1GYA | pdb_00001gya

N-GLYCAN AND POLYPEPTIDE NMR SOLUTION STRUCTURES OF THE ADHESION DOMAIN OF HUMAN CD2

• PDB DOI: https://doi.org/10.2210/pdb1GYA/pdb

• Classification: ADHESION GLYCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 1995-05-26 Released: 1996-11-08 
• Deposition Author(s): Wyss, D.F., Choi, J.S., Wagner, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 120 
• Conformers Submitted: 18 
• Selection Criteria: PROSTAT/STRUCT_CHECK 

Literature

Conformation and function of the N-linked glycan in the adhesion domain of human CD2.

Wyss, D.F., Choi, J.S., Li, J., Knoppers, M.H., Willis, K.J., Arulanandam, A.R., Smolyar, A., Reinherz, E.L., Wagner, G.

(1995) Science 269: 1273-1278

• PubMed: 7544493 
• DOI: https://doi.org/10.1126/science.7544493
• Primary Citation Related Structures: 
  1GYA


• PubMed Abstract: 
  

  The adhesion domain of human CD2 bears a single N-linked carbohydrate. The solution structure of a fragment of CD2 containing the covalently bound high-mannose N-glycan [-(N-acetylglucosamine)2-(mannose)5-8] was solved by nuclear magnetic resonance. The stem and two of three branches of the carbohydrate structure are well defined and the mobility of proximal glycan residues is restricted. Mutagenesis of all residues in the vicinity of the glycan suggests that the glycan is not a component of the CD2-CD58 interface; rather, the carbohydrate stabilizes the protein fold by counterbalancing an unfavorable clustering of five positive charges centered about lysine-61 of CD2.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.01 kDa 
• Atom Count: 982 
• Modeled Residue Count: 105 
• Deposited Residue Count: 105 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN CD2	A	105	Homo sapiens	Mutation(s): 0  Gene Names: SCD2=182=
UniProt & NIH Common Fund Data Resources
Find proteins for P06729 (Homo sapiens) Explore P06729  Go to UniProtKB:  P06729
PHAROS:  P06729 GTEx:  ENSG00000116824
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P06729-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	9		N-Glycosylation
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 120 
• Conformers Submitted: 18 
• Selection Criteria: PROSTAT/STRUCT_CHECK 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-11-08 
Deposition Author(s): Wyss, D.F., Choi, J.S., Wagner, G.

Revision History  

• Version 1.0: 1996-11-08
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary