6V7K | pdb_00006v7k

Crystal Structure of Vascular Endothelial Growth Factor (VEGF8-109) with one copy of HH4, an alpha/beta-Peptide with Irregular Secondary Structure

• PDB DOI: https://doi.org/10.2210/pdb6V7K/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-08 Released: 2020-12-09 
• Deposition Author(s): Thomas, N.C., Forest, K.T., Gellman, S.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.278 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

High-Resolution Structure for a Complex Between One Copy of a Non-Helical Foldamer and VEGF

Thomas, N.C., Forest, K.T., Gellman, S.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.63 kDa 
• Atom Count: 1,570 
• Modeled Residue Count: 205 
• Deposited Residue Count: 225 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	A, B	103	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha/beta-Peptide HH4	C [auth X]	19	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3E	C [auth X]	L-PEPTIDE LINKING	C6 H11 N O4		GLU
HT7	C [auth X]	L-PEPTIDE LINKING	C12 H14 N2 O2		TRP
NLE	C [auth X]	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.278 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.38	α = 90
b = 77.557	β = 90
c = 85.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Thomas, N.C., Forest, K.T., Gellman, S.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM056414

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Author supporting evidence, Database references
• Version 2.0: 2023-02-22
  Changes: Advisory, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations