MolNFT v1 · #56224 · protein
Crystal structure of escherichia COLI gamma-glutamyltranspeptidase in complex with acivicin
2Z8K: “Crystal structure of escherichia COLI gamma-glutamyltranspeptidase in complex with acivicin”. X-ray diffraction, 1 ligand (AVN), 6 pockets (best druggability 0.82). MolNFT v1 #56224 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2Z8K
- 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
- AVN
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% 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 | 20% helix, 27% strand | P18956 |
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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.82 | 0.83 | 96 | AVN |
| 2 | 505 | 0.75 | 0.83 | 50 | empty |
| 3 | 568 | 0.71 | 0.80 | 40 | empty |
| 4 | 84 | 0.34 | 0.75 | 23 | empty |
| 5 | 74 | 0.33 | 0.75 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 6324 Ų buried · 119 hydrogen bonds · protein-protein
- C–D · 6227 Ų buried · 122 hydrogen bonds · protein-protein
- A–D · 485 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 482 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 271 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2Z8K · Crystal Structure of Escherichia coli gamma-Glutamyltranspeptidase in Complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P18956 · AlphaFold monomer V2.0 prediction for glutathione hydrolase proenzyme (P18956) · a predicted model of the same protein · chain D 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 2Z8K · PDBe 2Z8K · UniProt P18956
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