Research workbench
Crystal structure of bacillus licheniformis gamma glutamyl transpeptidase with azaserine
Analyse Crystal structure of bacillus licheniformis gamma glutamyl transpeptidase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y8X
- Type
- protein
- Length
- 543 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma glutamyl transpeptidase
- EC
- 2.3.2.2
- Ligands
- AZS, CA
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma glutamyl transpeptidase (EC 2.3.2.2) | protein | 361 | 47% helix, 12% strand | — |
| B | Gamma glutamyl transpeptidase (EC 2.3.2.2) | protein | 182 | 20% helix, 30% strand | — |
Ligands and binding sites
- AZS · O-diazoacetyl-L-serine · ligand · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.74 | 0.80 | 64 | AZS |
Interfaces
1 interface between chains.
- A–B · 6761 Ų buried · 128 hydrogen bonds · protein-protein
Compared structures
- 5Y8X · Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine · 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
- Elsewhere: RCSB PDB 5Y8X · PDBe 5Y8X
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