MolNFT v1 · #34436 · protein
Crystal structure of gamma-glutamyl transpeptidase from escherichia COLI in complex with hydrolyzed glutathione
2DG5 · Gamma-glutamyltranspeptidase: “Crystal structure of gamma-glutamyl transpeptidase from escherichia COLI in complex with hydrolyzed…”. X-ray diffraction, 2 ligands (GLU, CA), 8 pockets (best druggability 0.75). MolNFT v1 #34436 on…
- PDB
- 2DG5
- Type
- protein
- Length
- 1,082 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltranspeptidase
- EC
- 2.3.2.2
- UniProt
- P18956
- Ligands
- GLU, CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 351 | 49% helix, 14% strand | P18956 |
| B, D | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 190 | 20% helix, 28% strand | P18956 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · chains A
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 | 500 | 0.75 | 0.83 | 52 | empty |
| 2 | 709 | 0.74 | 0.80 | 45 | CA |
| 3 | 619 | 0.73 | 0.81 | 53 | empty |
| 4 | 535 | 0.71 | 0.80 | 43 | empty |
| 5 | 77 | 0.33 | 0.75 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 6289 Ų buried · 120 hydrogen bonds · protein-protein
- C–D · 6275 Ų buried · 128 hydrogen bonds · protein-protein
- B–C · 469 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 271 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 2DG5 · Crystal Structure of Gamma-glutamyl transpeptidase from Escherichia coli in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P18956 · AlphaFold monomer V2.0 prediction for glutathione hydrolase proenzyme (P18956) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P18956
- Elsewhere: RCSB PDB 2DG5 · PDBe 2DG5 · UniProt P18956
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