3VRD · Crystal structure of flavocytochrome c from Thermochromatium tepidum · 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 D0G7Q3
- Every structure of UniProt D0G7Q4
- Elsewhere: RCSB PDB 3VRD · PDBe 3VRD · UniProt D0G7Q3 · UniProt D0G7Q4
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