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- PDB-1ck0: ANTI-ANTI-IDIOTYPIC ANTIBODY AGAINST HUMAN ANGIOTENSIN II, UNLIGA... -

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Basic information

Entry
Database: PDB / ID: 1ck0
TitleANTI-ANTI-IDIOTYPIC ANTIBODY AGAINST HUMAN ANGIOTENSIN II, UNLIGANDED FORM
Components
  • PROTEIN (IGG1-KAPPA ANTIBODY 131 (HEAVY CHAIN))
  • PROTEIN (IGG1-KAPPA ANTIBODY 131 (LIGHT CHAIN))
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
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/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
Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionApr 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (IGG1-KAPPA ANTIBODY 131 (LIGHT CHAIN))
H: PROTEIN (IGG1-KAPPA ANTIBODY 131 (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)47,5552
Polymers47,5552
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-21 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.850, 83.850, 142.060
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 (IGG1-KAPPA ANTIBODY 131 (LIGHT CHAIN))


Mass: 23904.543 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA / References: UniProt: P01837*PLUS
#2: Antibody PROTEIN (IGG1-KAPPA ANTIBODY 131 (HEAVY CHAIN))


Mass: 23650.486 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA / References: UniProt: P01869*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.5 Å3/Da / Density % sol: 50 %
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: 2.5→100 Å / Num. obs: 16538 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.094

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→6 Å / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
Details: GLY H131 - SER H138: THESE EIGHT RESIDUES WERE COMPLETELY DISORDERED IN THE STRUCTURE. TER ASN: THE SITE OF THE PROTEOLYSIS AT THE C TERMINUS OF THE HEAVY IS UNDEFINED, SO IT IS NOT KNOWN ...Details: GLY H131 - SER H138: THESE EIGHT RESIDUES WERE COMPLETELY DISORDERED IN THE STRUCTURE. TER ASN: THE SITE OF THE PROTEOLYSIS AT THE C TERMINUS OF THE HEAVY IS UNDEFINED, SO IT IS NOT KNOWN WEATHER THERE ARE RESIDUES MISSING THERE.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 677 5 %RANDOM
Rwork0.192 ---
obs-14063 84 %-
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 33 3324
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
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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