5VAX | pdb_00005vax

Bcl-2 complex with Beclin 1 BH3 domain

• PDB DOI: https://doi.org/10.2210/pdb5VAX/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-03-28 Released: 2018-04-04 
• Deposition Author(s): Lee, E.F., Smith, B.J., Yao, S., Fairlie, W.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Bcl-2 complex with Beclin 1 pT108 BH3 domain

Lee, E.F., Smith, B.J., Yao, S., Fairlie, W.D.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.88 kDa 
• Atom Count: 5,408 
• Modeled Residue Count: 651 
• Deposited Residue Count: 776 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-2 -- Bcl-2-like protein 1 Chimera	A, C [auth B], E [auth C], G [auth D]	168	Homo sapiens	Mutation(s): 0  Gene Names: BCL2, BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beclin-1	B [auth E], D [auth F], F [auth G], H	26	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14457 (Homo sapiens) Explore Q14457  Go to UniProtKB:  Q14457
PHAROS:  Q14457 GTEx:  ENSG00000126581

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B [auth E], D [auth F], F [auth G], H	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.474	α = 90
b = 87.174	β = 90
c = 126.631	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Lee, E.F., Smith, B.J., Yao, S., Fairlie, W.D.

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary