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
Deposition Author(s): Terzyan, S.S., Hanigan, M.H.
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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 60.37 kDa
Atom Count: 4,970
Modelled Residue Count: 531
Deposited Residue Count: 542
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione hydrolase 1 heavy chain	A	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione hydrolase 1 light chain	B	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 Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V7D (Subject of Investigation/LOI) Query on V7D Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	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		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B]	H [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

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 Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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

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Help and Resources

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2