7ALS | pdb_00007als

Alpha and beta Lactose isomer structure of Galectin 8, N-terminal domain

PDB DOI: https://doi.org/10.2210/pdb7ALS/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-10-07 Released: 2021-11-03
Deposition Author(s): Hakansson, M., Walse, B., Diehl, C., Kovacic, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.149 (Depositor), 0.149 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Alpha and beta Lactose isomer structure of Galectin 8, N-terminal domain

Hassan, M., Hakansson, M.

To be published.

Macromolecule Content

Total Structure Weight: 36.52 kDa
Atom Count: 2,939
Modeled Residue Count: 299
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-8	A, B	155	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

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C [auth E], E [auth G]	2		N/A	Interactions Focus chain C [auth E] Focus chain E [auth G] Interactions & Density Focus chain C [auth E] Focus chain E [auth G]
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	D [auth F], F [auth H]	2		N/A	Interactions Focus chain D [auth F] Focus chain F [auth H] Interactions & Density Focus chain D [auth F] Focus chain F [auth H]
Glycosylation Resources
GlyTouCan: G88362QR GlyCosmos: G88362QR GlyGen: G88362QR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	G [auth A], H [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B]

Biologically Interesting Molecules (External Reference)

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004 Query on PRD_900004	C [auth E], E [auth G]	beta-lactose	Oligosaccharide / Nutrient		Interactions Focus chain C [auth E] Focus chain E [auth G] Interactions & Density Focus chain C [auth E] Focus chain E [auth G]

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008 Query on PRD_900008	D [auth F], F [auth H]	alpha-lactose	Oligosaccharide / Nutrient		Interactions Focus chain D [auth F] Focus chain F [auth H] Interactions & Density Focus chain D [auth F] Focus chain F [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.199 (Depositor), 0.199 (DCC)
R-Value Work: 0.149 (Depositor), 0.149 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.56	α = 90
b = 62.54	β = 90
c = 84.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-11-03
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.