2YY1 | pdb_00002yy1

Crystal structure of N-terminal domain of human galectin-9 containing L-acetyllactosamine

PDB DOI: https://doi.org/10.2210/pdb2YY1/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2007-04-27 Released: 2008-04-29
Deposition Author(s): Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.244 (Depositor), 0.235 (DCC)
R-Value Work:
0.211 (Depositor), 0.202 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2YY1

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of N-terminal domain of human galectin-9 containing L-acetyllactosamine

Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 17.61 kDa
Atom Count: 1,194
Modeled Residue Count: 141
Deposited Residue Count: 160
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-9	A	160	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O00182 (Homo sapiens) Explore O00182 Go to UniProtKB: O00182
PHAROS: O00182 GTEx: ENSG00000168961
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00182
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G79333MY GlyCosmos: G79333MY GlyGen: G79333MY

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900019 Query on PRD_900019	B	N-acetyl-alpha-lactosamine	Oligosaccharide / Glycan component		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.244 (Depositor), 0.235 (DCC)
R-Value Work: 0.211 (Depositor), 0.202 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.407	α = 90
b = 47.407	β = 90
c = 121.609	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2020-09-09
Changes: Database references, Structure summary
Version 2.2: 2024-03-13
Changes: Data collection, Database references

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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.