MolNFT v1 · #143627 · protein
Frda-sdhe assembly intermediate
6B58 · Fumarate reductase flavoprotein subunit: “Frda-sdhe assembly intermediate”. X-ray diffraction, 2 ligands (FAD, K), 16 pockets (best druggability 0.80). MolNFT v1 #143627 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6B58
- Type
- protein
- Length
- 1,243 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit; FAD assembly factor sdhe
- EC
- 1.3.5.4
- UniProt
- P00363, P64561
- Ligands
- FAD, K
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate reductase flavoprotein subunit (EC 1.3.5.4) | protein | 542 | 40% helix, 20% strand | P00363 |
| B | FAD assembly factor sdhe | protein | 79 | 63% helix, 1% strand | P64561 |
| C | Fumarate reductase flavoprotein subunit (EC 1.3.5.4) | protein | 544 | 40% helix, 19% strand | P00363 |
| D | FAD assembly factor sdhe | protein | 78 | 62% helix, 1% strand | P64561 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C
- K · Potassium ion · metal · 2 copies · chains A, C
- ACT · Acetate ion · additive · 11 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains C
- MLI · Malonate ion · additive · chains C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.80 | 0.84 | 92 | FAD, MLI |
| 2 | 746 | 0.80 | 0.83 | 82 | FAD, ACT |
| 3 | 262 | 0.74 | 0.88 | 39 | empty |
| 4 | 261 | 0.70 | 0.85 | 38 | empty |
| 5 | 239 | 0.68 | 0.84 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1139 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1133 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (flavinylation, nonstandard).
Compared structures
- 6B58 · FrdA-SdhE assembly intermediate · the same entry in another collection · chain D against D, TM-score 1.00
- P00363 · AlphaFold monomer V2.0 prediction for fumarate reductase flavoprotein subunit (P00363) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P64561 · AlphaFold monomer V2.0 prediction for FAD assembly factor sdhe (P64561) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P00363
- Every structure of UniProt P64561
- Elsewhere: RCSB PDB 6B58 · PDBe 6B58 · UniProt P00363 · UniProt P64561
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