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

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Basic information

Entry
Database: PDB / ID: 1fvd
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 FAB (HEAVY CHAIN)
  • IGG1-KAPPA 4D5 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsEigenbrot, C. / Presta, L. / Randal, M. / Kossiakoff, A.A.
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 / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 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 / pdbx_unobs_or_zero_occ_residues / 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 FAB (LIGHT CHAIN)
B: IGG1-KAPPA 4D5 FAB (HEAVY CHAIN)
C: IGG1-KAPPA 4D5 FAB (LIGHT CHAIN)
D: IGG1-KAPPA 4D5 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)94,3094
Polymers94,3094
Non-polymers00
Water3,585199
1
A: IGG1-KAPPA 4D5 FAB (LIGHT CHAIN)
B: IGG1-KAPPA 4D5 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,1552
Polymers47,1552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-27 kcal/mol
Surface area18930 Å2
MethodPISA
2
C: IGG1-KAPPA 4D5 FAB (LIGHT CHAIN)
D: IGG1-KAPPA 4D5 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,1552
Polymers47,1552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-29 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.200, 80.200, 86.100
Angle α, β, γ (deg.)113.10, 92.70, 102.60
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES 8, 95, 141 OF CHAINS A AND C AND RESIDUES 154 AND 156 OF CHAINS B AND D ARE CIS PROLINES.
2: 127 ATOMS OF THE FINAL MODEL WERE ASSIGNED AN OCCUPANCY OF ZERO. THEY ARE IN CDR-H3, THE C-TERMINAL REGIONS, AND A CONSTANT DOMAIN LOOP REGION.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99983, 0.0176, -0.00577), (0.01451, 0.55092, -0.83443), (-0.0115, -0.83437, -0.55108)
Vector: 92.98331, 67.76248, 128.50787)
DetailsTHE 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 FAB (LIGHT CHAIN)


Mass: 23431.973 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: EMBL: X95750
#2: Antibody IGG1-KAPPA 4D5 FAB (HEAVY CHAIN)


Mass: 23722.617 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: EMBL: Y14735
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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 108-223 101-216

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %(w/v)PEG34001reservoir
350 mMimidazole malate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / Num. obs: 27905 / Observed criterion σ(I): 0 / Num. measured all: 50304 / Rmerge(I) obs: 0.119

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→10 Å / Rfactor Rwork: 0.179 / Rfactor obs: 0.179 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 0 199 6831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.4
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 26210 / σ(F): 2 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_d3.4
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_deg
X-RAY DIFFRACTIONx_mcbond_it2.71
X-RAY DIFFRACTIONx_scbond_it4.51.5
X-RAY DIFFRACTIONx_mcangle_it4.21.5
X-RAY DIFFRACTIONx_scangle_it6.62

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