MolNFT v1 · #114216 · protein
Crystal structure of escherichia COLI gamma-glutamyltranspeptidase in complex with peptidyl phosphonate inhibitor 1B
5B5T · Gamma-glutamyltranspeptidase large chain: “Crystal structure of escherichia COLI gamma-glutamyltranspeptidase in complex with peptidyl phosphonate…”. X-ray diffraction, 2 ligands (6FY, CA), 7 pockets (best druggability 0.80). MolNFT…
- PDB
- 5B5T
- Type
- protein
- Length
- 1,078 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyltranspeptidase large chain; Gamma-glutamyltranspeptidase small chain
- EC
- 2.3.2.2, 3.4.19.13
- UniProt
- P18956
- Ligands
- 6FY, CA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gamma-glutamyltranspeptidase large chain (EC 2.3.2.2, 3.4.19.13) | protein | 349 | 50% helix, 14% strand | P18956 |
| B, D | Gamma-glutamyltranspeptidase small chain (EC 2.3.2.2, 3.4.19.13) | protein | 190 | 20% helix, 27% strand | P18956 |
Ligands and binding sites
- 6FY · (2~{S})-2-azanyl-4-[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-butan-2-yl]oxyphosphonoyl-butanoic acid · ligand · 2 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.80 | 0.81 | 76 | 6FY, CA |
| 2 | 498 | 0.76 | 0.83 | 46 | empty |
| 3 | 493 | 0.69 | 0.80 | 43 | 6FY |
| 4 | 75 | 0.64 | 0.92 | 33 | empty |
| 5 | 82 | 0.33 | 0.75 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 6359 Ų buried · 125 hydrogen bonds · protein-protein
- C–D · 6241 Ų buried · 123 hydrogen bonds · protein-protein
- A–D · 416 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 279 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5B5T · 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 5B5T · PDBe 5B5T · UniProt P18956
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