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Crystal structure of the uncomplexed form of the flavocytochrome C fumarate reductase of shewanella putrefaciens strain mr-1
Analyse Crystal structure of the uncomplexed form of the flavocytochrome C fumarate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D4C
- Type
- protein
- Length
- 2,274 residues
- Chains
- 4
- 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, SO4
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Flavocytochrome C fumarate reductase (EC 1.3.99.1) | protein | 570 | 35% helix, 17% strand | P83223 |
| B | Flavocytochrome C fumarate reductase (EC 1.3.99.1) | protein | 566 | 35% helix, 19% strand | P83223 |
| C | Flavocytochrome C fumarate reductase (EC 1.3.99.1) | protein | 568 | 34% helix, 17% strand | P83223 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, C, B, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.88 | 0.89 | 156 | SO4, HEC, FAD |
| 2 | 956 | 0.84 | 0.86 | 115 | SO4, HEC, FAD |
| 3 | 1059 | 0.84 | 0.85 | 119 | SO4, HEC, FAD |
| 4 | 788 | 0.83 | 0.86 | 100 | HEC, FAD |
| 5 | 947 | 0.81 | 0.82 | 92 | HEC |
Interfaces
3 interfaces between chains.
- A–C · 394 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 387 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 1D4C · Crystal structure of the uncomplexed form of the flavocytochrome C fumarate reductase of… · the same entry in another collection · chain D against D, 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 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 P83223
- Elsewhere: RCSB PDB 1D4C · PDBe 1D4C · UniProt P83223
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