Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.07 kDa 
• Atom Count: 287 
• Modelled Residue Count: 33 
• Deposited Residue Count: 33 
• Unique protein chains: 1

2M9F

NMR solution structure of Pin1 WW domain mutant 5-1g

• DOI: 10.2210/pdb2M9F/pdb
• BMRB: 19292

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-06-07 Released: 2013-06-26 
• Deposition Author(s): Enck, S., Chen, W., Price, J.L., Powers, E.T., Wong, C., Dyson, H.J., Kelly, J.W.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural and energetic basis of carbohydrate-aromatic packing interactions in proteins.

Chen, W., Enck, S., Price, J.L., Powers, D.L., Powers, E.T., Wong, C.H., Dyson, H.J., Kelly, J.W.

(2013) J Am Chem Soc 135: 9877-9884

• PubMed: 23742246 
• DOI: 10.1021/ja4040472
• Primary Citation of Related Structures:  
  2M9E, 2M9J, 2M9I, 2M9F


• PubMed Abstract: 
  

Carbohydrate-aromatic interactions mediate many biological processes. However, the structure-energy relationships underpinning direct carbohydrate-aromatic packing interactions in aqueous solution have been difficult to assess experimentally and remain elusive. Here, we determine the structures and folding energetics of chemically synthesized glycoproteins to quantify the contributions of the hydrophobic effect and CH-π interactions to carbohydrate-aromatic packing interactions in proteins. We find that the hydrophobic effect contributes significantly to protein-carbohydrate interactions. Interactions between carbohydrates and aromatic amino acid side chains, however, are supplemented by CH-π interactions. The strengths of experimentally determined carbohydrate CH-π interactions do not correlate with the electrostatic properties of the involved aromatic residues, suggesting that the electrostatic component of CH-π interactions in aqueous solution is small. Thus, tight binding of carbohydrates and aromatic residues is driven by the hydrophobic effect and CH-π interactions featuring a dominating dispersive component.

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Organizational Affiliation: 

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	A	33	Homo sapiens	Mutation(s): 0  Gene Names: PIN1 EC: 5.2.1.8
Find proteins for Q13526 (Homo sapiens) Explore Q13526  Go to UniProtKB:  Q13526
NIH Common Fund Data Resources
PHAROS:  Q13526 GTEx:  ENSG00000127445

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2M9F Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-07 
• Released Date: 2013-06-26 
Deposition Author(s): Enck, S., Chen, W., Price, J.L., Powers, E.T., Wong, C., Dyson, H.J., Kelly, J.W.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2013-07-17
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary