6QYL

Structure of MBP-Mcl-1 in complex with compound 8a

• PDB DOI: https://doi.org/10.2210/pdb6QYL/pdb

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


• Deposited: 2019-03-09 Released: 2019-08-07 
• Deposition Author(s): Dokurno, P., Szlavik, Z., Ondi, L., Csekei, M., Paczal, A., Szabo, Z.B., Radics, G., Murray, J., Davidson, J., Chen, I., Davis, B., Hubbard, R.E., Pedder, C., Surgenor, A.E., Smith, J., Robertson, A., LeToumelin-Braizat, G., Cauquil, N., Zarka, M., Demarles, D., Perron-Sierra, F., Geneste, O., Kotschy, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

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: 58.03 kDa 
• Atom Count: 4,293 
• Modelled Residue Count: 513 
• 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, 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
JLE (Subject of Investigation/LOI)	C [auth A]	(2~{R})-2-[[6-ethyl-5-(1~{H}-indol-4-yl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoic acid C25 H22 N4 O2 S IZDAFHXFYWJQKU-LJQANCHMSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.12	α = 90
b = 136.26	β = 90
c = 37.85	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Dokurno, P., Szlavik, Z., Ondi, L., Csekei, M., Paczal, A., Szabo, Z.B., Radics, G., Murray, J., Davidson, J., Chen, I., Davis, B., Hubbard, R.E., Pedder, C., Surgenor, A.E., Smith, J., Robertson, A., LeToumelin-Braizat, G., Cauquil, N., Zarka, M., Demarles, D., Perron-Sierra, F., Geneste, O., Kotschy, A.

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Database references
• Version 1.2: 2019-09-18
  Changes: Data collection, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary