8ZEB | pdb_00008zeb

Crystal structure of BCL-XL bound by cp-B6X-4

• PDB DOI: https://doi.org/10.2210/pdb8ZEB/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, Phage 203
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-05 Released: 2025-01-29 
• Deposition Author(s): Sun, X.N., Liu, J.X., Wu, D.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Biphenyl-Dihydrothiazole-Cyclized Peptide Libraries for Peptide Lig-and and Drug Discovery

Liu, J.J., Sun, X.N., Zhuang, J., Liu, Z.Y., Xu, C.Y., Wu, D.L., Wu, C.L.

(2025) Sci China B Chem 

• DOI: https://doi.org/10.1007/s11426-024-2291-x

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: surface plasmon resonance

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)

Macromolecule Content 

• Total Structure Weight: 35.95 kDa 
• Atom Count: 2,661 
• Modeled Residue Count: 308 
• Deposited Residue Count: 312 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A, B	141	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THR-PRO-GLU-TRP-ALA-SER-THR-LEU-ARG-PRO-GLU-(CCS)-(EDN)-(Z7Z)-(PRS)	C [auth D], D [auth C]	15	Phage 203	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCS	C [auth D], D [auth C]	L-PEPTIDE LINKING	C5 H9 N O4 S		CYS
PRS	C [auth D], D [auth C]	L-PEPTIDE LINKING	C4 H7 N O2 S		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.022	α = 90
b = 97.605	β = 90
c = 93.149	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Sun, X.N., Liu, J.X., Wu, D.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31800664

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release