7LA5 | pdb_00007la5

Structure of human GGT1 in complex with Lnt1-172 compound.

PDB DOI: https://doi.org/10.2210/pdb7LA5/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2021-01-05 Released: 2022-01-12
Deposition Author(s): Terzyan, S.S., Hanigan, M., Nguen, L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.281 (Depositor), 0.284 (DCC)
R-Value Work:
0.223 (Depositor), 0.228 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of human GGT1 in complex with Lnt1-172 compound.

Terzyan, S.S., Hanigan, M.

To be published.

Macromolecule Content

Total Structure Weight: 60.15 kDa
Atom Count: 4,321
Modeled Residue Count: 532
Deposited Residue Count: 542
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione hydrolase 1 heavy chain	A	353	Homo sapiens	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19440
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A	Go to GlyGen: P19440-1
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19440
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: P19440-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
XSM (Subject of Investigation/LOI) Query on XSM Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	(2R)-4-borono-2-{[(1H-imidazol-4-yl)methyl]amino}butanoic acid C₈ H₁₄ B N₃ O₄ JBISBMUZBNLAPG-SSDOTTSWSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [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 I [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 I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	C [auth A], D [auth A], E [auth A], F [auth A], I [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 I [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 I [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]