MolNFT v1 · #144680 · protein
Sdha-sdhe complex
6C12 · Succinate dehydrogenase flavoprotein subunit: “Sdha-sdhe complex”. X-ray diffraction, 2 ligands (FAD, NA), 18 pockets (best druggability 0.76). MolNFT v1 #144680 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6C12
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase flavoprotein subunit; FAD assembly factor sdhe
- EC
- 1.3.5.1
- UniProt
- P0AC41, P64559
- Ligands
- FAD, NA
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | protein | 537 | 41% helix, 21% strand | P0AC41 |
| D | FAD assembly factor sdhe | protein | 86 | 69% helix, 0% strand | P64559 |
| A | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | protein | 536 | 40% helix, 21% strand | P0AC41 |
| C | FAD assembly factor sdhe | protein | 85 | 68% helix, 0% strand | P64559 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, A
- NA · Sodium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.76 | 0.83 | 83 | FAD |
| 2 | 492 | 0.76 | 0.84 | 62 | FAD |
| 3 | 550 | 0.70 | 0.79 | 64 | empty |
| 4 | 481 | 0.68 | 0.79 | 43 | empty |
| 5 | 237 | 0.53 | 0.76 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1504 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1471 Ų buried · 27 hydrogen bonds · protein-protein
- B–A · 709 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 6C12 · SDHA-SDHE complex · the same entry in another collection · chain C against C, TM-score 1.00
- P64559 · AlphaFold monomer V2.0 prediction for FAD assembly factor sdhe (P64559) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P0AC41 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase flavoprotein subunit… · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P0AC41
- Every structure of UniProt P64559
- Elsewhere: RCSB PDB 6C12 · PDBe 6C12 · UniProt P0AC41 · UniProt P64559
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