4WMW

The structure of MBP-MCL1 bound to ligand 5 at 1.9A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 

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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MBP-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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

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A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
FMT
Query on FMT

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Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3R6
Query on 3R6

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Download CCD File 
A
2-hydroxy-5-(methylsulfanyl)benzoic acid
C8 H8 O3 S
DATDARDTUZHWMK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3R6IC50: 160000 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.940α = 90.00
b = 136.300β = 90.00
c = 37.800γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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