5V83

Structure of DCN1 bound to NAcM-HIT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 5V83

Classification: LIGASE

Total Structure Weight: 44684.75

Macromolecule Entities
Molecule Chains Length Organism Details
Lysozyme,DCN1-like protein 1 chimera A 384 Homo sapiens Escherichia virus t4 EC#: 3.2.1.17 IUBMB
Mutation: C54T, C97A, A146T
Gene Name(s): E DCUN1D1 Gene View DCUN1L1 RP42 SCCRO
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
8Z7
Query on 8Z7

A N-(1-benzylpiperidin-4-yl)-N'-[3-(trifluoromethyl)phenyl]urea
C20 H22 F3 N3 O
MXZRHPHRSQJCML-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.171
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 34.97 α = 90.00
b = 97.28 β = 104.39
c = 58.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-21
  • Released Date: 2017-05-24
  • Deposition author(s): Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

Revision History

  • Version 1_0: 2017-05-24

    Type: Initial release

  • Version 1_1: 2017-06-21

    Type: Database references, Refinement description

  • Version 1_2: 2017-09-06

    Type: Database references

  • Version 1_3: 2017-09-20

    Type: Author supporting evidence