5K64

Crystal structure of VEGF binding IgG1-Fc (Fcab 448)

• PDB DOI: https://doi.org/10.2210/pdb5K64/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-05-24 Released: 2017-09-06 
• Deposition Author(s): Humm, A., Lobner, E., Kitzmuller, M., Mlynek, G., Obinger, C., Djinovic-Carugo, K.
• Funding Organization(s): Christian Doppler Research Association, Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.249 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 53.94 kDa 
• Atom Count: 3,633 
• Modelled Residue Count: 426 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, B	228	Homo sapiens	Mutation(s): 13  Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857  Go to UniProtKB:  P01857
PHAROS:  P01857 GTEx:  ENSG00000211896

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G64481DJ GlyCosmos:  G64481DJ GlyGen:  G64481DJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	E [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.249 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.72	α = 90
b = 38.86	β = 94.23
c = 97.2	γ = 90

Software Package:

Software Name	Purpose
EDNA	data collection
XDS	data scaling
XDS	data reduction
PHENIX	phasing
PHENIX	refinement
BUSTER	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Humm, A., Lobner, E., Kitzmuller, M., Mlynek, G., Obinger, C., Djinovic-Carugo, K.

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Funding Organization	Location	Grant Number
Christian Doppler Research Association	Austria	Christian Doppler Laboratory for Antibody Engineering
Austrian Science Fund	Austria	FWF W1224 (Doctoral Program on Biomolecular Technology of Proteins, BioTop)

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Database references
• Version 1.2: 2017-10-11
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary