MolNFT v1 · #64956 · protein
Crystal structure of N-acyl-D-glutamate deacylase from bordetella bronchiseptica complexed with zinc, acetate and formate ions.
3GIP: “Crystal structure of N-acyl-D-glutamate deacylase from bordetella bronchiseptica complexed with zinc, acetate…”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.76). MolNFT v1 #64956 on GenesisL1: 3D structure…
- PDB
- 3GIP
- 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
- ZN
- Pockets
- 6 · best druggability 0.76
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
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- ACY · Acetic acid · additive · 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 | 1028 | 0.76 | 0.79 | 97 | empty |
| 2 | 171 | 0.55 | 0.80 | 41 | ACY, FMT |
| 3 | 106 | 0.54 | 0.83 | 29 | ACY, FMT, ZN |
| 4 | 73 | 0.38 | 0.78 | 13 | empty |
| 5 | 70 | 0.31 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 868 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3GIP · Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica… · 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 Q7WHC3
- Elsewhere: RCSB PDB 3GIP · PDBe 3GIP · UniProt Q7WHC3
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