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- PDB-1clz: IGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NON... -

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Basic information

Entry
Database: PDB / ID: 1clz
TitleIGG FAB (IGG3, KAPPA) FRAGMENT (MBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER
Components(IGG FAB (IGG3, KAPPA)) x 2
KeywordsIMMUNOGLOBULIN / IMMUNOGLOBULIN C REGION / GLYCOPROTEIN / TRANSMEMBRANE
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / antibacterial humoral response / 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) / : / Ig gamma-3 chain C region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 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: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: 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
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 (IGG3, KAPPA)
H: IGG FAB (IGG3, KAPPA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8554
Polymers48,0072
Non-polymers8482
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2


  • Idetical with deposited unit in distinct coordinate
  • defined by software
TypeNameSymmetry operationNumber
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area4960 Å2
ΔGint-2 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.400, 84.900, 86.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IGG FAB (IGG3, KAPPA) / MBR96 FAB (IMMUNOGLOBULIN)


Mass: 24246.910 Da / Num. of mol.: 1 / Fragment: FRAGMENT (MBR96) / Source method: isolated from a natural source / Details: HYBRIDIZED WITH P2X63-AG MOUSE / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: PIR: PC4203
#2: Antibody IGG FAB (IGG3, KAPPA) / MBR96 FAB (IMMUNOGLOBULIN)


Mass: 23759.754 Da / Num. of mol.: 1 / Fragment: FRAGMENT (MBR96) / Source method: isolated from a natural source / Details: HYBRIDIZED WITH P2X63-AG MOUSE / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P22436
#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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.8 / Details: pH 7.8
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Chang, C.Y., (1994) J.Mol.Biol., 235, 372.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMimidazole-HCl1drop
28 mg/mlprotein1drop
34 Msodium formate1reservoir
41 mM1reservoirCuCl2

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jan 1, 1993 / Details: MIRROR (SUPPER 6 CM)
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.78→38.1 Å / Num. obs: 9937 / % possible obs: 73.9 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 2.78→2.95 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.151 / % possible all: 43.8
Reflection
*PLUS
Num. measured all: 23962 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 43.8 %

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORrefinement
XENGENdata scaling
RefinementResolution: 2.8→8 Å / Cross valid method: EX POST FACTO / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.295 969 10 %
Rwork0.197 --
obs0.197 8858 70 %
Displacement parametersBiso mean: 14.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 58 0 3431
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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: 2.75→2.87 Å
RfactorNum. reflection% reflection
Rfree0.312 28 1.9 %
Rwork0.255 237 -
obs--18 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRO (ENGH & HUBETOPHCSDX.PRO (ENGL & HUBER)
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.78 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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