Research workbench
Crystal structure of B. subtilis 168 glpq in complex with glycerol-3- phosphate (1 hour soak)
Analyse Crystal structure of B. subtilis 168 glpq in complex with glycerol-3- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T9C
- Type
- protein
- Length
- 263 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphoryl diester phosphodiesterase
- EC
- 3.1.4.46
- UniProt
- P37965
- Ligands
- G3P, CA, NA, PO4
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Glycerophosphoryl diester phosphodiesterase (EC 3.1.4.46) | protein | 263 | 40% helix, 17% strand | P37965 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · chains E
- CA · Calcium ion · metal · chains E
- NA · Sodium ion · metal · chains E
- PO4 · Phosphate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.38 | 0.78 | 24 | empty |
Compared structures
- 5T9C · Crystal structure of B. subtilis 168 GlpQ in complex with glycerol-3-phosphate (1 hour… · the same entry in another collection · chain E against E, TM-score 1.00
- P37965 · AlphaFold monomer V2.0 prediction for glycerophosphodiester phosphodiesterase (P37965) · a predicted model of the same protein · chain E 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 P37965
- Elsewhere: RCSB PDB 5T9C · PDBe 5T9C · UniProt P37965
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.