MolNFT v1 · #15761 · protein
Complex II (succinate dehydrogenase) from E. COLI with dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site
1NEN · Succinate dehydrogenase flavoprotein subunit: “Complex II (succinate dehydrogenase) from E. COLI with dinitrophenol-17 inhibitor co-crystallized at the…”. X-ray diffraction, 10 ligands (OAA, FAD, FES), 17 pockets (best druggability…
- PDB
- 1NEN
- Type
- protein
- Length
- 1,068 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase flavoprotein subunit; Succinate dehydrogenase iron-sulfur…
- EC
- 1.3.99.1, 1.3.5.1
- UniProt
- P0AC41, P07014, P69054, P0AC44
- Ligands
- OAA, FAD, FES, SF4, F3S, HEM, DNT, CDN, EPH, CA
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase flavoprotein subunit (EC 1.3.99.1, 1.3.5.1) | protein | 588 | 37% helix, 18% strand | P0AC41 |
| B | Succinate dehydrogenase iron-sulfur protein (EC 1.3.99.1, 1.3.5.1) | protein | 238 | 30% helix, 13% strand | P07014 |
| C | Succinate dehydrogenase cytochrome B-556 subunit | protein | 129 | 78% helix, 1% strand | P69054 |
| D | Succinate dehydrogenase hydrophobic membrane anchor protein | protein | 113 | 80% helix, 0% strand | P0AC44 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
- SF4 · Iron/sulfur cluster · ligand · chains B
- F3S · FE3-S4 cluster · ligand · chains B
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
- DNT · 2-[1-methylhexyl]-4,6-dinitrophenol · ligand · chains B, C, D
- CDN · Cardiolipin · ligand · chains C, D
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains C
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 329 | 0.86 | 0.96 | 56 | OAA, FAD |
| 2 | 1167 | 0.86 | 0.86 | 95 | HEM, DNT, CDN |
| 3 | 557 | 0.71 | 0.80 | 44 | empty |
| 4 | 51 | 0.71 | 0.99 | 17 | empty |
| 5 | 229 | 0.66 | 0.84 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2660 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 1281 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1154 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 589 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 77 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 1NEN · Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor… · the same entry in another collection · chain D against D, TM-score 1.00
- P07014 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase iron- sulfur subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0AC41 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase flavoprotein subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P0AC44 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase hydrophobic membrane anchor… · a predicted model of the same protein · chain D against A, TM-score 0.95
- P69054 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase cytochrome B556 subunit… · a predicted model of the same protein · chain C against A, TM-score 0.91
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 P07014
- Every structure of UniProt P69054
- Every structure of UniProt P0AC44
- Elsewhere: RCSB PDB 1NEN · PDBe 1NEN · UniProt P0AC41 · UniProt P07014 · UniProt P69054 · UniProt P0AC44
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