5N38

S65DParkin and pUB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 5N38

Classification: LIGASE

Total Structure Weight: 54933.73

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkin A 405 Homo sapiens EC#: 6.3.2 IUBMB
Mutation: S65D, Q347C
Gene Name(s): PARK2 PRKN Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Polyubiquitin-B B 76 Homo sapiens Details: Ser65 is phosphorylated
Gene Name(s): UBB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
SEP
Query on SEP
B L-PEPTIDE LINKING C3 H8 N O6 P SER
3CN
Query on 3CN
B NON-POLYMER C3 H9 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.186
  • Space Group: P 63 2 2

Unit Cell:

Length (Å) Angle (°)
a = 146.54 α = 90.00
b = 146.54 β = 90.00
c = 88.44 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-02-08
  • Released Date: 2017-04-19
  • Deposition author(s): Kumar, A., Chaugule, V.K., Johnson, C., Toth, R., Sundaramoorthy, R., Knebel, A., Walden, H.

Revision History

  • Version 1_0: 2017-04-19

    Type: Initial release

  • Version 1_1: 2017-04-26

    Type: Database references

  • Version 1_2: 2017-05-17

    Type: Database references

  • Version 1_3: 2017-09-13

    Type: Author supporting evidence