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- PDB-1pdc: REFINED SOLUTION STRUCTURE AND LIGAND-BINDING PROPERTIES OF PDC-1... -

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Basic information

Entry
Database: PDB / ID: 1pdc
TitleREFINED SOLUTION STRUCTURE AND LIGAND-BINDING PROPERTIES OF PDC-109 DOMAIN B. A COLLAGEN-BINDING TYPE II DOMAIN
ComponentsSEMINAL FLUID PROTEIN PDC-109
KeywordsCOLLAGEN-BINDING TYPE II DOMAIN
Function / homology
Function and homology information


positive regulation of sperm capacitation / phospholipid efflux / sperm capacitation / single fertilization / heparin binding / cell surface / extracellular space
Similarity search - Function
Seminal plasma protein, PDC-109-like / : / Fibronectin, type II, collagen-binding / Seminal Fluid Protein PDC-109 (Domain B) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain ...Seminal plasma protein, PDC-109-like / : / Fibronectin, type II, collagen-binding / Seminal Fluid Protein PDC-109 (Domain B) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Ribbon / Mainly Beta
Similarity search - Domain/homology
Seminal plasma protein PDC-109
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR
AuthorsLlinas, M. / Constantine, K.L. / Patthy, L.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain.
Authors: Constantine, K.L. / Madrid, M. / Banyai, L. / Trexler, M. / Patthy, L. / Llinas, M.
#1: Journal: Biochemistry / Year: 1991
Title: Sequence-Specific 1H NMR Assignments and Structural Characterization of Bovine Seminal Fluid Protein Pdc-109 Domain B
Authors: Constantine, K.L. / Ramesh, V. / Banyai, L. / Trexler, M. / Patthy, L. / Llinas, M.
#2: Journal: Eur.J.Biochem. / Year: 1990
Title: The Collagen-Binding Site of Type-II Units of Bovine Seminal Fluid Protein Pdc-109 and Fibronectin
Authors: Banyai, L. / Trexler, M. / Koncz, S. / Gyenes, M. / Sipos, G. / Patthy, L.
History
DepositionOct 10, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: SEMINAL FLUID PROTEIN PDC-109


Theoretical massNumber of molelcules
Total (without water)5,3791
Polymers5,3791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: RESIDUE PRO 4 IS A CIS PROLINE.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide SEMINAL FLUID PROTEIN PDC-109


Mass: 5379.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P02784
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
DIANAGUENTERT,BRAUN,WUTHRICHrefinement
MIDGEMADRIDrefinement
X-PLORBRUNGERrefinement
NMR ensembleConformers submitted total number: 1

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