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- PDB-3ck0: ANTI-ANTI-IDIOTYPIC ANTIBODY AGAINST HUMAN ANGIOTENSIN II, COMPLE... -

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Basic information

Entry
Database: PDB / ID: 3ck0
TitleANTI-ANTI-IDIOTYPIC ANTIBODY AGAINST HUMAN ANGIOTENSIN II, COMPLEX WITH HUMAN ANGIOTENSIN II
Components
  • PROTEIN (8-MER; HUMAN ANGIOTENSIN II)
  • PROTEIN (IMMUNOGLOBULIN; HEAVY CHAIN)
  • PROTEIN (IMMUNOGLOBULIN; LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homology
Function and homology information


regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / : / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger ...regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / : / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of macrophage derived foam cell differentiation / positive regulation of extracellular matrix assembly / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of CoA-transferase activity / vasoconstriction / low-density lipoprotein particle remodeling / type 1 angiotensin receptor binding / response to angiotensin / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of protein tyrosine kinase activity / positive regulation of gap junction assembly / regulation of cardiac conduction / regulation of vasoconstriction / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / nitric oxide-cGMP-mediated signaling / negative regulation of MAP kinase activity / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / B cell differentiation / Peptide ligand-binding receptors / positive regulation of cytokine production / kidney development / angiotensin-activated signaling pathway / regulation of cell growth / growth factor activity / serine-type endopeptidase inhibitor activity / PPARA activates gene expression / hormone activity / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / regulation of apoptotic process / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Angiotensinogen, serpin domain / Angiotensinogen / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Angiotensinogen / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPan, Y.H. / Amzel, L.M.
CitationJournal: To be Published
Title: Structures of Angiotensin II and a Phage-Display Selected Cyclic Peptide in Complex with Fab131: Making Angiotensin II Analogs
Authors: Pan, Y.H. / Lee, K.H. / Li, M. / Ronco, P. / Amzel, L.M.
History
DepositionJun 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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
L: PROTEIN (IMMUNOGLOBULIN; LIGHT CHAIN)
H: PROTEIN (IMMUNOGLOBULIN; HEAVY CHAIN)
P: PROTEIN (8-MER; HUMAN ANGIOTENSIN II)


Theoretical massNumber of molelcules
Total (without water)48,6033
Polymers48,6033
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-27 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.440, 84.440, 158.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody PROTEIN (IMMUNOGLOBULIN; LIGHT CHAIN)


Mass: 23904.543 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: IGG1, KAPPA / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA / References: UniProt: P01837*PLUS
#2: Antibody PROTEIN (IMMUNOGLOBULIN; HEAVY CHAIN)


Mass: 23650.486 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: IGG1, KAPPA / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA
#3: Protein/peptide PROTEIN (8-MER; HUMAN ANGIOTENSIN II)


Mass: 1048.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SYNTHETIC / Source: (natural) synthetic construct (others) / References: UniProt: P01019*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: MONOCHROMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 10218 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.099

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→8 Å / Data cutoff low absF: 0.1 / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 10060 88.3 %
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 1 3367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.52
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT

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