6YBJ

Structure of MBP-Mcl-1 in complex with compound 3e

• PDB DOI: https://doi.org/10.2210/pdb6YBJ/pdb

• Classification: APOPTOSIS
• Organism(s): Escherichia coli O157:H7, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2020-03-17 Released: 2020-11-18 
• Deposition Author(s): Dokurno, P., Surgenor, A.E., Murray, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.36 kDa 
• Atom Count: 4,299 
• Modelled Residue Count: 514 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1	A	518	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 6  Gene Names: malE, Z5632, ECs5017, MCL1, BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q07820 (Homo sapiens) Explore Q07820  Go to UniProtKB:  Q07820
PHAROS:  Q07820 GTEx:  ENSG00000143384
UniProt Groups	P0AEX9Q07820

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OJW (Subject of Investigation/LOI)	D [auth A]	(2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(5-fluoranylfuran-2-yl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-[2-[(2-methylpyrazol-3-yl)methoxy]phenyl]propanoic acid C38 H38 Cl F N6 O6 S AQVKIYGPKKZICS-SSEXGKCCSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
OJW	Binding MOAD:  6YBJ	Ki: 0.86 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.93	α = 90
b = 136.71	β = 90
c = 38.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Dokurno, P., Surgenor, A.E., Murray, J.B.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description