2YXS

Crystal Structure of N-terminal domain of human galectin-8 with D-lactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystal Structure of N-terminal domain of human galectin-8 with D-lactose

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galectin-8 variantA164Homo sapiensMutation(s): 0 
Gene Names: LGALS8
Find proteins for O00214 (Homo sapiens)
Explore O00214 
Go to UniProtKB:  O00214
NIH Common Fund Data Resources
PHAROS  O00214
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
B
2 N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LATKd:  62000   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900004
Query on PRD_900004
Bbeta-lactoseOligosaccharide /  Nutrient

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.913α = 90
b = 50.551β = 90
c = 69.336γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, 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