Research workbench
Crystal structure of helicobacter pylori glutamate racemase in complex with D-glutamate
Analyse Crystal structure of helicobacter pylori glutamate racemase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JFY
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q9ZLT0
- Ligands
- DGL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate racemase (EC 5.1.1.3) | protein | 255 | 46% helix, 17% strand | Q9ZLT0 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.78 | 0.93 | 43 | DGL |
| 2 | 237 | 0.62 | 0.81 | 32 | empty |
| 3 | 245 | 0.61 | 0.80 | 37 | empty |
| 4 | 55 | 0.38 | 0.79 | 12 | empty |
| 5 | 77 | 0.33 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1102 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2JFY · Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZLT0 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q9ZLT0) · 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 Q9ZLT0
- Elsewhere: RCSB PDB 2JFY · PDBe 2JFY · UniProt Q9ZLT0
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