Research workbench
1.85 ångström crystal structure of O-succinylbenzoate synthase from salmonella typhimurium in complex with succinic acid
Analyse 1.85 ångström crystal structure of O-succinylbenzoate synthase from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GC2
- Type
- protein
- Length
- 322 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-succinylbenzoate synthase
- EC
- 4.2.1.113
- UniProt
- P58486
- Ligands
- NA, CL
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-succinylbenzoate synthase (EC 4.2.1.113) | protein | 322 | 37% helix, 23% strand | P58486 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- SIN · Succinic acid · additive · 2 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.70 | 0.83 | 46 | SIN |
| 2 | 100 | 0.35 | 0.74 | 22 | empty |
| 3 | 58 | 0.33 | 0.77 | 17 | empty |
| 4 | 56 | 0.31 | 0.76 | 17 | empty |
| 5 | 50 | 0.29 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3GC2 · 1.85 Angstrom Crystal Structure of O-succinylbenzoate Synthase from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- P58486 · AlphaFold monomer V2.0 prediction for O-succinylbenzoate synthase (P58486) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P58486
- Elsewhere: RCSB PDB 3GC2 · PDBe 3GC2 · UniProt P58486
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.