Research workbench
Crystal structure of mitochondrial respiratory complex II from porcine heart at 2.4 ångströms
Analyse Crystal structure of mitochondrial respiratory complex II from porcine heart at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZOY
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-binding protein; Iron-sulfur protein; Large cytochrome binding protein; Small…
- EC
- 1.3.5.1
- UniProt
- Q0QF01, Q007T0, A5GZW8
- Ligands
- EPH, FAD, FES, SF4, F3S, UQ1, HEM
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-binding protein (EC 1.3.5.1) | protein | 613 | 33% helix, 22% strand | Q0QF01 |
| B | Iron-sulfur protein (EC 1.3.5.1) | protein | 239 | 30% helix, 15% strand | Q007T0 |
| C | Large cytochrome binding protein | protein | 138 | 74% helix, 1% strand | — |
| D | Small cytochrome binding protein | protein | 102 | 85% helix, 0% strand | A5GZW8 |
Ligands and binding sites
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · 2 copies · chains C, D
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
- SF4 · Iron/sulfur cluster · ligand · chains B
- F3S · FE3-S4 cluster · ligand · chains B
- UQ1 · Ubiquinone-1 · ligand · chains B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.85 | 0.86 | 87 | UQ1, HEM, EPH |
| 2 | 337 | 0.85 | 0.95 | 59 | FAD |
| 3 | 114 | 0.78 | 0.97 | 28 | empty |
| 4 | 373 | 0.72 | 0.84 | 39 | empty |
| 5 | 51 | 0.71 | 0.98 | 21 | SF4 |
Interfaces
5 interfaces between chains.
- A–B · 2724 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 1725 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1329 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 634 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 102 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 1ZOY · Crystal Structure of Mitochondrial Respiratory Complex II from porcine heart at 2.4… · the same entry in another collection · chain A against A, 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 1.00
- 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 0.99
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 Q0QF01
- Every structure of UniProt Q007T0
- Every structure of UniProt A5GZW8
- Elsewhere: RCSB PDB 1ZOY · PDBe 1ZOY · UniProt Q0QF01 · UniProt Q007T0 · UniProt A5GZW8
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