MolNFT v1 · #49375 · protein
Crystal structure of helicobacter pylori gamma-glutamyltranspeptidase in complex with glutamate
2QM6: “Crystal structure of helicobacter pylori gamma-glutamyltranspeptidase in complex with glutamate”. X-ray diffraction, 1 ligand (GLU), 5 pockets (best druggability 0.79). MolNFT v1 #49375 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2QM6
- Type
- protein
- Length
- 1,062 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltranspeptidase
- EC
- 2.3.2.2
- UniProt
- O25743
- Ligands
- GLU
- Pockets
- 5 · best druggability 0.79
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 | 342 | 48% helix, 14% strand | O25743 |
| B, D | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 186 | 18% helix, 26% strand | O25743 |
| C | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 348 | 49% helix, 12% strand | O25743 |
Ligands and binding sites
- GLU · Glutamic 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.79 | 0.82 | 86 | empty |
| 2 | 442 | 0.64 | 0.78 | 39 | empty |
| 3 | 370 | 0.62 | 0.78 | 34 | empty |
| 4 | 85 | 0.40 | 0.77 | 22 | empty |
| 5 | 70 | 0.36 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5652 Ų buried · 113 hydrogen bonds · protein-protein
- C–D · 5583 Ų buried · 110 hydrogen bonds · protein-protein
- B–D · 413 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 183 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 174 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2QM6 · Crystal Structure of Helicobacter Pylori Gamma-Glutamyltranspeptidase in Complex with… · the same entry in another collection · chain D against D, 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 2QM6 · PDBe 2QM6 · UniProt O25743
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