5VC8

Crystal structure of the WHSC1 PWWP1 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 5VC8

Classification: DNA BINDING PROTEIN

Total Structure Weight: 44130.07


Macromolecule Entities
Molecule Chains Length Organism Details
Histone-lysine N-methyltransferase NSD2 A, B 141 Homo sapiens EC#: 2.1.1.43 IUBMB
Gene Name(s): WHSC1 KIAA1090 MMSET NSD2 Gene View TRX5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
dodeca-2-deoxy-nucleotide, poorly resolved by electron density W, X, Y 12 Synthetic construct
DNA (5'-D(P*CP*TP*(DN))-3') Z 3 Synthetic construct Interpretation of weak electron density in terms of an unidentified fragment of the dodecadeoxynucleotide.

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UNX
Query on UNX

A, B UNKNOWN ATOM OR ION
X
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET
DN
Query on DN
Z DNA LINKING C5 H11 O6 P --

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 82.99 α = 90.00
b = 82.99 β = 90.00
c = 115.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-31
  • Released Date: 2017-06-28
  • Deposition author(s): Qin, S., Tempel, W., Dong, A., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History

  • Version 1_0: 2017-06-28

    Type: Initial release