MolNFT v1 · #53421 · protein
Crystal structure of the E. COLI SUCCINATE:QUINONE oxidoreductase (sqr) sdhd HIS71MET mutant
2WU5 · Succinate dehydrogenase flavoprotein subunit: “Crystal structure of the E. COLI SUCCINATE:QUINONE oxidoreductase (sqr) sdhd HIS71MET mutant”. X-ray diffraction, 8 ligands (FAD, TEO, FES), 20 pockets (best druggability 0.86). MolNFT…
- PDB
- 2WU5
- Type
- protein
- Length
- 3,159 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase flavoprotein subunit; Succinate dehydrogenase iron-sulfur…
- EC
- 1.3.5.1, 1.3.99.1
- UniProt
- P0AC41, P07014, P69054, P0AC44
- Ligands
- FAD, TEO, FES, SF4, F3S, HEM, CBE, NA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1, 1.3.99.1) | protein | 588 | 37% helix, 21% strand | P0AC41 |
| B, F, J | Succinate dehydrogenase iron-sulfur subunit (EC 1.3.5.1, 1.3.99.1) | protein | 238 | 34% helix, 16% strand | P07014 |
| C, G, K | Succinate dehydrogenase cytochrome B556 subunit (EC 1.3.5.1) | protein | 122 | 81% helix, 1% strand | P69054 |
| D, H, L | Succinate dehydrogenase hydrophobic membrane anchor protein subunit (EC 1.3.5.1) | protein | 105 | 85% helix, 0% strand | P0AC44 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, E, F, I, J
- TEO · Malate like intermediate · 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
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains B, C, D, F, G, H, J, K, L
- CBE · 2-methyl-N-phenyl-5,6-dihydro-1,4-oxathiine-3-carboxamide · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.86 | 0.87 | 90 | HEM, CBE |
| 2 | 1157 | 0.86 | 0.87 | 97 | HEM, CBE |
| 3 | 1128 | 0.86 | 0.86 | 97 | HEM, CBE |
| 4 | 287 | 0.85 | 0.97 | 54 | FAD, TEO |
| 5 | 286 | 0.85 | 0.96 | 52 | FAD, TEO |
Interfaces
31 interfaces between chains.
- A–B · 2553 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2547 Ų buried · 42 hydrogen bonds · protein-protein
- I–J · 2541 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1219 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 1199 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (flavinylation).
Compared structures
- 2WU5 · Crystal structure of the E. coli succinate:qui oxidoreductase (SQR) SdhD His71Met mutant · 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 P0AC44
- Elsewhere: RCSB PDB 2WU5 · PDBe 2WU5 · UniProt P0AC41 · UniProt P07014 · UniProt P69054 · UniProt P0AC44
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