Research workbench
Succinate: quinone oxidoreductase sqr from E.COLI K12
Analyse Succinate: quinone oxidoreductase sqr from E.COLI K12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JZ2
- Type
- protein
- Length
- 2,871 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase flavoprotein subunit; Succinate dehydrogenase iron-sulfur…
- EC
- 1.3.5.1
- UniProt
- P0AC41, P07014, P69054, I2WBK2
- Ligands
- FAD, FES, SF4, F3S, 3PE, HEM, UQ2, NA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | protein | 481 | 36% helix, 20% strand | P0AC41 |
| B, F, J | Succinate dehydrogenase iron-sulfur subunit (EC 1.3.5.1) | protein | 238 | 32% helix, 14% strand | P07014 |
| C, G, K | Succinate dehydrogenase cytochrome B556 subunit | protein | 125 | 78% helix, 1% strand | P69054 |
| D, H, L | Succinate dehydrogenase hydrophobic membrane anchor subunit | protein | 113 | 80% helix, 0% strand | I2WBK2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, E, I
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains B, F, J
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B, F, J
- F3S · FE3-S4 cluster · ligand · 3 copies · chains B, F, J
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains C, D, G, H, K, L
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains B, C, D, F, G, H, J, K, L
- UQ2 · Ubiquinone-2 · ligand · 3 copies · chains B, C, D, F, G, H, J, K, L
- NA · Sodium ion · metal · 3 copies · chains A, E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.88 | 0.88 | 105 | HEM, 3PE, UQ2 |
| 2 | 853 | 0.88 | 0.89 | 101 | empty |
| 3 | 1172 | 0.86 | 0.87 | 107 | 3PE, HEM, UQ2 |
| 4 | 1200 | 0.86 | 0.86 | 108 | HEM, 3PE, UQ2 |
| 5 | 365 | 0.80 | 0.89 | 51 | FAD |
Interfaces
29 interfaces between chains.
- E–F · 2307 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 2296 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2295 Ų buried · 31 hydrogen bonds · protein-protein
- J–K · 1319 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1316 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 3 covalent (flavinylation, covalent ligand).
Compared structures
- 7JZ2 · Succinate: qui oxidoreductase SQR from E.coli K12 · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P0AC41
- Every structure of UniProt P07014
- Every structure of UniProt P69054
- Every structure of UniProt I2WBK2
- Elsewhere: RCSB PDB 7JZ2 · PDBe 7JZ2 · UniProt P0AC41 · UniProt P07014 · UniProt P69054 · UniProt I2WBK2
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