Research workbench
Avian respiratory complex II with 3-nitropropionate and ubiquinone
Analyse Avian respiratory complex II with 3-nitropropionate and ubiquinone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YQ4
- 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
- Ligands
- PEE, FAD, 3NP, FES, SF4, F3S, JZR, HEM, UQ
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | protein | 614 | 36% helix, 22% strand | — |
| B | Succinate dehydrogenase ip subunit (EC 1.3.5.1) | protein | 242 | 31% helix, 15% strand | — |
| C | Succinate dehydrogenase cytochrome B, large subunit (EC 1.3.5.1) | protein | 139 | 75% helix, 1% strand | — |
| D | Succinate dehydrogenase cytochrome B, small subunit (EC 1.3.5.1) | protein | 102 | 85% helix, 0% strand | — |
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
- 3NP · 3-nitropropanoic acid · 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
- JZR · hexyl beta-D-glucopyranoside · ligand · chains B, C
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
- UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · chains B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.84 | 0.85 | 86 | HEM, UQ, PEE |
| 2 | 271 | 0.83 | 0.95 | 52 | FAD, 3NP |
| 3 | 442 | 0.78 | 0.86 | 53 | empty |
| 4 | 501 | 0.68 | 0.79 | 51 | empty |
| 5 | 201 | 0.59 | 0.81 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2671 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 1769 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1378 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 618 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 145 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 covalent (flavinylation, covalent ligand).
Compared structures
- 1YQ4 · Avian respiratory complex ii with 3-nitropropionate and ubiqui · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1YQ4 · PDBe 1YQ4
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