MolNFT v1 · #57653 · protein
Crystal structure of porcine heart mitochondrial complex II bound with N-biphenyl-3-yl-2-iodo-benzamide
3AEG · Succinate dehydrogenase [ubiquinone] flavoprotein subunit…: “Crystal structure of porcine heart mitochondrial complex II bound with N-biphenyl-3-yl-2-iodo-benzamide”. X-ray diffraction, 6 ligands (FAD, FES, SF4), 16 pockets (best…
- PDB
- 3AEG
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial; Succinate…
- EC
- 1.3.5.1
- UniProt
- Q0QF01, Q007T0, D0VWV4, A5GZW8
- Ligands
- FAD, FES, SF4, F3S, HEM, 11J
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1) | protein | 613 | 32% helix, 22% strand | Q0QF01 |
| B | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1) | protein | 239 | 30% helix, 15% strand | Q007T0 |
| C | Succinate dehydrogenase cytochrome B560 subunit, mitochondrial | protein | 138 | 75% helix, 1% strand | D0VWV4 |
| D | Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial | protein | 102 | 81% helix, 0% strand | A5GZW8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · 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
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
- 11J · N-biphenyl-3-yl-2-iodobenzamide · ligand · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.86 | 0.96 | 61 | FAD |
| 2 | 1144 | 0.83 | 0.84 | 99 | HEM, 11J |
| 3 | 86 | 0.74 | 0.96 | 19 | empty |
| 4 | 287 | 0.70 | 0.84 | 29 | empty |
| 5 | 415 | 0.67 | 0.79 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2855 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 1763 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1389 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 712 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 109 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3AEG · Crystal structure of porcine heart mitochondrial complex II bound with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q0QF01 · 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
- Q007T0 · 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
- A5GZW8 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain D against A, TM-score 0.98
- D0VWV4 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase cytochrome B560 subunit… · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q0QF01
- Every structure of UniProt Q007T0
- Every structure of UniProt D0VWV4
- Every structure of UniProt A5GZW8
- Elsewhere: RCSB PDB 3AEG · PDBe 3AEG · UniProt Q0QF01 · UniProt Q007T0 · UniProt D0VWV4 · UniProt A5GZW8
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