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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.226 (Depositor), 0.227 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8ZEB

This is version 1.0 of the entry. See complete history.

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

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07817
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Query on CCS	C [auth D], D [auth C]	L-PEPTIDE LINKING	C₅ H₉ N O₄ S		CYS
PRS Query on 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), 0.227 (DCC)
R-Value Work: 0.181 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.