Research workbench
Crystal structure of helicobacter pylori glutamate racemase in complex with D-glutamate and an inhibitor
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
- 2JFZ
- Type
- protein
- Length
- 503 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
- 003, DGL
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 255 | 47% helix, 16% strand | Q9ZLT0 |
| B | Glutamate racemase (EC 5.1.1.3) | protein | 248 | 49% helix, 18% strand | Q9ZLT0 |
Ligands and binding sites
- 003 · 5-methyl-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-3-pyridin-4-yl-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione · ligand · 2 copies · chains A, B
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.80 | 0.81 | 109 | 003, DGL |
| 2 | 66 | 0.32 | 0.75 | 17 | empty |
| 3 | 80 | 0.31 | 0.73 | 19 | empty |
| 4 | 52 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 967 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2JFZ · 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 B 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 2JFZ · PDBe 2JFZ · UniProt Q9ZLT0
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