Research workbench
Kinetics and structural properties of triosephosphate isomerase from helicobacter pylori
Analyse Kinetics and structural properties of triosephosphate isomerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JGQ
- Type
- protein
- Length
- 462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P56076
- Ligands
- QGA, PO4
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 231 | 40% helix, 17% strand | P56076 |
Ligands and binding sites
- QGA · 1-[(3-cyclohexylpropanoyl)(2-hydroxyethyl)amino]-1-deoxy-D-allitol · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.44 | 0.77 | 16 | empty |
| 2 | 52 | 0.33 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1649 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 2JGQ · Kinetics and structural properties of triosephosphate isomerase from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- P56076 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P56076) · 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 P56076
- Elsewhere: RCSB PDB 2JGQ · PDBe 2JGQ · UniProt P56076
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