Research workbench
Crystal structure of bacillus subtilis gamma-glutamyltranspeptidase in complex with acivicin
Analyse Crystal structure of bacillus subtilis gamma-glutamyltranspeptidase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WHS
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltranspeptidase large chain; Gamma-glutamyltranspeptidase small chain
- EC
- 2.3.2.2, 3.4.19.13
- UniProt
- P54422
- Ligands
- AVN
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyltranspeptidase large chain (EC 2.3.2.2, 3.4.19.13) | protein | 359 | 48% helix, 12% strand | P54422 |
| B | Gamma-glutamyltranspeptidase small chain (EC 2.3.2.2, 3.4.19.13) | protein | 183 | 19% helix, 31% strand | P54422 |
Ligands and binding sites
- AVN · (2S)-amino[(5s)-3-chloro-4,5-dihydroisoxazol-5-yl]acetic acid · ligand · 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 | 656 | 0.67 | 0.76 | 62 | AVN |
| 2 | 56 | 0.32 | 0.77 | 11 | empty |
| 3 | 53 | 0.30 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 6641 Ų buried · 121 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3WHS · Crystal structure of Bacillus subtilis gamma-glutamyltranspeptidase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P54422 · AlphaFold monomer V2.0 prediction for glutathione hydrolase proenzyme (P54422) · a predicted model of the same protein · 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 P54422
- Elsewhere: RCSB PDB 3WHS · PDBe 3WHS · UniProt P54422
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