Research workbench
Mycobacterium smegmatis SDH1 complex in the apo form
Analyse Mycobacterium smegmatis SDH1 complex in the apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D6X
- Type
- protein
- Length
- 1,097 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase subunit a; Fumarate reductase iron-sulfur subunit; Succinate…
- EC
- 1.3.-.-
- UniProt
- A0A0D6G5S3, A0A0D6G6K3, A0A0D6G6P6
- Ligands
- FES, FAD, SF4, F3S, PEV
- Pockets
- 12 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase subunit a (EC 1.3.-.-) | protein | 594 | 36% helix, 13% strand | A0A0D6G5S3 |
| B | Fumarate reductase iron-sulfur subunit | protein | 239 | 33% helix, 15% strand | A0A0D6G6K3 |
| C | Succinate dehydrogenase (membrane anchor subunit) | protein | 264 | 53% helix, 3% strand | A0A0D6G6P6 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, C
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains B
- F3S · FE3-S4 cluster · ligand · chains B
- PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.81 | 0.82 | 125 | FAD |
| 2 | 497 | 0.77 | 0.84 | 45 | empty |
| 3 | 247 | 0.67 | 0.83 | 31 | empty |
| 4 | 205 | 0.66 | 0.84 | 37 | empty |
| 5 | 176 | 0.57 | 0.81 | 33 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2695 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2554 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 7D6X · Mycobacterium smegmatis Sdh1 complex in the apo form · the same entry in another collection · chain A against A, 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 A0A0D6G5S3
- Every structure of UniProt A0A0D6G6K3
- Every structure of UniProt A0A0D6G6P6
- Elsewhere: RCSB PDB 7D6X · PDBe 7D6X · UniProt A0A0D6G5S3 · UniProt A0A0D6G6K3 · UniProt A0A0D6G6P6
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