MolNFT v1 · #53323 · protein
Remodelling of carboxin binding to the Q-site of avian respiratory complex II
2WQY · Succinate dehydrogenase flavoprotein subunit: “Remodelling of carboxin binding to the Q-site of avian respiratory complex II”. X-ray diffraction, 12 ligands (UNL, FAD, OAA), 20 pockets (best druggability 0.86). MolNFT v1 #53323 on…
- PDB
- 2WQY
- Type
- protein
- Length
- 2,185 residues
- Chains
- 8
- 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
- UNL, FAD, OAA, FES, SF4, F3S, BHG, HEM, CBE, PEE, K, AZI
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | protein | 613 | 34% helix, 23% strand | Q9YHT1 |
| B, O | Succinate dehydrogenase ip subunit (EC 1.3.5.1) | protein | 239 | 32% helix, 15% strand | Q9YHT2 |
| C, P | Succinate dehydrogenase cytochrome B, large subunit (EC 1.3.5.1) | protein | 140 | 74% helix, 1% strand | — |
| D, Q | Succinate dehydrogenase cytochrome B, small subunit (EC 1.3.5.1) | protein | 101 | 86% helix, 0% strand | Q5ZIS0 |
| N | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | protein | 612 | 34% helix, 23% strand | Q9YHT1 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 95 copies · chains A, B, C, P, D, N, O, Q
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, N, O
- OAA · Oxaloacetate ion · ligand · 2 copies · chains A, N
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, O
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, O
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, O
- BHG · hexyl beta-D-galactopyranoside · ligand · 2 copies · chains B, C, P, O
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C, D, O, P, Q
- CBE · 2-methyl-N-phenyl-5,6-dihydro-1,4-oxathiine-3-carboxamide · ligand · 2 copies · chains B, C, D, O, P, Q
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains C, D, P, Q
- K · Potassium ion · metal · 4 copies · chains A, B, N, O
- AZI · Azide ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains B, C, D, O, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.86 | 0.96 | 53 | FAD, OAA |
| 2 | 1068 | 0.85 | 0.86 | 91 | HEM, CBE, GOL, UNL, PEE |
| 3 | 318 | 0.85 | 0.95 | 55 | FAD, OAA |
| 4 | 1028 | 0.85 | 0.86 | 93 | HEM, CBE, GOL, PEE |
| 5 | 120 | 0.79 | 0.97 | 32 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2674 Ų buried · 44 hydrogen bonds · protein-protein
- N–O · 2663 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1819 Ų buried · 18 hydrogen bonds · protein-protein
- O–P · 1813 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1393 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2WQY · Remodelling of carboxin binding to the Q-site of avian respiratory complex II · the same entry in another collection · chain Q against Q, TM-score 1.00
- Q9YHT1 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] flavoprotein… · a predicted model of the same protein · chain N 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 Q9YHT1
- Every structure of UniProt Q9YHT2
- Every structure of UniProt Q5ZIS0
- Elsewhere: RCSB PDB 2WQY · PDBe 2WQY · UniProt Q9YHT1 · UniProt Q9YHT2 · UniProt Q5ZIS0
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