MolNFT v1 · #167108 · protein
Crystal structure of human sdha-ADHAF2 assembly intermediate
6VAX · Succinate dehydrogenase [ubiquinone] flavoprotein subunit…: “Crystal structure of human sdha-ADHAF2 assembly intermediate”. X-ray diffraction, 3 ligands (FAD, OAA, K), 15 pockets (best druggability 0.81). MolNFT v1 #167108 on…
- PDB
- 6VAX
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial; Succinate…
- EC
- 1.3.5.1
- UniProt
- P31040, Q9NX18
- Ligands
- FAD, OAA, K
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1) | protein | 611 | 34% helix, 21% strand | P31040 |
| B, D | Succinate dehydrogenase assembly factor 2, mitochondrial | protein | 113 | 56% helix, 0% strand | Q9NX18 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C
- OAA · Oxaloacetate ion · ligand · 2 copies · chains A, C
- K · Potassium ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.81 | 0.85 | 81 | FAD, OAA |
| 2 | 1134 | 0.80 | 0.82 | 98 | FAD, OAA |
| 3 | 883 | 0.74 | 0.78 | 97 | empty |
| 4 | 75 | 0.73 | 0.97 | 19 | empty |
| 5 | 525 | 0.72 | 0.81 | 57 | GOL, EDO |
Interfaces
3 interfaces between chains.
- C–D · 2019 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2014 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 337 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 6VAX · Crystal structure of human SDHA-SDHAF2 assembly intermediate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NX18 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase assembly factor 2… · a predicted model of the same protein · chain B against A, TM-score 0.94
- P31040 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] flavoprotein… · a predicted model of the same protein · chain A 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 P31040
- Every structure of UniProt Q9NX18
- Elsewhere: RCSB PDB 6VAX · PDBe 6VAX · UniProt P31040 · UniProt Q9NX18
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