4WMV

STRUCTURE OF MBP-MCL1 BOUND TO ligand 4 AT 2.4A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1.

Clifton, M.C.Dranow, D.M.Leed, A.Fulroth, B.Fairman, J.W.Abendroth, J.Atkins, K.A.Wallace, E.Fan, D.Xu, G.Ni, Z.J.Daniels, D.Van Drie, J.Wei, G.Burgin, A.B.Golub, T.R.Hubbard, B.K.Serrano-Wu, M.H.

(2015) Plos One 10: e0125010-e0125010

  • DOI: 10.1371/journal.pone.0125010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advan ...

    Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.


    Organizational Affiliation

    Beryllium, Bedford, Massachusetts, United States of America.,Van Drie Research, North Andover, Massachusetts, United States of America.,The Broad Institute, Cambridge, Massachusetts, United States of America.,Acme Bioscience, Palo Alto, California, United States of America.,The Broad Institute, Cambridge, Massachusetts, United States of America; Dana-Farber Cancer Institute and Howard Hughes Medical Institute, Boston, Massachusetts, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MBL-MCL1 chimera protein
A
518Homo sapiensEscherichia coli (strain K12)
This entity is chimeric
Mutation(s): 3 
Gene Names: MCL1 (BCL2L3), malE
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3R4
Query on 3R4

Download SDF File 
Download CCD File 
A
3-chloro-6-fluoro-1-benzothiophene-2-carboxylic acid
C9 H4 Cl F O2 S
HSRSWUJIPYUCSE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3R4IC50: 93000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.890α = 90.00
b = 136.070β = 90.00
c = 37.820γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release