Research workbench
Crystal structure of acivicin-inhibited gamma-glutamyltranspeptidase reveals critical roles for its C-terminus in autoprocessing and catalysis
Analyse Crystal structure of acivicin-inhibited gamma-glutamyltranspeptidase reveals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FNM
- Type
- protein
- Length
- 1,066 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Helicobacter pylori
- Molecule
- Gamma-glutamyltranspeptidase (Ggt) Large subunit; Gamma-glutamyltranspeptidase (Ggt)…
- EC
- 2.3.2.2
- UniProt
- O25743
- Ligands
- AVN
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.7 · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyltranspeptidase (Ggt) Large subunit (EC 2.3.2.2) | protein | 342 | 49% helix, 14% strand | O25743 |
| B, D | Gamma-glutamyltranspeptidase (Ggt) Small subunit (EC 2.3.2.2) | protein | 188 | 18% helix, 26% strand | O25743 |
| C | Gamma-glutamyltranspeptidase (Ggt) Large subunit (EC 2.3.2.2) | protein | 348 | 50% helix, 13% strand | O25743 |
Ligands and binding sites
- AVN · (2S)-amino[(5s)-3-chloro-4,5-dihydroisoxazol-5-yl]acetic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.79 | 0.82 | 80 | empty |
| 2 | 160 | 0.40 | 0.73 | 24 | empty |
| 3 | 77 | 0.40 | 0.79 | 16 | empty |
| 4 | 134 | 0.38 | 0.73 | 16 | empty |
| 5 | 78 | 0.37 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5766 Ų buried · 113 hydrogen bonds · protein-protein
- C–D · 5661 Ų buried · 112 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 192 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 173 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3FNM · Crystal structure of acivicin-inhibited gamma-glutamyltranspeptidase reveals critical… · 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
- Every structure of UniProt O25743
- Elsewhere: RCSB PDB 3FNM · PDBe 3FNM · UniProt O25743
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