Research workbench
Crystal structure of N-acyl-D-glutamate deacylase from bordetella bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate.
Analyse Crystal structure of N-acyl-D-glutamate deacylase from bordetella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GIQ
- Type
- protein
- Length
- 948 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acyl-D-glutamate deacylase
- EC
- 3.5.1.82
- UniProt
- Q7WHC3
- Ligands
- G01, ZN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acyl-D-glutamate deacylase (EC 3.5.1.82) | protein | 474 | 33% helix, 22% strand | Q7WHC3 |
Ligands and binding sites
- G01 · N-[(R)-hydroxy(methyl)phosphoryl]-D-glutamic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.77 | 0.82 | 64 | empty |
| 2 | 161 | 0.61 | 0.84 | 39 | G01 |
| 3 | 121 | 0.59 | 0.85 | 31 | G01 |
| 4 | 152 | 0.51 | 0.79 | 32 | empty |
| 5 | 76 | 0.39 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3GIQ · Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica… · the same entry in another collection · chain B against B, 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 Q7WHC3
- Elsewhere: RCSB PDB 3GIQ · PDBe 3GIQ · UniProt Q7WHC3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.