5T89

Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6

• PDB DOI: https://doi.org/10.2210/pdb5T89/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-09-07 Released: 2017-02-01 
• Deposition Author(s): Markovic-Mueller, S., Stuttfeld, E., Asthana, M., Weinert, T., Bliven, S., Goldie, K.N., Kisko, K., Capitani, G., Ballmer-Hofer, K.
• Funding Organization(s): Swiss National Science Foundation, Oncosuisse

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.315 
• R-Value Work: 0.285 
• R-Value Observed: 0.286 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 182.19 kDa 
• Atom Count: 11,357 
• Modelled Residue Count: 1,385 
• Deposited Residue Count: 1,554 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	A [auth V], B [auth W]	131	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 receptor 1	C [auth X], D [auth Y]	646	Homo sapiens	Mutation(s): 0  Gene Names: FLT1, FLT, FRT, VEGFR1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P17948 (Homo sapiens) Explore P17948  Go to UniProtKB:  P17948
PHAROS:  P17948 GTEx:  ENSG00000102755

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A], F [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth V], H [auth W], I [auth X], J [auth X], K [auth X], L [auth X], M [auth X], N [auth X], O [auth X], P [auth X], Q [auth Y], R [auth Y], S [auth Y], T [auth Y], U [auth Y], V [auth Y], W [auth Y], X [auth Y], Y	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.315 
• R-Value Work: 0.285 
• R-Value Observed: 0.286 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.71	α = 90
b = 123.09	β = 109.56
c = 167.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Markovic-Mueller, S., Stuttfeld, E., Asthana, M., Weinert, T., Bliven, S., Goldie, K.N., Kisko, K., Capitani, G., Ballmer-Hofer, K.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A-130463
Oncosuisse	Switzerland	OC2 01200-08-2007

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-02-15
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Advisory, Author supporting evidence, Data collection
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary