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- PDB-7lsi: Structure of KD035, a VEGFR2 monoclonal antibody -

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Basic information

Entry
Database: PDB / ID: 7lsi
TitleStructure of KD035, a VEGFR2 monoclonal antibody
Components
  • KD035 Fab heavy chain
  • KD035 Fab light chain
KeywordsANTITUMOR PROTEIN / IMMUNE SYSTEM / VEGFR2 / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDepetris, R.S.
CitationJournal: To Be Published
Title: Structure of KD035, a VEGFR2 monoclonal antibody
Authors: Depetris, R.S.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KD035 Fab heavy chain
B: KD035 Fab heavy chain
C: KD035 Fab light chain
D: KD035 Fab light chain


Theoretical massNumber of molelcules
Total (without water)91,4164
Polymers91,4164
Non-polymers00
Water2,504139
1
A: KD035 Fab heavy chain
C: KD035 Fab light chain


Theoretical massNumber of molelcules
Total (without water)45,7082
Polymers45,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-20 kcal/mol
Surface area19160 Å2
MethodPISA
2
B: KD035 Fab heavy chain
D: KD035 Fab light chain


Theoretical massNumber of molelcules
Total (without water)45,7082
Polymers45,7082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.164, 90.236, 81.529
Angle α, β, γ (deg.)90.000, 93.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody KD035 Fab heavy chain


Mass: 23132.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody KD035 Fab light chain


Mass: 22574.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2M Na Phosphate monobasic monohydrate,20% PEG3350

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Data collection

DiffractionMean temperature: 62 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.99→39.46 Å / Num. obs: 50743 / % possible obs: 96.5 % / Redundancy: 3.3 % / CC1/2: 0.9 / Net I/σ(I): 6.7
Reflection shellResolution: 1.99→2.06 Å / Num. unique obs: 4626 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N9G

3n9g


Resolution: 2.4→39.456 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 1155 3.91 %
Rwork0.1969 28408 -
obs0.2 29563 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.5 Å2 / Biso mean: 33.9262 Å2 / Biso min: 13.74 Å2
Refinement stepCycle: final / Resolution: 2.4→39.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 0 139 6415
Biso mean---34.08 -
Num. residues----842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016414
X-RAY DIFFRACTIONf_angle_d1.368745
X-RAY DIFFRACTIONf_chiral_restr0.05987
X-RAY DIFFRACTIONf_plane_restr0.0071121
X-RAY DIFFRACTIONf_dihedral_angle_d14.9882249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.50920.38931430.2626356699
2.5092-2.64150.341520.2481351998
2.6415-2.80690.33651410.2316345896
2.8069-3.02360.30831410.2195356699
3.0236-3.32770.3051460.2157358399
3.3277-3.80890.2881400.1882357799
3.8089-4.79750.21541430.1572354297
4.7975-39.4560.22561490.1817359798

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