MolNFT v1 · #52561 · protein
Crystal structure of helicobacter pylori glutamate racemase in complex with D-glutamate and an inhibitor
2W4I: “Crystal structure of helicobacter pylori glutamate racemase in complex with D-glutamate and an inhibitor”. X-ray diffraction, 2 ligands (DGL, VGA), 12 pockets (best druggability 0.82). MolNFT v1 #52561 on GenesisL1: 3D structure…
- PDB
- 2W4I
- Type
- protein
- Length
- 1,017 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q9ZLT0
- Ligands
- DGL, VGA
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 255 | 49% helix, 17% strand | Q9ZLT0 |
| B, E, F | Glutamate racemase (EC 5.1.1.3) | protein | 254 | 49% helix, 17% strand | Q9ZLT0 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 4 copies · chains A, B, E, F
- VGA · 1-[(3S)-5-phenyl-3-thiophen-2-yl-3H-1,4-benzodiazepin-2-yl]azetidin-3-ol · ligand · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.82 | 0.86 | 92 | DGL, VGA |
| 2 | 601 | 0.81 | 0.86 | 79 | DGL, VGA |
| 3 | 191 | 0.49 | 0.76 | 26 | empty |
| 4 | 114 | 0.40 | 0.75 | 29 | empty |
| 5 | 61 | 0.36 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1084 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1079 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 605 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2W4I · Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9ZLT0 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q9ZLT0) · a predicted model of the same protein · chain F 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 Q9ZLT0
- Elsewhere: RCSB PDB 2W4I · PDBe 2W4I · UniProt Q9ZLT0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.