Research workbench
Crystal structure of escherichia COLI gamma-glutamyltranspeptidase in complex with azaserine prepared in the dark
Analyse Crystal structure of escherichia COLI gamma-glutamyltranspeptidase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z8J
- Type
- protein
- Length
- 1,080 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
- AZS
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 350 | 49% helix, 14% strand | P18956 |
| B, D | Gamma-glutamyltranspeptidase (EC 2.3.2.2) | protein | 190 | 19% helix, 28% strand | P18956 |
Ligands and binding sites
- AZS · O-diazoacetyl-L-serine · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.76 | 0.82 | 42 | empty |
| 2 | 453 | 0.75 | 0.84 | 52 | empty |
| 3 | 568 | 0.73 | 0.81 | 51 | empty |
| 4 | 490 | 0.70 | 0.80 | 44 | empty |
| 5 | 82 | 0.35 | 0.76 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 6373 Ų buried · 116 hydrogen bonds · protein-protein
- C–D · 6252 Ų buried · 110 hydrogen bonds · protein-protein
- A–D · 489 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 276 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2Z8J · Crystal Structure of Escherichia coli gamma-Glutamyltranspeptidase in Complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- P18956 · AlphaFold monomer V2.0 prediction for glutathione hydrolase proenzyme (P18956) · a predicted model of the same protein · chain B 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 2Z8J · PDBe 2Z8J · UniProt P18956
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