2X1X

CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 IN A TETRAGONAL CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.334
  • R-Value Work: 0.266

Literature

Macromolecules
Sequence Display for 2X1X

Classification: HORMONE / SIGNALING PROTEIN

Total Structure Weight: 38851.24

Macromolecule Entities
Molecule Chains Length Organism Details
VASCULAR ENDOTHELIAL GROWTH FACTOR C E 110 Homo sapiens Fragment: VEGF HOMOLOGY DOMAIN, RESIDUES 112-215
Mutation: C137A
Gene Name(s): VEGFC Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 R 213 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: IG-LIKE DOMAINS 2 AND 3, RESIDUES 120-326
Gene Name(s): KDR Gene View FLK1 VEGFR2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

E, R N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HG
Query on HG

R MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

E BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.334
  • R-Value Work: 0.266
  • Space Group: P 42 21 2

Unit Cell:

Length (Å) Angle (°)
a = 88.73 α = 90.00
b = 88.73 β = 90.00
c = 105.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-01-08
  • Released Date: 2010-02-09
  • Deposition author(s): Leppanen, V.-M., Prota, A.E., Jeltsch, M., Anisimov, A., Kalkkinen, N., Strandin, T., Lankinen, H., Goldman, A., Ballmer-Hofer, K., Alitalo, K.

Revision History

  • 2011-08-10
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • 2017-07-12
    Type: Advisory, Derived calculations