4YK9 | pdb_00004yk9

Complex structure of BCL-XL and mutated BIM BH3 domain

• PDB DOI: https://doi.org/10.2210/pdb4YK9/pdb

• Classification: APOPTOSIS
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-04 Released: 2016-04-13 
• Deposition Author(s): Ha, N.C., Kim, J.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Complex structure of BCL-XL and mutated BIM BH3 domain

Ha, N.C., Kim, J.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.47 kDa 
• Atom Count: 2,824 
• Modeled Residue Count: 326 
• Deposited Residue Count: 432 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A, C [auth F]	195	Mus musculus	Mutation(s): 0  Gene Names: Bcl2l1, Bcl2l, Bclx
UniProt
Find proteins for Q64373 (Mus musculus) Explore Q64373  Go to UniProtKB:  Q64373

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BH3BIM	B, D [auth G]	21	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], H [auth A], I [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A], G [auth A], J [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AAR	B, D [auth G]	L-PEPTIDE LINKING	C6 H16 N5 O		ARG
SEP	B, D [auth G]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.738	α = 90
b = 81.738	β = 90
c = 42.568	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
Coot	model building
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Ha, N.C., Kim, J.S.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary