7AEN | pdb_00007aen

Galectin-8 N-terminal carbohydrate recognition domain in complex with methyl 3-O-((7-carboxy)quinolin-2-yl)-methoxy)-beta-D-galactopyranoside

PDB DOI: https://doi.org/10.2210/pdb7AEN/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-17 Released: 2021-07-28
Deposition Author(s): Hassan, M., Klavern, V.S., Hakansson, M., Anderluh, M., Tomasic, T., Jakopin, Z., Nilsson, J.U., Kovacic, R., Walse, B., Diehl, C.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.212 (Depositor), 0.213 (DCC)
R-Value Work:
0.139 (Depositor), 0.141 (DCC)
R-Value Observed:
0.143 (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-Guided Design of d-Galactal Derivatives with High Affinity and Selectivity for the Galectin-8 N-Terminal Domain

Hassan, M., Baussiere, F., Guzelj, S., Sundin, A.P., Hakansson, M., Kovacic, R., Leffler, H., Tomasic, T., Anderluh, M., Jakopin, Z., Nilsson, U.J.

(2021) ACS Med Chem Lett 12: 1745-1752

DOI: https://doi.org/10.1021/acsmedchemlett.1c00371

Macromolecule Content

Total Structure Weight: 34.82 kDa
Atom Count: 2,740
Modeled Residue Count: 298
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Galectin-8	A, B	150	Homo sapiens	Mutation(s): 0 Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens) Explore O00214 Go to UniProtKB: O00214
PHAROS: O00214 GTEx: ENSG00000116977
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00214
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R8B (Subject of Investigation/LOI) Query on R8B Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	methyl 3-O-((7-carboxy) quinolin-2-yl)-methyl)-beta-D-galactopyranoside C₁₈ H₂₁ N O₈ OBYVIVUJQDGTKI-RIUYPTKQSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
R8B	BindingDB: 7AEN	Kd: 1.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.212 (Depositor), 0.213 (DCC)
R-Value Work: 0.139 (Depositor), 0.141 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.452	α = 90
b = 61.124	β = 90
c = 84.712	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
PHASER	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	Sweden	765581

Revision History (Full details and data files)

Version 1.0: 2021-07-28
Type: Initial release
Version 1.1: 2022-02-09
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2024-01-31
Changes: Data collection, Refinement description