6S8K | pdb_00006s8k

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

• PDB DOI: https://doi.org/10.2210/pdb6S8K/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Bos taurus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-10 Released: 2019-11-27 
• Deposition Author(s): Sharma, A., Olieric, N., Steinmetz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

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

La Sala, G., Olieric, N., Sharma, A.

(2019) Chem 5

• DOI: https://doi.org/10.1016/j.chempr.2019.08.022

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 116.43 kDa 
• Atom Count: 9,012 
• Modeled Residue Count: 1,017 
• Deposited Residue Count: 1,037 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A	437	Bos taurus	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947  Go to UniProtKB:  P81947

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856  Go to UniProtKB:  Q6B856

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed ankyrin repeat protein (DARPIN) D1	C [auth F]	155	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	D [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	G [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PN6 (Subject of Investigation/LOI)	F [auth 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
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.565	α = 90
b = 91.351	β = 96.851
c = 83.221	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-27 
Deposition Author(s): Sharma, A., Olieric, N., Steinmetz, M.

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references, Derived calculations