MolNFT v1 · #134600 · protein
Crystal structure of B. subtilis 168 glpq in complex with bicine
5T91 · Glycerophosphoryl diester phosphodiesterase: “Crystal structure of B. subtilis 168 glpq in complex with bicine”. X-ray diffraction, 3 ligands (BCN, CA, NA), 1 pocket (best druggability 0.37). MolNFT v1 #134600 on GenesisL1: 3D…
- PDB
- 5T91
- Type
- protein
- Length
- 258 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
- BCN, CA, NA
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerophosphoryl diester phosphodiesterase (EC 3.1.4.46) | protein | 258 | 40% helix, 17% strand | P37965 |
Ligands and binding sites
- BCN · Bicine · ligand · chains A
- CA · Calcium ion · metal · chains A
- NA · Sodium ion · metal · chains A
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 | 60 | 0.37 | 0.79 | 13 | CA, BCN |
Compared structures
- 5T91 · Crystal structure of B. subtilis 168 GlpQ in complex with bicine · the same entry in another collection · chain A against A, TM-score 1.00
- P37965 · AlphaFold monomer V2.0 prediction for glycerophosphodiester phosphodiesterase (P37965) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 5T91 · PDBe 5T91 · UniProt P37965
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