6BFT | pdb_00006bft

Structure of Bevacizumab Fab mutant in complex with VEGF

• PDB DOI: https://doi.org/10.2210/pdb6BFT/pdb

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


• Deposited: 2017-10-27 Released: 2018-10-31 
• Deposition Author(s): Christie, M., Christ, D.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Stable human IgG antibody therapeutics with native framework structure

Christie, M., Rouet, R., Nevoltris, D., Langley, D., Schofield, P., Fabri, L., Tingey, K., Lowe, D., Jermutus, L., Christ, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 121.34 kDa 
• Atom Count: 8,359 
• Modeled Residue Count: 1,057 
• Deposited Residue Count: 1,094 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avastin Light Chain Fab fragment mutant	A [auth B], C [auth L]	214	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q8TCD0 (Homo sapiens) Explore Q8TCD0  Go to UniProtKB:  Q8TCD0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Avastin Heavy Chain Fab fragment mutant	B [auth A], D [auth H]	231	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	E [auth G], F [auth C]	102	Homo sapiens	Mutation(s): 0  Gene Names: VEGFA, VEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692  Go to UniProtKB:  P15692
GTEx:  ENSG00000112715

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	I [auth H], J [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	G [auth B], H [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
CSO	E [auth G], F [auth C]	CYS	Hydroxylation	C3 H7 N O3 S

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.279	α = 90
b = 88.749	β = 111.87
c = 106.676	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Christie, M., Christ, D.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DE160100608
Australian Research Council (ARC)	Australia	DP160104915

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary