6S8L

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes

La Sala, G.Olieric, N.

(2019) Chem --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A
451Homo sapiensMutation(s): 0 
Gene Names: TUBA1B
Find proteins for P68363 (Homo sapiens)
Go to Gene View: TUBA1B
Go to UniProtKB:  P68363
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta-3 chain
B
450Homo sapiensMutation(s): 0 
Gene Names: TUBB3 (TUBB4)
Find proteins for Q13509 (Homo sapiens)
Go to Gene View: TUBB3
Go to UniProtKB:  Q13509
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Designed ankyrin repeat protein (DARPIN) D1
F
157N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
PN6
Query on PN6

Download SDF File 
Download CCD File 
B
(3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione
Plinabulin
C19 H20 N4 O2
UNRCMCRRFYFGFX-TYPNBTCFSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.630α = 90.00
b = 91.200β = 97.49
c = 82.640γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release