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- PDB-1apo: THREE-DIMENSIONAL STRUCTURE OF THE APO FORM OF THE N-TERMINAL EGF... -

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Entry
Database: PDB / ID: 1apo
TitleTHREE-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
ComponentsEGF-LIKE MODULE OF BLOOD COAGULATION 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
HYDROXIDE ION / Coagulation factor X
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodSOLUTION NMR
AuthorsUllner, M. / Selander, M. / Persson, E. / Stenflo, J. / Drakenberg, T. / Teleman, O.
Citation
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. / Drakenberg, T. / Teleman, O.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: Calcium Binding to the Isolated Beta-Hydroxyaspartic Acid-Containing Epidermal Growth Factor-Like Domain of Bovine Factor X
Authors: Persson, E. / Selander, M. / Linse, S. / Drakenberg, T. / Ohlin, A.-K.
History
DepositionApr 21, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5782
Polymers4,5611
Non-polymers171
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: GLU 82 - PHE 83 MODEL 5 OMEGA =211.97 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLU 82 - PHE 83 MODEL 11 OMEGA =210.27 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLU 82 - PHE 83 MODEL 12 OMEGA =210.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / -
Representative

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Components

#1: Protein/peptide EGF-LIKE MODULE OF BLOOD COAGULATION FACTOR X


Mass: 4560.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00743
#2: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
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: 13

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