4GNG

Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide

Structural Biology Knowledgebase: 4GNG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.182

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GNG

Classification: TRANSFERASE / NUCLEAR PROTEIN

Total Structure Weight: 28132.70

Macromolecule Entities
Molecule Chains Length Organism Details
Histone-lysine N-methyltransferase NSD3 A, D 107 Homo sapiens EC#: 2.1.1.43 IUBMB
Fragment: UNP RESIDUES 1310-1413
Gene Name(s): WHSC1L1 Gene View NSD3 DC28
Histone H3.3 B, F 15 Homo sapiens Fragment: UNP RESIDUES 2-16
Gene Name(s): H3F3A Gene View H3.3A H3F3 PP781 H3F3B Gene View H3.3B

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

A, B GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
M3L
Query on M3L
B, F L-PEPTIDE LINKING C9 H21 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.182
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.20 α = 90.00
b = 59.96 β = 90.00
c = 95.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-17
  • Released Date: 2013-01-02
  • Deposition author(s): Li, F., He, C., Wu, J., Shi, Y.

Revision History

  • 2013-09-04
    Type: Citation | Details: Citation update