MolNFT v1 · #140391 · protein
Crystal structure of bacillus licheniformis gamma glutamyl transpeptidase with don
5Y9B: “Crystal structure of bacillus licheniformis gamma glutamyl transpeptidase with don”. X-ray diffraction, 2 ligands (DON, CA), 2 pockets (best druggability 0.72). MolNFT v1 #140391 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5Y9B
- Type
- protein
- Length
- 542 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
- DON, CA
- Pockets
- 2 · best druggability 0.72
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 | 360 | 47% helix, 12% strand | — |
| B | Gamma glutamyl transpeptidase (EC 2.3.2.2) | protein | 182 | 20% helix, 31% strand | — |
Ligands and binding sites
- DON · 6-diazenyl-5-oxo-L-norleucine · ligand · chains A, B
- CA · Calcium ion · metal · 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.72 | 0.79 | 63 | DON |
| 2 | 53 | 0.30 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 6784 Ų buried · 125 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Y9B · Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with DON · 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
- Elsewhere: RCSB PDB 5Y9B · PDBe 5Y9B
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