MolNFT v1 · #29966 · protein
Crystal structure of mitochondrial respiratory complex II from porcine heart at 2.4 ångströms
1ZOY · FAD-binding protein: “Crystal structure of mitochondrial respiratory complex II from porcine heart at 2.4 ångströms”. X-ray diffraction, 7 ligands (EPH, FAD, FES), 15 pockets (best druggability 0.85). MolNFT v1 #29966 on GenesisL1…
- 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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