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Complex II (succinate dehydrogenase) from E. COLI with atpenin A5 inhibitor co-crystallized at the ubiquinone binding site
Analyse Complex II (succinate dehydrogenase) from E. COLI with atpenin A5 inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ACZ
- 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
- UniProt
- P10444, P07014, P69054, P10445
- Ligands
- OAA, FAD, FES, SF4, F3S, HEB, AT5, CDN
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase flavoprotein subunit (EC 1.3.99.1) | protein | 588 | 35% helix, 18% strand | P10444 |
| B | Succinate dehydrogenase iron-sulfur protein (EC 1.3.99.1) | protein | 238 | 33% helix, 15% strand | P07014 |
| C | Succinate dehydrogenase cytochrome B556 subunit | protein | 129 | 75% helix, 1% strand | P69054 |
| D | Succinate dehydrogenase hydrophobic membrane anchor protein | protein | 113 | 79% helix, 0% strand | P10445 |
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
- HEB · Heme B/C · ligand · chains B, C, D
- AT5 · 3-[(2S,4S,5R)-5,6-dichloro-2,4-dimethyl-1-oxohexyl]-4-hydroxy-5,6-dimethoxy-2(1H)-pyridinone · ligand · chains B, C, D
- CDN · Cardiolipin · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.86 | 0.96 | 53 | OAA, FAD |
| 2 | 1186 | 0.86 | 0.86 | 95 | HEB, AT5, CDN |
| 3 | 534 | 0.70 | 0.79 | 49 | empty |
| 4 | 241 | 0.68 | 0.84 | 37 | empty |
| 5 | 480 | 0.67 | 0.79 | 62 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2677 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1284 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1145 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 601 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 2ACZ · Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor… · the same entry in another collection · chain A against A, 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
- 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 P10444
- Every structure of UniProt P07014
- Every structure of UniProt P69054
- Every structure of UniProt P10445
- Elsewhere: RCSB PDB 2ACZ · PDBe 2ACZ · UniProt P10444 · UniProt P07014 · UniProt P69054 · UniProt P10445
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