MolNFT v1 · #141800 · protein
Gamma-glutamyltranspeptidase from pseudomonas nitroreducens complexed with gly-gly
5ZJG · Gamma-glutamyltransferase 1 threonine peptidase. merops…: “Gamma-glutamyltranspeptidase from pseudomonas nitroreducens complexed with gly-gly”. X-ray diffraction, 1 ligand (GLY), 10 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5ZJG
- Type
- protein
- Length
- 1,064 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltransferase 1 threonine peptidase. merops family T03 L-subunit…
- UniProt
- A0A239KXH0
- Ligands
- GLY
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyltransferase 1 threonine peptidase. merops family T03 L-subunit | protein | 338 | 50% helix, 13% strand | A0A239KXH0 |
| B | Gamma-glutamyltransferase 1 threonine peptidase. merops family T03 S-subunit | protein | 196 | 18% helix, 30% strand | A0A239KXH0 |
| C | Gamma-glutamyltransferase 1 threonine peptidase. merops family T03 L-subunit | protein | 336 | 50% helix, 13% strand | A0A239KXH0 |
| D | Gamma-glutamyltransferase 1 threonine peptidase. merops family T03 S-subunit | protein | 194 | 19% helix, 30% strand | A0A239KXH0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.73 | 0.81 | 49 | empty |
| 2 | 206 | 0.70 | 0.87 | 30 | empty |
| 3 | 138 | 0.66 | 0.88 | 22 | empty |
| 4 | 78 | 0.58 | 0.88 | 35 | GLY |
| 5 | 125 | 0.45 | 0.77 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5898 Ų buried · 108 hydrogen bonds · protein-protein
- C–D · 5885 Ų buried · 110 hydrogen bonds · protein-protein
- A–C · 347 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 142 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZJG · Gamma-glutamyltranspeptidase from Pseudomonas nitroreducens complexed with Gly-Gly · the same entry in another collection · chain C against C, 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 5ZJG · PDBe 5ZJG · UniProt A0A239KXH0
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