4CZS

Discovery of Glycomimetic Ligands via Genetically-encoded Library of Phage displaying Mannose-peptides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Genetically-Encoded Fragment-Based Discovery of Glycopeptide Ligands for Carbohydrate-Binding Proteins.

Ng, S.Lin, E.Kitov, P.I.Tjhung, K.F.Gerlits, O.O.Deng, L.Kasper, B.Sood, A.Paschal, B.M.Zhang, P.Ling, C.C.Klassen, J.S.Noren, C.J.Mahal, L.K.Woods, R.J.Coates, L.Derda, R.

(2015) J.Am.Chem.Soc. 137: 5248

  • DOI: 10.1021/ja511237n

  • PubMed Abstract: 
  • We describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based discovery (GE-FBD) uses selection of phage-displayed glycopeptides to dock a glycan fragment a ...

    We describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based discovery (GE-FBD) uses selection of phage-displayed glycopeptides to dock a glycan fragment at the CRD and guide selection of synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 10(8) glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40-50-fold enhancement in affinity over methyl α-d-mannopyranoside (MeMan). Lectin array suggested specificity: Man-WYD derivative bound only to 3 out of 17 proteins—ConA, LcH, and PSA—that bind to Man. An X-ray structure of ConA:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking, but their extra-CRD binding modes are significantly different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.


    Organizational Affiliation

    ‡Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States.,#Alberta Glycomics Centre, Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada.,∥Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602,United States.,∇School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland.,⊥New England Biolabs, Ipswich, Massachusetts 01938, United States.,†Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.,§Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CONCANAVALIN-A
A, B, C, D
237Canavalia catharticaMutation(s): 0 
Find proteins for P81461 (Canavalia cathartica)
Go to UniProtKB:  P81461
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MAN-WYD
E, F, G, H
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
XSN
Query on XSN
E, F, G, H
L-peptide linkingC4 H8 N2 O3ASN
8LR
Query on 8LR
E, F, G, H
non-polymerC8 H16 O7

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.995α = 90.00
b = 62.761β = 96.10
c = 124.827γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references
  • Version 1.2: 2015-07-08
    Type: Atomic model, Database references, Structure summary