MolNFT v1 · #114659 · protein
Benzylsuccinate alpha-gamma bound to fumarate
5BWD · Benzylsuccinate synthase alpha chain: “Benzylsuccinate alpha-gamma bound to fumarate”. X-ray diffraction, 1 ligand (FUM), 7 pockets (best druggability 0.78). MolNFT v1 #114659 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5BWD
- Type
- protein
- Length
- 892 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzylsuccinate synthase alpha chain; Benzylsuccinate synthase gamma chain
- EC
- 4.1.99.11
- UniProt
- O68395, O68394
- Ligands
- FUM
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzylsuccinate synthase alpha chain (EC 4.1.99.11) | protein | 853 | 49% helix, 10% strand | O68395 |
| C | Benzylsuccinate synthase gamma chain | protein | 39 | 0% helix, 51% strand | O68394 |
Ligands and binding sites
- FUM · Fumaric acid · ligand · chains A
- PGE · Triethylene glycol · additive · 5 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.78 | 0.82 | 69 | FUM |
| 2 | 128 | 0.54 | 0.82 | 22 | empty |
| 3 | 147 | 0.46 | 0.77 | 31 | empty |
| 4 | 68 | 0.31 | 0.75 | 13 | empty |
| 5 | 61 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 1154 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5BWD · Benzylsuccinate alpha-gamma bound to 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 O68394
- Elsewhere: RCSB PDB 5BWD · PDBe 5BWD · UniProt O68395 · UniProt O68394
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.