MolNFT v1 · #114660 · protein
Benzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate
5BWE · Benzylsuccinate synthase alpha chain: “Benzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate”. X-ray diffraction, 3 ligands (FUM, MBN, SF4), 20 pockets (best druggability 0.81). MolNFT v1 #114660 on…
- PDB
- 5BWE
- Type
- protein
- Length
- 1,926 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzylsuccinate synthase alpha chain; Benzylsuccinate synthase beta chain…
- EC
- 4.1.99.11
- UniProt
- O68395, O68396, O68394
- Ligands
- FUM, MBN, SF4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Benzylsuccinate synthase alpha chain (EC 4.1.99.11) | protein | 857 | 50% helix, 10% strand | O68395 |
| B, F | Benzylsuccinate synthase beta chain | protein | 69 | 9% helix, 25% strand | O68396 |
| C, G | Benzylsuccinate synthase gamma chain | protein | 37 | 0% helix, 51% strand | O68394 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · 2 copies · chains A, D
- MBN · Toluene · ligand · 2 copies · chains A, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.81 | 0.83 | 99 | empty |
| 2 | 54 | 0.68 | 0.96 | 18 | SF4 |
| 3 | 211 | 0.59 | 0.81 | 33 | empty |
| 4 | 200 | 0.58 | 0.81 | 30 | empty |
| 5 | 136 | 0.56 | 0.82 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1661 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1594 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1578 Ų buried · 24 hydrogen bonds · protein-protein
- D–G · 1121 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1121 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5BWE · Benzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate · 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 5BWE · PDBe 5BWE · UniProt O68395 · UniProt O68396 · UniProt O68394
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