7LSB | pdb_00007lsb

Structure of B1, a monoclonal VEGFR2 antibody parental of KD035

• PDB DOI: https://doi.org/10.2210/pdb7LSB/pdb

• Classification: ANTITUMOR PROTEIN,IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-02-18 Released: 2021-02-24 
• Deposition Author(s): Depetris, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure of B1, a monoclonal VEGFR2 parental of KD035

Depetris, R.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 45.86 kDa 
• Atom Count: 3,173 
• Modeled Residue Count: 424 
• Deposited Residue Count: 430 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B1 Fab heavy chain	A [auth B]	218	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
B1 Fab light chain	B [auth D]	212	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.691	α = 90
b = 66.416	β = 101.93
c = 66.543	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Depetris, R.S.

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary