MolNFT v1 · #34302 · protein
Crystal structure of gamma-glutamyltranspeptidase from escherichia COLI acyl-enzyme intermediate
2DBW: “Crystal structure of gamma-glutamyltranspeptidase from escherichia COLI acyl-enzyme intermediate”. X-ray diffraction, 1 ligand (GGL), 6 pockets (best druggability 0.82). MolNFT v1 #34302 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2DBW
- Type
- protein
- Length
- 1,095 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
- GGL
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 359 | 48% helix, 13% strand | P18956 |
| B, D | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 190 | 21% helix, 28% strand | P18956 |
| C | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 356 | 48% helix, 13% strand | P18956 |
Ligands and binding sites
- GGL · Gamma-L-glutamic acid · ligand · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, D, C, A
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 | 804 | 0.82 | 0.85 | 72 | GOL |
| 2 | 379 | 0.76 | 0.86 | 40 | empty |
| 3 | 546 | 0.75 | 0.82 | 53 | empty |
| 4 | 85 | 0.38 | 0.77 | 24 | empty |
| 5 | 73 | 0.30 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 6541 Ų buried · 124 hydrogen bonds · protein-protein
- C–D · 6512 Ų buried · 122 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 461 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 288 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 2DBW · Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli Acyl-Enzyme… · the same entry in another collection · chain D against D, 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 2DBW · PDBe 2DBW · UniProt P18956
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