4Y1V | pdb_00004y1v

Complex of human Galectin-1 and Galbeta1-3GlcNAc

• PDB DOI: https://doi.org/10.2210/pdb4Y1V/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-09 Released: 2016-04-06 
• Deposition Author(s): Lin, H.Y., Hsieh, T.J., Lin, C.H.
• Funding Organization(s): Academia Sinica, Ministry of Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural basis of human galectin-1 inhibition with Ki values in the micro- to nanomolar range

Lin, H.Y., Hsieh, T.J., Tu, Z., Huang, B.S., Wu, S.C., Chien, C.T., Hsu, S.T., Lin, C.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.62 kDa 
• Atom Count: 2,162 
• Modeled Residue Count: 266 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	A, B	154	Homo sapiens	Mutation(s): 0  Gene Names: LGALS1
UniProt & NIH Common Fund Data Resources
Find proteins for P09382 (Homo sapiens) Explore P09382  Go to UniProtKB:  P09382
PHAROS:  P09382 GTEx:  ENSG00000100097

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G44759DI GlyCosmos:  G44759DI

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.715	α = 90
b = 58.291	β = 90
c = 111.591	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data processing
HKL-2000	data scaling
PHASER	phasing
PHENIX	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Lin, H.Y., Hsieh, T.J., Lin, C.H.

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Funding Organization	Location	Grant Number
Academia Sinica	Taiwan	As-022316
Ministry of Science and Technology	Taiwan	103-2113-M-001-023-MY3
Ministry of Science and Technology	Taiwan	102-2113-M-001-001-MY3
Ministry of Science and Technology	Taiwan	102-2923-M-001-001-MY3

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-11-15
  Changes: Data collection
• Version 2.3: 2024-10-23
  Changes: Structure summary