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- PDB-1mim: IGG FAB FRAGMENT (CD25-BINDING) -

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Basic information

Entry
Database: PDB / ID: 1mim
TitleIGG FAB FRAGMENT (CD25-BINDING)
Components(CHIMERIC SDZ CHI621) x 2
KeywordsIMMUNOGLOBULIN / C REGION
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMikol, V.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of the fab fragment of SDZ CHI621: a chimeric antibody against CD25.
Authors: Mikol, V.
#1: Journal: Transplantation / Year: 1995
Title: Prolonged Action of a Chimeric Interleukin-2 Receptor (Cd25) Monoclonal Antibody Used in Cadaveric Renal Transplantation
Authors: Amlot, P.L. / Rawlings, E. / Fernando, O.N. / Griffin, P.J. / Heinrich, G. / Schreier, M.H. / Castaigne, J.P. / Moore, R. / Sweny, P.
History
DepositionDec 4, 1995Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: CHIMERIC SDZ CHI621
H: CHIMERIC SDZ CHI621


Theoretical massNumber of molelcules
Total (without water)46,0272
Polymers46,0272
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-21 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.580, 59.760, 102.090
Angle α, β, γ (deg.)90.00, 99.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody CHIMERIC SDZ CHI621


Mass: 22882.338 Da / Num. of mol.: 1 / Fragment: IGG FAB
Source method: isolated from a genetically manipulated source
Details: MURINE ANTI-CD25 MONOCLONAL ANTIBODY, RFT5, CHIMERIZED WITH THE CONSTANT REGIONS OF HUMAN 1GG1 HEAVY AND KAPPA LIGHT CHAINS
Source: (gene. exp.) Homo sapiens (human)
Fragment: CONSTANT REGIONS OF 1GG1 HEAVY AND KAPPA LIGHT CHAINS
References: UniProt: P01834
#2: Antibody CHIMERIC SDZ CHI621


Mass: 23144.826 Da / Num. of mol.: 1 / Fragment: IGG FAB
Source method: isolated from a genetically manipulated source
Details: MURINE ANTI-CD25 MONOCLONAL ANTIBODY, RFT5, CHIMERIZED WITH THE CONSTANT REGIONS OF HUMAN 1GG1 HEAVY AND KAPPA LIGHT CHAINS
Source: (gene. exp.) Homo sapiens (human)
Fragment: CONSTANT REGIONS OF 1GG1 HEAVY AND KAPPA LIGHT CHAINS
References: GenBank: 9857755
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE WATER MOLECULE 2 WAS POSITIONED ON A STRONG ELECTRON DENSITY PEAK WHICH WAS OBSERVED BETWEEN ...THE WATER MOLECULE 2 WAS POSITIONED ON A STRONG ELECTRON DENSITY PEAK WHICH WAS OBSERVED BETWEEN TWO STRANDS OF THE BETA SHEET OF THE VARIABLE DOMAIN OF THE HEAVY CHAIN. IT MAKES SHORT CONTACTS WITH TWO CARBONYL OXYGENS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
27.5 %(w/v)PEG80001drop
30.02 %(w/v)1dropNaN3
40.33 mMprotein1drop
5100 mMTris-HCl1reservoir
615.0 %(w/v)PEG80001reservoir
70.04 %(w/v)1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 14331 / % possible obs: 90.6 % / Observed criterion σ(I): 2
Reflection
*PLUS
Num. measured all: 32477 / Rmerge(I) obs: 0.057

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.196 -
obs0.196 13210
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 0 69 3303
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.38
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2

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