Research workbench
Avian mitochondrial complex II with Atpenin A5 bound, sidechain in pocket
Analyse Avian mitochondrial complex II with Atpenin A5 bound, sidechain in pocket in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MYT
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.27
- Source
- Gallus gallus
- Molecule
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial; Succinate…
- EC
- 1.3.5.1
- UniProt
- F1NPJ4, Q9YHT2, D0VWW3, Q5ZIS0
- Ligands
- UNL, FAD, OAA, FES, SF4, F3S, AT5, HEM, UMQ, 3PE, K
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.27 · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1) | protein | 611 | 34% helix, 23% strand | F1NPJ4 |
| B | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1) | protein | 240 | 31% helix, 15% strand | Q9YHT2 |
| C | Succinate dehydrogenase cytochrome b, large subunit (EC 1.3.5.1) | protein | 139 | 73% helix, 1% strand | D0VWW3 |
| D | Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial | protein | 102 | 86% helix, 0% strand | Q5ZIS0 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 59 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- OAA · Oxaloacetate ion · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
- SF4 · Iron/sulfur cluster · ligand · chains B
- F3S · FE3-S4 cluster · ligand · chains B
- 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
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
- UMQ · Undecyl-maltoside · ligand · chains B, C
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains C, D
- K · Potassium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.86 | 0.87 | 93 | AT5, HEM, UNL, 3PE |
| 2 | 298 | 0.85 | 0.95 | 51 | FAD, OAA, UNL |
| 3 | 101 | 0.76 | 0.96 | 19 | UNL |
| 4 | 296 | 0.72 | 0.86 | 37 | UNL |
| 5 | 435 | 0.68 | 0.80 | 37 | PEG, UNL |
Interfaces
5 interfaces between chains.
- A–B · 2668 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 1810 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1409 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 634 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 151 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 modified (flavinylation, methylation).
Compared structures
- 6MYT · Avian mitochondrial complex II with atpenin A5 bound, sidechain in pocket · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YHT2 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] iron-sulfur… · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q5ZIS0 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain D against A, TM-score 0.99
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 F1NPJ4
- Every structure of UniProt Q9YHT2
- Every structure of UniProt D0VWW3
- Every structure of UniProt Q5ZIS0
- Elsewhere: RCSB PDB 6MYT · PDBe 6MYT · UniProt F1NPJ4 · UniProt Q9YHT2 · UniProt D0VWW3 · UniProt Q5ZIS0
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