Research workbench
Benzylsuccinate synthase alpha-beta-gamma complex
Analyse Benzylsuccinate synthase alpha-beta-gamma complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PKF
- Type
- protein
- Length
- 963 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tutd; Tutg; Tutf
- EC
- 4.1.99.11
- UniProt
- O68395, O68396, O68394
- Ligands
- SF4, CL
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tutd (EC 4.1.99.11) | protein | 857 | 50% helix, 10% strand | O68395 |
| B | Tutg (EC 4.1.99.11) | protein | 69 | 9% helix, 25% strand | O68396 |
| C | Tutf (EC 4.1.99.11) | protein | 37 | 0% helix, 51% strand | O68394 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.66 | 0.93 | 21 | empty |
| 2 | 157 | 0.58 | 0.82 | 23 | empty |
| 3 | 206 | 0.56 | 0.79 | 29 | empty |
| 4 | 171 | 0.45 | 0.75 | 27 | empty |
| 5 | 93 | 0.40 | 0.77 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1584 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1117 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4PKF · Benzylsuccinate synthase alpha-beta-gamma complex · 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 O68395
- Every structure of UniProt O68396
- Every structure of UniProt O68394
- Elsewhere: RCSB PDB 4PKF · PDBe 4PKF · UniProt O68395 · UniProt O68396 · UniProt O68394
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