MolNFT v1 · #137866 · protein
Crystal structure of alternate isoform of glutamate racemase from helicobacter pylori bound to D-glutamate
5W1Q: “Crystal structure of alternate isoform of glutamate racemase from helicobacter pylori bound to D-glutamate”. X-ray diffraction, 1 ligand (DGL), 3 pockets (best druggability 0.79). MolNFT v1 #137866 on GenesisL1: 3D structure…
- PDB
- 5W1Q
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- K2K6A3
- Ligands
- DGL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate racemase (EC 5.1.1.3) | protein | 254 | 49% helix, 17% strand | K2K6A3 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.79 | 0.85 | 72 | DGL, GOL |
| 2 | 82 | 0.32 | 0.74 | 22 | empty |
| 3 | 62 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1084 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5W1Q · Crystal structure of alternate isoform of glutamate racemase from Helicobacter pylori… · the same entry in another collection · chain A 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 K2K6A3
- Elsewhere: RCSB PDB 5W1Q · PDBe 5W1Q · UniProt K2K6A3
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