Research workbench
Flavocytochrome C3 with mesaconate bound
Analyse Flavocytochrome C3 with mesaconate bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y0P
- Type
- protein
- Length
- 568 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit
- EC
- 1.3.99.1
- UniProt
- Q02469
- Ligands
- HEM, FAD, MEZ, NA
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate reductase flavoprotein subunit (EC 1.3.99.1) | protein | 568 | 36% helix, 18% strand | Q02469 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- MEZ · (2E)-2-methylbut-2-enedioic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.87 | 0.88 | 131 | HEM, FAD, MEZ |
| 2 | 246 | 0.62 | 0.81 | 29 | empty |
| 3 | 108 | 0.51 | 0.82 | 25 | empty |
| 4 | 87 | 0.37 | 0.76 | 20 | empty |
| 5 | 90 | 0.37 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 8 cofactor (heme attachment).
Compared structures
- 1Y0P · Flavocytochrome c3 with mesaconate bound · 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 Q02469
- Elsewhere: RCSB PDB 1Y0P · PDBe 1Y0P · UniProt Q02469
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