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- PDB-1fvc: X-RAY STRUCTURES OF THE ANTIGEN-BINDING DOMAINS FROM THREE VARIAN... -

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Entry
Database: PDB / ID: 1fvc
TitleX-RAY STRUCTURES OF THE ANTIGEN-BINDING DOMAINS FROM THREE VARIANTS OF HUMANIZED ANTI-P185-HER2 ANTIBODY 4D5 AND COMPARISON WITH MOLECULAR MODELING
Components
  • IGG1-KAPPA 4D5 FV (HEAVY CHAIN)
  • IGG1-KAPPA 4D5 FV (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsEigenbrot, C. / Randal, M. / Kossiakoff, A.A. / Presta, L.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: X-ray structures of the antigen-binding domains from three variants of humanized anti-p185HER2 antibody 4D5 and comparison with molecular modeling.
Authors: Eigenbrot, C. / Randal, M. / Presta, L. / Carter, P. / Kossiakoff, A.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Humanization of an Anti-P185-Her2 Antibody for Human Cancer Therapy
Authors: Carter, P. / Presta, L. / Gorman, C.M. / Ridgway, J.B. / Henner, D. / Wong, W.L.T. / Rowland, A.M. / Kotts, C. / Carver, M.E. / Shepard, H.M.
History
DepositionOct 20, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG1-KAPPA 4D5 FV (LIGHT CHAIN)
B: IGG1-KAPPA 4D5 FV (HEAVY CHAIN)
C: IGG1-KAPPA 4D5 FV (LIGHT CHAIN)
D: IGG1-KAPPA 4D5 FV (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)50,2824
Polymers50,2824
Non-polymers00
Water2,270126
1
A: IGG1-KAPPA 4D5 FV (LIGHT CHAIN)
B: IGG1-KAPPA 4D5 FV (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)25,1412
Polymers25,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-12 kcal/mol
Surface area10220 Å2
MethodPISA
2
C: IGG1-KAPPA 4D5 FV (LIGHT CHAIN)
D: IGG1-KAPPA 4D5 FV (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)25,1412
Polymers25,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-12 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.600, 63.400, 90.200
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: EIGHT ATOMS HAVE BEEN ASSIGNED ZERO OCCUPANCY IN THE FINAL MODEL. THEY ARE ATOMS CG, CD, OE1, AND OE2 OF RESIDUE GLU B 1 AND ATOMS CG, CD, OE1, AND NE2 OF RESIDUE GLN C 3.
2: RESIDUES 8 AND 95 IN CHAINS A AND C ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99776, 0.03673, 0.05595), (0.03703, -0.9993, -0.00435), (0.05576, -0.00641, 0.99842)
Vector: 36.96113, 27.31182, -0.46846)
DetailsTHERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT. THE LIGHT AND HEAVY CHAINS OF MOLECULE 1 ARE DENOTED BY CHAIN IDENTIFIERS *A* AND *B*. THE LIGHT AND HEAVY CHAINS OF MOLECULE 2 ARE DENOTED BY THE CHAIN IDENTIFIERS *C* AND *D*. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *C* AND *D*.

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Components

#1: Antibody IGG1-KAPPA 4D5 FV (LIGHT CHAIN)


Mass: 11964.308 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 185985
#2: Antibody IGG1-KAPPA 4D5 FV (HEAVY CHAIN)


Mass: 13176.638 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERING IS SEQUENTIAL WITHIN EACH CHAIN. THE SEQUENTIAL NUMBERING OF THE LIGHT CHAIN ...THE RESIDUE NUMBERING IS SEQUENTIAL WITHIN EACH CHAIN. THE SEQUENTIAL NUMBERING OF THE LIGHT CHAIN CORRESPONDS TO THE KABAT NUMBERING SCHEME. THE FOLLOWING IS THE RELATIONSHIP OF THE SEQUENTIAL NUMBERING SCHEME OF THE HEAVY CHAIN TO THE KABAT NUMBERING SCHEME: ENTRY KABAT 1-52 1-52 53 52A 54-83 53-82 84-86 82A,82B,82C 87-104 83-100 105-107 100A,100B,100C 108-120 101-113

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMimidazole malate1reservoir
232 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Num. obs: 18259 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.116

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / Rfactor Rwork: 0.183 / Rfactor obs: 0.183 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 0 126 3647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.2
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 17110 / Rfactor obs: 0.183 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.2
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_deg

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