6D3O | pdb_00006d3o

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

• PDB DOI: https://doi.org/10.2210/pdb6D3O/pdb

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


• Deposited: 2018-04-16 Released: 2019-04-24 
• 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: 3.10 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

High-Resolution Structures for a Complex Between a Non-Helical Foldamer and VEGF

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.8 kDa 
• Atom Count: 1,722 
• Modeled Residue Count: 219 
• Deposited Residue Count: 234 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	A	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
PHAROS:  P15692 GTEx:  ENSG00000112715

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	B	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
PHAROS:  P15692 GTEx:  ENSG00000112715

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HH4 alpha/beta-Peptide	C, D	15	synthetic construct	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.649	α = 90
b = 101.649	β = 90
c = 59.988	γ = 120

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: 2019-04-24 
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: 2019-04-24
  Type: Initial release
  
• Version 2.0: 2019-08-14
  Changes: Data collection, Database references, Polymer sequence
• Version 2.1: 2020-01-01
  Changes: Author supporting evidence
• Version 2.2: 2020-06-10
  Changes: Database references, Structure summary
• Version 3.0: 2021-02-24
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 4.0: 2023-02-22
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 4.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 5.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations