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- PDB-1cly: IGG FAB (HUMAN IGG1, KAPPA) CHIMERIC FRAGMENT (CBR96) COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1cly
TitleIGG FAB (HUMAN IGG1, KAPPA) CHIMERIC FRAGMENT (CBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER
Components(IGG FAB (HUMAN IGG1, KAPPA)) x 2
KeywordsIMMUNOGLOBULIN / IMMUNOGLOBULIN C REGION / GLYCOPROTEIN / ANTIB
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
Lewis Y antigen, beta anomer / METHYL NONANOATE (ESTER) / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSheriff, S. / Bajorath, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: The x-ray structure of an anti-tumour antibody in complex with antigen.
Authors: Jeffrey, P.D. / Bajorath, J. / Chang, C.Y. / Yelton, D. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of the Monoclonal Anti-Tumor Antibody Br96 and its Complex with the Lewis Y Determinant
Authors: Chang, C.Y. / Jeffrey, P.D. / Bajorath, J. / Hellstrom, I. / Hellstrom, K.E. / Sheriff, S.
History
DepositionMar 15, 1995Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: IGG FAB (HUMAN IGG1, KAPPA)
H: IGG FAB (HUMAN IGG1, KAPPA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5354
Polymers47,6872
Non-polymers8482
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-2 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.700, 81.700, 166.300
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 IGG FAB (HUMAN IGG1, KAPPA) / CBR96 FAB (IMMUNOGLOBULIN)


Mass: 24077.883 Da / Num. of mol.: 1 / Fragment: CHIMERIC FRAGMENT (BR96)
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER / Source: (gene. exp.) Homo sapiens (human)
Description: HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH P2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION
Fragment: CH1, IGG1 / References: UniProt: P01834*PLUS
#2: Antibody IGG FAB (HUMAN IGG1, KAPPA) / CBR96 FAB (IMMUNOGLOBULIN)


Mass: 23609.449 Da / Num. of mol.: 1 / Fragment: CHIMERIC FRAGMENT (BR96)
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER / Source: (gene. exp.) Homo sapiens (human)
Description: HYBRIDOMA PRODUCED BY FUSIONING BALB/C SPLEEN CELLS WITH P2X63-AG 8.653 MOUSE MYELOMA CELLS. HUMAN CONSTANT REGIONS INTRODUCED BY HOMOLOGOUS RECOMBINATION
Fragment: CH1, IGG1
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis Y antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis Y antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-NON / METHYL NONANOATE (ESTER)


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
Has protein modificationY
Sequence detailsTHE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN ...THE FAB LIGHT CHAIN (RESIDUES 1 - 214) HAS BEEN ASSIGNED CHAIN INDICATOR L. THE FAB HEAVY CHAIN (RESIDUES 1 - 231) HAS BEEN ASSIGNED CHAIN INDICATOR H. THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN, C. FOELLER SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED., (1991), NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD.).

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion / Details: Chang, C.Y., (1994) J.Mol.Biol., 235, 372. / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium acetate1reservoirpH4.6
20.1 Mammonium sulfate1reservoir
313-15 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.51→57.8 Å / Num. obs: 20051 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.9
Reflection shellResolution: 2.51→2.75 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2 / % possible all: 90.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 59769
Reflection shell
*PLUS
% possible obs: 90.8 %

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Processing

Software
NameClassification
R-AXISdata collection
R-AXISdata reduction
X-PLORrefinement
R-AXISdata scaling
RefinementResolution: 2.5→8 Å / Cross valid method: EX POST FACTO / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.298 1741 10 %
Rwork0.238 --
obs0.238 17177 91 %
Displacement parametersBiso mean: 47.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 58 0 3395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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: 2.5→2.61 Å
RfactorNum. reflection% reflection
Rfree0.376 160 7.5 %
Rwork0.334 1558 -
obs--71.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRO (ENGH & HUBETOPHCSDX.PRO (ENGH & HUBER)
X-RAY DIFFRACTION2PARAME_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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