3UGD

Structural and functional characterization of an anesthetic binding site in the second cysteine-rich domain of protein kinase C delta

Structural Biology Knowledgebase: 3UGD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3UGD

Classification: METAL BINDING PROTEIN

Total Structure Weight: 15658.60

Macromolecule Entities
Molecule Chains Length Organism Details
Protein kinase C delta type A, B 65 Mus musculus EC#: 2.7.11.13 IUBMB
Fragment: C1B Subdomain of PKC delta, UNP residues 231-280
Mutation: Y236H
Gene Name(s): Prkcd Pkcd

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.173
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.95 α = 90.00
b = 32.50 β = 94.21
c = 49.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-11-02
  • Released Date: 2012-12-12
  • Deposition author(s): Shanmugasundararaj, S., Stehle, T., Miller, K.W.

Revision History

  • 2013-08-28
    Type: Citation | Details: Citation update