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- PDB-1hak: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLACENTAL ANNEXIN V COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1hak
TitleCRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLACENTAL ANNEXIN V COMPLEXED WITH K-201 AS A CALCIUM CHANNEL ACTIVITY INHIBITOR
ComponentsANNEXIN V
KeywordsCALCIUM/PHOSPHOLIPID-BINDING / ANNEXIN V / LIPOCORTIN V / ENDONEXIN II / PLACENTA ANTICOAGULANT PROTEIN-I / 35KDA CALELECTRIN / INHIBITOR OF BLOOD COAGULATION / CALCIUM-PHOSPHOLIPID-BINDING complex
Function / homology
Function and homology information


phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / sarcolemma / phospholipid binding / blood coagulation / Platelet degranulation ...phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / sarcolemma / phospholipid binding / blood coagulation / Platelet degranulation / : / external side of plasma membrane / focal adhesion / calcium ion binding / negative regulation of apoptotic process / signal transduction / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A5 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A5 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-K21 / Annexin A5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAgo, H. / Inagaki, E. / Miyano, M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of annexin V with its ligand K-201 as a calcium channel activity inhibitor.
Authors: Kaneko, N. / Ago, H. / Matsuda, R. / Inagaki, E. / Miyano, M.
#1: Journal: Drug Dev.Res. / Year: 1994
Title: New 1,4-Bezothiazepin Derivative, K201, Demonstrates Cardioprotective Effects Against Sudden Cardiac Cell Death and Intracellular Calcium Blocking Action
Authors: Kaneko, N.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal and Molecular Structure of Human Annexin V After Refinement. Implications for Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
Authors: Huber, R. / Berendes, R. / Burger, A. / Schneider, M. / Karshikov, A. / Luecke, H. / Romisch, J. / Paques, E.
#3: Journal: J.Biochem.(Tokyo) / Year: 1987
Title: Structure and Expression of Cdna for an Inhibitor of Blood Coagulation Isolated from Human Placenta: A New Lipocortin-Like Protein
Authors: Iwasaki, A. / Suda, M. / Nakao, H. / Nagoya, T. / Saino, Y. / Arai, K. / Mizoguchi, T. / Sato, F. / Yoshizaki, H. / Hirata, M. / Miyata, T. / Shidara, Y. / Murata, M. / Maki, M.
History
DepositionDec 10, 1997Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ANNEXIN V
A: ANNEXIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8114
Polymers71,9612
Non-polymers8492
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.300, 99.300, 130.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein ANNEXIN V / LIPOCORTIN V / ENDONEXIN II / PLACENTA ANTICOAGULANT PROTEIN-I / 35KDA CALELECTRIN / INHIBITOR OF ...LIPOCORTIN V / ENDONEXIN II / PLACENTA ANTICOAGULANT PROTEIN-I / 35KDA CALELECTRIN / INHIBITOR OF BLOOD COAGULATION


Mass: 35980.707 Da / Num. of mol.: 2 / Fragment: ANNEXIN FOLD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Cellular location: CYTOPLASM / Gene: CDNA / Organ: PLACENTA / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P08758
#2: Chemical ChemComp-K21 / 4-[3-{1-(4-BENZYL)PIPERODINYL}PROPIONYL]-7-METHOXY-2,3,4,5-TERTRAHYDRO-1,4-BENZOTHIAZEPINE / K201


Mass: 424.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32N2O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
21 mMcalcium chloride11
1ammonium sulfate11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 14, 1995 / Details: ASYMMETRIC DOUBLE MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 104199 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AK0

1ak0


Resolution: 3→20 Å / Rfactor Rfree error: 0.0125 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE PSF FILE FOR X-PLOR REFINEMENT WAS CREATED USING QUANTA/CHARMM.
RfactorNum. reflection% reflectionSelection details
Rfree0.331 701 5 %RANDOM
Rwork0.206 ---
obs0.206 14609 97.4 %-
Displacement parametersBiso mean: 12.6 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 60 109 5195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.428
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 78 5 %
Rwork0.273 1626 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROAMINO.RTF
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.428
LS refinement shell
*PLUS
Rfactor obs: 0.273

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