6XPB
Structure of human GGT1 in complex with 2-amino-4-(((1-((carboxymethyl)amino)-1-oxobutan-2-yl)oxy)(phenoxy)phosphoryl)butanoic acid (ACPB) molecule
- PDB DOI: https://doi.org/10.2210/pdb6XPB/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Komagataella pastoris
- Mutation(s): No 
- Deposited: 2020-07-08 Released: 2020-11-25 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.74 Å
- R-Value Free: 0.189 
- R-Value Work: 0.153 
- R-Value Observed: 0.155 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutathione hydrolase 1 heavy chain | 353 | Homo sapiens | Mutation(s): 0  Gene Names: GGT1, GGT EC: 3.4.19.13 (PDB Primary Data), 2.3.2.2 (PDB Primary Data), 3.4.19.14 (PDB Primary Data) | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P19440 (Homo sapiens) Explore P19440  Go to UniProtKB:  P19440 | |||||
PHAROS:  P19440 GTEx:  ENSG00000100031  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P19440 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutathione hydrolase 1 light chain | 189 | Homo sapiens | Mutation(s): 0  Gene Names: GGT1, GGT EC: 3.4.19.13 (PDB Primary Data), 2.3.2.2 (PDB Primary Data), 3.4.19.14 (PDB Primary Data) | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P19440 (Homo sapiens) Explore P19440  Go to UniProtKB:  P19440 | |||||
PHAROS:  P19440 GTEx:  ENSG00000100031  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P19440 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
V7D (Subject of Investigation/LOI) Query on V7D | L [auth B] | 2,2-diamino-4-[(S)-({(2S)-1-[(carboxymethyl)amino]-1-oxobutan-2-yl}oxy)(hydroxy)phosphanyl]butanoic acid C16 H24 N3 O7 P TVQHRKKZDSLIPL-JWNZJDHWSA-N | |||
NAG Query on NAG | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | H [auth A], K [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | I [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.74 Å
- R-Value Free: 0.189 
- R-Value Work: 0.153 
- R-Value Observed: 0.155 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 106.362 | α = 90 |
b = 124.218 | β = 90 |
c = 104.232 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-11-25  Deposition Author(s): Terzyan, S.S., Hanigan, M.H.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01GM125952 |
Revision History (Full details and data files)
- Version 1.0: 2020-11-25
Type: Initial release - Version 2.0: 2021-07-21
Changes: Advisory, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-10-18
Changes: Data collection, Database references, Refinement description