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- PDB-1ccf: How an Epidermal Growth Factor (EGF)-Like Domain Binds Calcium-Hi... -

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Entry
Database: PDB / ID: 1ccf
TitleHow an Epidermal Growth Factor (EGF)-Like Domain Binds Calcium-High Resolution NMR Structure of the Calcium Form of the NH2-Terminal EGF-Like Domain in Coagulation Factor X
ComponentsCOAGULATION FACTOR X
KeywordsCOAGULATION FACTOR
Function / homology
Function and homology information


coagulation factor Xa / blood coagulation / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Coagulation factor X
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR
AuthorsSelander-Sunnerhagen, M. / Ullner, M. / Persson, M. / Teleman, O. / Stenflo, J. / Drakenberg, T.
Citation
Journal: J.Biol.Chem. / Year: 1992
Title: How an epidermal growth factor (EGF)-like domain binds calcium. High resolution NMR structure of the calcium form of the NH2-terminal EGF-like domain in coagulation factor X.
Authors: Selander-Sunnerhagen, M. / Ullner, M. / Persson, E. / Teleman, O. / Stenflo, J. / Drakenberg, T.
#1: Journal: Biochemistry / Year: 1992
Title: Three-Dimensional Structure of the Apo Form of the N-Terminal Egf-Like Module of Blood Coagulation Factor X as Determined by NMR Spectroscopy and Simulated Folding
Authors: Ullner, M. / Selander, M. / Persson, E. / Stenflo, J. / Teleman, O. / Drakenberg, T.
#2: Journal: Biochemistry / Year: 1990
Title: 1H NMR Assignment and Secondary Structure of the Ca2+-Free Form of the Amino-Terminal Epidermal Growth Factor Like Domain in Coagulation Factor X
Authors: Selander, M. / Persson, E. / Stenflo, J. / Drakenberg, T.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Calcium Binding to the Isolated Beta-Hydroxyaspartic Acid-Containing Epidermal Growth Factor-Like Domain of the Bovine Factor X
Authors: Selander, M. / Persson, E. / Drakenberg, T. / Linse, S.
History
DepositionMay 19, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 16, 2017Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Polymer sequence / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conn / struct_sheet_range
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_label_comp_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAGULATION FACTOR X


Theoretical massNumber of molelcules
Total (without water)4,5771
Polymers4,5771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: THE HYDROXYLATED ASPARTIC ACID RESIDUE IS REPRESENTED AS ASP 63 AND HETATM HYD 63.
2: PHE 83 - SER 84 MODEL 3 OMEGA =216.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: SER 84 - THR 85 MODEL 3 OMEGA =148.06 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: PHE 83 - SER 84 MODEL 4 OMEGA =213.40 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: SER 84 - THR 85 MODEL 4 OMEGA =148.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: SER 84 - THR 85 MODEL 5 OMEGA =211.34 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: PHE 83 - SER 84 MODEL 9 OMEGA =214.90 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: SER 84 - THR 85 MODEL 9 OMEGA =147.72 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / -
Representative

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Components

#1: Protein/peptide COAGULATION FACTOR X


Mass: 4576.948 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00743
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR ensembleConformers submitted total number: 15

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