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- PDB-1b9p: NMR STRUCTURE OF HEPARIN BINDING SITE OF NON COLLAGENOUS DOMAIN I... -

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Basic information

Entry
Database: PDB / ID: 1b9p
TitleNMR STRUCTURE OF HEPARIN BINDING SITE OF NON COLLAGENOUS DOMAIN I (NC1) OF COLLAGEN FACIT XIV
ComponentsPROTEIN (COLLAGEN ALPHA 1)
KeywordsCOLLAGEN FACIT XIV / HEPARIN-BINDING SITE / NC1
Function / homology
Function and homology information


interstitial matrix / collagen trimer / cell adhesion / extracellular region
Similarity search - Function
: / Thrombospondin N-terminal -like domains. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type III domain ...: / Thrombospondin N-terminal -like domains. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Collagen alpha-1(XIV) chain
Similarity search - Component
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / distance geometry
AuthorsMontserret, R. / Deleage, G. / Penin, F.
Citation
Journal: Biochemistry / Year: 1999
Title: Structural analysis of the heparin-binding site of the NC1 domain of collagen XIV by CD and NMR.
Authors: Montserret, R. / Aubert-Foucher, E. / McLeish, M.J. / Hill, J.M. / Ficheux, D. / Jaquinod, M. / van der Rest, M. / Deleage, G. / Penin, F.
#1: Journal: Matrix Biol. / Year: 1998
Title: Identification and characterization of a heparin binding site within the NC1 domain of chicken collagen XIV.
Authors: Giry-Lozinguez, C. / Aubert-Foucher, E. / Penin, F. / Deleage, G. / Dublet, B. / van der Rest, M.
History
DepositionFeb 15, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (COLLAGEN ALPHA 1)


Theoretical massNumber of molelcules
Total (without water)4,0211
Polymers4,0211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50NO RESTRAINT VIOLATION
Representative

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Components

#1: Protein/peptide PROTEIN (COLLAGEN ALPHA 1) / ALPHA 1 TYPE XIV COLLAGEN


Mass: 4020.755 Da / Num. of mol.: 1 / Fragment: FRAGMENT 84-116 OF NC1 (HEPARIN BINDING SITE) / Mutation: E1C / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND EXTRACELLULARLY IN THE EMBRYO OF GALLUS GALLUS (CHICKEN).
Source: (synth.) synthetic construct (others) / References: UniProt: P32018

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
NMR detailsText: AVERAGED STRUCTURE

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Sample preparation

Sample conditionspH: 6.0 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
VNMRstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 1

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