GL1X · GenesisL1 explorer

MolNFT v1 · #28825 · protein

Avian respiratory complex II with oxaloacetate and ubiquinone

1YQ3 · Succinate dehydrogenase flavoprotein subunit: “Avian respiratory complex II with oxaloacetate and ubiquinone”. X-ray diffraction, 10 ligands (PEE, FAD, TEO), 17 pockets (best druggability 0.84). MolNFT v1 #28825 on GenesisL1: 3D…

PDB
1YQ3
Type
protein
Length
1,097 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Succinate dehydrogenase flavoprotein subunit; Succinate dehydrogenase ip subunit…
EC
1.3.5.1
UniProt
Q9YHT1, Q9YHT2, Q5ZIS0
Ligands
PEE, FAD, TEO, FES, SF4, F3S, UQ, JZR, HEM, UNL
Pockets
17 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ASuccinate dehydrogenase flavoprotein subunit (EC 1.3.5.1)protein61436% helix, 23% strandQ9YHT1
BSuccinate dehydrogenase ip subunit (EC 1.3.5.1)protein24232% helix, 15% strandQ9YHT2
CSuccinate dehydrogenase cytochrome B, large subunit (EC 1.3.5.1)protein13973% helix, 1% strand—
DSuccinate dehydrogenase cytochrome B, small subunit (EC 1.3.5.1)protein10285% helix, 0% strandQ5ZIS0

Ligands and binding sites

  • PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains C, D
  • FAD · Flavin-adenine dinucleotide · ligand · chains A, B
  • TEO · Malate like intermediate · 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
  • UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · chains B, C, D
  • JZR · hexyl beta-D-glucopyranoside · ligand · chains B, C
  • HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
  • UNL · Unknown ligand · ion · 30 copies · chains A, B, C, D
  • GOL · Glycerol · additive · chains 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, 8 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12950.840.9553FAD, TEO
210350.840.8589UQ, HEM, PEE
3820.750.9720empty
43330.700.8338UNL
54070.660.7938empty

Interfaces

5 interfaces between chains.

  • A–B · 2706 Ų buried · 51 hydrogen bonds · protein-protein
  • B–C · 1787 Ų buried · 20 hydrogen bonds · protein-protein
  • C–D · 1357 Ų buried · 9 hydrogen bonds · protein-protein
  • B–D · 606 Ų buried · 14 hydrogen bonds · protein-protein
  • A–C · 140 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor (flavinylation).

Compared structures

  • 1YQ3 · Avian respiratory complex ii with oxaloacetate and ubiqui · the same entry in another collection · chain B against B, TM-score 1.00
  • Q9YHT1 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] flavoprotein… · a predicted model of the same protein · 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 0.99
  • 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

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.