Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 30.55 kDa 
• Atom Count: 2311 
• Modelled Residue Count: 268 
• Deposited Residue Count: 268 
• Unique protein chains: 2

1W6P

X-RAY CRYSTAL STRUCTURE OF C2S HUMAN GALECTIN-1 COMPLEXED WITH N- Acetyl-LACTOSAMINE

• DOI: 10.2210/pdb1W6P/pdb

• Classification: LECTIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-08-20 Released: 2004-10-20 
• Deposition Author(s): Lopez-Lucendo, M.I.F., Gabius, H.J., Romero, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

Growth-Regulatory Human Galectin-1: Crystallographic Characterisation of the Structural Changes Induced by Single-Site Mutations and Their Impact on the Thermodynamics of Ligand Binding

Lopez-Lucendo, M.I.F., Solis, D., Andre, S., Hirabayashi, J., Kasai, K., Kaltner, H., Gabius, H.J., Romero, A.

(2004) J Mol Biol 343: 957

• PubMed: 15476813 
• DOI: 10.1016/j.jmb.2004.08.078
• Primary Citation of Related Structures:  
  1GZW, 1W6O, 1W6N, 1W6M, 1W6Q, 1W6P


• PubMed Abstract: 
  

Human galectin-1 is a potent multifunctional effector that participates in specific protein-carbohydrate and protein-protein (lipid) interactions. By determining its X-ray structure, we provide the basis to define the structure of its ligand-binding pocket and to perform rational drug design. We have also analysed whether single-site mutations introduced at some distance from the carbohydrate recognition domain can affect the lectin fold and influence sugar binding. Both the substitutions introduced in the C2S and R111H mutants altered the presentation of the loop, harbouring Asp123 in the common "jelly-roll" fold. The orientation of the side-chain was inverted 180 degrees and the positions of two key residues in the sugar-binding site of the R111H mutant were notably shifted, i.e. His52 and Trp68. Titration calorimetry was used to define the decrease in ligand affinity in both mutants and a significant increase in the entropic penalty was found to outweigh a slight enhancement of the enthalpic contribution. The position of the SH-groups in the galectin appeared to considerably restrict the potential to form intramolecular disulphide bridges and was assumed to be the reason for the unstable lectin activity in the absence of reducing agent. However, this offers no obvious explanation for the improved stability of the C2S mutant under oxidative conditions. The noted long-range effects in single-site mutants are relevant for the functional divergence of closely related galectins and in more general terms, the functionality definition of distinct amino acids.

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Organizational Affiliation: 

Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GALECTIN-1	A	134	Homo sapiens	Mutation(s): 2  Gene Names: LGALS1
Find proteins for P09382 (Homo sapiens) Explore P09382  Go to UniProtKB:  P09382
NIH Common Fund Data Resources
PHAROS:  P09382 GTEx:  ENSG00000100097

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GALECTIN-1	B	134	Homo sapiens	Mutation(s): 2  Gene Names: LGALS1
Find proteins for P09382 (Homo sapiens) Explore P09382  Go to UniProtKB:  P09382
NIH Common Fund Data Resources
PHAROS:  P09382 GTEx:  ENSG00000100097

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	C, D	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	A, B	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900019	C, D	N-acetyl-alpha-lactosamine	Oligosaccharide /  Glycan component		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.76	α = 90
b = 88.1	β = 90
c = 93.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-20 
• Released Date: 2004-10-20 
Deposition Author(s): Lopez-Lucendo, M.I.F., Gabius, H.J., Romero, A.

Revision History  

• Version 1.0: 2004-10-20
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-07-24
  Changes: Data collection
• Version 1.5: 2020-07-01
  Changes: Advisory, Data collection, Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary