7Y8D

Crystal structure of cp1 bound BCLxl

PDB DOI: https://doi.org/10.2210/pdb7Y8D/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens, synthetic construct
Expression System: ecological metagenomes
Mutation(s): No

Deposited: 2022-06-23 Released: 2023-11-15
Deposition Author(s): Li, F.W., Liu, C., Wu, C.L., Wu, D.L.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.243
R-Value Work: 0.188
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

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

Literature

Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-xL by engaging a single-residue discrepancy

Li, F.W., Liu, Z.Y., Liu, C., Liu, J.J., Wu, C.L., Wu, D.L.

To be published.

Macromolecule Content

Total Structure Weight: 18.09 kDa
Atom Count: 1,323
Modelled Residue Count: 152
Deposited Residue Count: 153
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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
cp1 peptide	B	12	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JFF Query on JFF Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	(2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamoyl]phenyl]prop-1-enyl]sulfanyl-2-(carboxyamino)propanoic acid C₁₉ H₂₆ Cl N₅ O₆ S SHRIZMDECXYRNC-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.243
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.803	α = 90
b = 99.366	β = 90
c = 51.359	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2023-11-15
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.