MolNFT v1 · #176048 · protein
Highly active mutant W525D of gamma-glutamyltranspeptidase from pseudomonas nitroreducens
7D9X · Gamma-glutamyltransferase 1 threonine peptidase. merops…: “Highly active mutant W525D of gamma-glutamyltranspeptidase from pseudomonas nitroreducens”. X-ray diffraction, 2 ligands (GLY, GBL), 11 pockets (best druggability 0.70).…
- PDB
- 7D9X
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltransferase 1 threonine peptidase. merops family T03
- UniProt
- A0A239KXH0
- Ligands
- GLY, GBL
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gamma-glutamyltransferase 1 threonine peptidase. merops family T03 | protein | 336 | 49% helix, 13% strand | A0A239KXH0 |
| B, D | Gamma-glutamyltransferase 1 threonine peptidase. merops family T03 | protein | 194 | 19% helix, 30% strand | A0A239KXH0 |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains B, A, D, C
- GBL · Gamma-butyrolactone · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.70 | 0.85 | 32 | GLY |
| 2 | 311 | 0.69 | 0.83 | 38 | GLY, GBL |
| 3 | 50 | 0.67 | 0.97 | 26 | GLY |
| 4 | 362 | 0.61 | 0.77 | 33 | empty |
| 5 | 142 | 0.54 | 0.81 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 5879 Ų buried · 107 hydrogen bonds · protein-protein
- A–B · 5860 Ų buried · 110 hydrogen bonds · protein-protein
- A–C · 440 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 81 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7D9X · Highly active mutant W525D of Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens · 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 A0A239KXH0
- Elsewhere: RCSB PDB 7D9X · PDBe 7D9X · UniProt A0A239KXH0
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