Research workbench
Crystal structure of the flavocytochrome C fumarate reductase of shewanella putrefaciens strain mr-1 complexed with fumarate
Analyse Crystal structure of the flavocytochrome C fumarate reductase of shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D4E
- Type
- protein
- Length
- 560 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavocytochrome C fumarate reductase
- EC
- 1.3.99.1
- UniProt
- P83223
- Ligands
- HEC, FAD, FUM
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavocytochrome C fumarate reductase (EC 1.3.99.1) | protein | 560 | 33% helix, 18% strand | P83223 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- FUM · Fumaric acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.83 | 0.86 | 98 | HEC, FAD, FUM |
| 2 | 890 | 0.77 | 0.80 | 95 | HEC |
| 3 | 74 | 0.36 | 0.76 | 19 | empty |
| 4 | 52 | 0.35 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 1D4E · Crystal structure of the flavocytochrome C fumarate reductase of shewanella putrefaciens… · the same entry in another collection · chain A against A, TM-score 1.00
- P83223 · AlphaFold monomer V2.0 prediction for fumarate reductase flavoprotein subunit (P83223) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P83223
- Elsewhere: RCSB PDB 1D4E · PDBe 1D4E · UniProt P83223
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