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 
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 
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1 | 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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Groups | P0AEX9Q07820 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
OJW (Subject of Investigation/LOI) Query on OJW | 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 Query on CL | C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900001 Query on 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 Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2020-11-18  Deposition Author(s): Dokurno, P., Surgenor, A.E., Murray, J.B.
Revision History (Full details and data files)
- 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