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- PDB-1kyj: Tumor Associated Mucin Motif from CD43 protein -

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Basic information

Entry
Database: PDB / ID: 1kyj
TitleTumor Associated Mucin Motif from CD43 protein
ComponentsLeukosialin (CD43) fragment
Keywordsglycoprotein / immune system / Leukosialin / CD43 / Mucin glycoprotein
Function / homology2-acetamido-2-deoxy-alpha-D-galactopyranose
Function and homology information
MethodSOLUTION NMR / VNMR, NMRPIPE, X-PLOR, Torsion Space Simulated Annealing
AuthorsColtart, D.M. / Williams, L.J. / Glunz, P.W. / Sames, D. / Kuduk, S.D. / Schwarz, J.B. / Chen, X.-T. / Royyuru, A.K. / Danishefsky, S.D. / Live, D.H.
Citation
Journal: J.Am.Chem.Soc. / Year: 2002
Title: Principles of Mucin Architecture: Structural Studies on Synthetic Glycopeptides Bearing Clustered Mono-, Di-, Tri-, and Hexasaccharide Glycodomains
Authors: Coltart, D.M. / Royyuru, A.K. / Williams, L.J. / Glunz, P.W. / Sames, D. / Kuduk, S.D. / Schwarz, J.B. / Chen, X.T. / Danishefsky, S.J. / Live, D.H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Probing Cell-Surface Architecture Through Synthesis: An NMR Determined Structural Motif for Tumor-Associated Mucins
Authors: Live, D.H. / Williams, L.J. / Kuduk, S.D. / Schwarz, J.B. / Glunz, P.W. / Chen, X.-T. / Sames, D. / Kumar, R.A. / Danishefsky, S.J.
History
DepositionFeb 4, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 20, 2002ID: 1SIA
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukosialin (CD43) fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,1674
Polymers5041
Non-polymers6643
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)59 / 200No NOE violations greter than 0.15A, no coupling violation greater than 0.5 Hz, no angle violation greater than 5 deg.
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Leukosialin (CD43) fragment / pentapeptide fragment of sialophorin


Mass: 503.547 Da / Num. of mol.: 1 / Fragment: N-terminal glycopentapeptide / Source method: obtained synthetically / Details: Fragment of human sequence
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D TOCSY NOESY
NMR detailsText: Coordinates are given only for the experimentally defined glycopeptide core residues. These are comprised of the amino acid units in the peptide and the N-acetyl-galactosamine. Coordinates for ...Text: Coordinates are given only for the experimentally defined glycopeptide core residues. These are comprised of the amino acid units in the peptide and the N-acetyl-galactosamine. Coordinates for the terminal galactose and sialic acid of each of the glycans are not included.

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Sample preparation

DetailsContents: 10 mM glycopeptide / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.5 / Pressure: 1 atm / Temperature: 291 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Inc.collection
VNMR6.1Varian Inc.data analysis
NMRPipe2.1Delagliodata analysis
X-PLOR98Brunger/MSIrefinement
RefinementMethod: VNMR, NMRPIPE, X-PLOR, Torsion Space Simulated Annealing
Software ordinal: 1
Details: refinement based on 107 NOE's 11 J coupling restraints and 3 dihedral restraints. See citation for full description.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: No NOE violations greter than 0.15A, no coupling violation greater than 0.5 Hz, no angle violation greater than 5 deg.
Conformers calculated total number: 200 / Conformers submitted total number: 59

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