7TKX | pdb_00007tkx

Crystal structure of R14A human Galectin-7 mutant in presence of 4-O-beta-D-Galactopyranosyl-D-glucose

PDB DOI: https://doi.org/10.2210/pdb7TKX/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-01-17 Released: 2023-01-25
Deposition Author(s): Pham, N.T.H., Calmettes, C., Doucet, N.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of R14A human Galectin-7 mutant in presence of 4-O-beta-D-Galactopyranosyl-D-glucose

Pham, N.T.H., Calmettes, C., Doucet, N.

To be published.

Macromolecule Content

Total Structure Weight: 30.78 kDa
Atom Count: 2,407
Modelled Residue Count: 267
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-7	A, B	135	Homo sapiens	Mutation(s): 1 Gene Names: LGALS7, PIG1, LGALS7B
UniProt & NIH Common Fund Data Resources
Find proteins for P47929 (Homo sapiens) Explore P47929 Go to UniProtKB: P47929
PHAROS: P47929 GTEx: ENSG00000178934 ENSG00000205076
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47929
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBL (Subject of Investigation/LOI) Query on LBL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	(2~{R},3~{R},4~{R},5~{R})-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,3,5, 6-tetrakis(oxidanyl)hexanal C₁₂ H₂₂ O₁₁ DKXNBNKWCZZMJT-JVCRWLNRSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.25	α = 90
b = 76.38	β = 90
c = 111.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Pham, N.T.H.

Calmettes, C.

Doucet, N.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)		RGPIN 2016-05557
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		R01GM105978
Other government		Fonds de Recherche du Quebec - Sante (FRQ-S) - Research Scholar Senior Career Award (281993)
Other government		Fonds de Recherche du Quebec - Sante (FRQ-S) - Junior 1 (251848)
Natural Sciences and Engineering Research Council (NSERC, Canada)		RGPIN-2017-06091
Other government		Fonds de Recherche du Quebec - Sante (FRQ-S) - Doctoral Training scholarship (287239)