6S8L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chain A451Homo sapiensMutation(s): 0 
Gene Names: TUBA1B
Find proteins for P68363 (Homo sapiens)
Explore P68363 
Go to UniProtKB:  P68363
NIH Common Fund Data Resources
PHAROS:  P68363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-3 chain B450Homo sapiensMutation(s): 0 
Gene Names: TUBB3TUBB4
Find proteins for Q13509 (Homo sapiens)
Explore Q13509 
Go to UniProtKB:  Q13509
NIH Common Fund Data Resources
PHAROS:  Q13509
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Designed ankyrin repeat protein (DARPIN) D1 F157synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

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

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

Download Ideal Coordinates CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PN6IC50:  1800   nM  BindingDB
PN6Kd:  1000   nM  BindingDB
PN6Kd:  1060   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.63α = 90
b = 91.2β = 97.49
c = 82.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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