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- PDB-1avh: CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEME... -

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Basic information

Entry
Database: PDB / ID: 1avh
TitleCRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS
ComponentsANNEXIN V
KeywordsCALCIUM/PHOSPHOLIPID BINDING / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsHuber, R. / Berendes, R. / Burger, A. / Schneider, M. / Karshikov, A. / Luecke, H. / Roemisch, J. / Paques, E.
Citation
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.
#1: Journal: FEBS Lett. / Year: 1990
Title: The Calcium Binding Sites in Human Annexin V by Crystal Structure Analysis at 2.0 Angstroms Resolution
Authors: Huber, R. / Schneider, M. / Mayr, I. / Roemisch, J. / Paques, E.-P.
#2: Journal: Embo J. / Year: 1990
Title: The Crystal and Molecular Structure of Human Annexin V, an Anticoagulant Protein that Binds to Calcium and Membranes
Authors: Huber, R. / Roemisch, J. / Paques, E.-P.
History
DepositionOct 17, 1991Processing 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 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,54611
Polymers71,9612
Non-polymers5859
Water4,954275
1
A: ANNEXIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2936
Polymers35,9811
Non-polymers3125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANNEXIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2535
Polymers35,9811
Non-polymers2724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: ANNEXIN V
hetero molecules

B: ANNEXIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,54611
Polymers71,9612
Non-polymers5859
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/21
Buried area1570 Å2
ΔGint-82 kcal/mol
Surface area29400 Å2
MethodPISA
4
A: ANNEXIN V
hetero molecules

B: ANNEXIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,54611
Polymers71,9612
Non-polymers5859
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z+1/21
Buried area2030 Å2
ΔGint-81 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.800, 98.800, 129.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Atom site foot note1: GLY B 231 - ASN B 232 OMEGA ANGLE = 211.920 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein ANNEXIN V


Mass: 35980.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P08758
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
23 mMMOPS1drop
320 mM1dropCaCl2
40.0015 mlprecipitant1drop
52.1 Mammonium sulphate1reservoir
60.1 MTris-chloride1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.184 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 25 275 5326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_angle_deg2.319
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d2.319
X-RAY DIFFRACTIONo_angle_deg

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