5IT6 | pdb_00005it6

Galectin-related protein: an integral member of the network of chicken galectins

PDB DOI: https://doi.org/10.2210/pdb5IT6/pdb

Classification: CELL ADHESION
Organism(s): Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-16 Released: 2016-07-13
Deposition Author(s): Flores-Ibarra, A., Garcia-Caballero, G., Michalak, M., Bovin, N.V., Andre, S., Manning, J.C., Vertesy, S., Ruiz, F.M., Kaltner, H., Kopitz, J., Romero, A., Gabius, H.-J.
Funding Organization(s): Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.188 (Depositor), 0.194 (DCC)
R-Value Work:
0.171 (Depositor), 0.178 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Galectin-related protein: An integral member of the network of chicken galectins 1. From strong sequence conservation of the gene confined to vertebrates to biochemical characteristics of the chicken protein and its crystal structure.

Garcia Caballero, G., Flores-Ibarra, A., Michalak, M., Khasbiullina, N., Bovin, N.V., Andre, S., Manning, J.C., Vertesy, S., Ruiz, F.M., Kaltner, H., Kopitz, J., Romero, A., Gabius, H.J.

(2016) Biochim Biophys Acta 1860: 2285-2297

PubMed: 27268118 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bbagen.2016.06.001
Primary Citation Related Structures:
5IT6

Organizational Affiliation

Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany.

Macromolecule Content

Total Structure Weight: 15.84 kDa
Atom Count: 1,212
Modeled Residue Count: 134
Deposited Residue Count: 134
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-related protein	A	134	Gallus gallus	Mutation(s): 0 Gene Names: LGALSL, GRP, RCJMB04_34j3
UniProt
Find proteins for Q5ZHQ2 (Gallus gallus) Explore Q5ZHQ2 Go to UniProtKB: Q5ZHQ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZHQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.188 (Depositor), 0.194 (DCC)
R-Value Work: 0.171 (Depositor), 0.178 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.584	α = 90
b = 106.865	β = 90
c = 114.087	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Economy and Competitiveness	Spain	BFU2014-55448-P

Revision History (Full details and data files)

Version 1.0: 2016-07-13
Type: Initial release
Version 1.1: 2016-08-03
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description