4B8M | pdb_00004b8m

Aurora B kinase in complex with VX-680

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.236 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Structural and Biochemical Analysis of an Aurora B Kinase Mutant Reveals a Multistep Activation Mechanism

Sessa, F., Villa, F.

To be published.

Macromolecule Content 

  • Total Structure Weight: 78.52 kDa 
  • Atom Count: 5,407 
  • Modeled Residue Count: 635 
  • Deposited Residue Count: 660 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AURORA KINASE B-A
A, B
286Xenopus laevisMutation(s): 0 
EC: 2.7.11.1
UniProt
Find proteins for Q6DE08 (Xenopus laevis)
Explore Q6DE08 
Go to UniProtKB:  Q6DE08
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DE08
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
INNER CENTROMERE PROTEIN A
C, D
44Xenopus laevisMutation(s): 0 
UniProt
Find proteins for O13024 (Xenopus laevis)
Explore O13024 
Go to UniProtKB:  O13024
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13024
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VX6

Query on VX6


Download:Ideal Coordinates CCD File
E [auth A],
F [auth B]		CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE
C23 H28 N8 O S
GCIKSSRWRFVXBI-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.236 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.787α = 90
b = 67.259β = 96.58
c = 116.755γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary