4KZN | pdb_00004kzn

crystal structure of human VEGF-A receptor binding domain

• PDB DOI: https://doi.org/10.2210/pdb4KZN/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2014-06-04 
• Deposition Author(s): Liaw, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for the Bivalent Glycosylated Human VEGF-A121 and VEGF-A165 in recruiment of Receptor and Co-receptor

Shen, S.T., Huang, P.T., Shuau, Y.S., Lee, Y.M., Chen, Y.J., Liaw, Y.C., Lou, K.L.

To be published.

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: 13.59 kDa 
• Atom Count: 927 
• Modeled Residue Count: 95 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	A	104	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
PHAROS:  P15692 GTEx:  ENSG00000112715
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P15692-13

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.573	α = 90
b = 32.014	β = 92.99
c = 42.981	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Liaw, Y.C.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary