5B1Z | pdb_00005b1z

Crystal structure of Bcl-xL in complex with HBx-BH3 motif

PDB DOI: https://doi.org/10.2210/pdb5B1Z/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens, Hepatitis B virus
Expression System: Escherichia coli BL21(DE3), Peptide display vector fth1
Mutation(s): No

Deposited: 2015-12-22 Released: 2016-12-28
Deposition Author(s): Yuan, Y.A.
Funding Organization(s): Ministry of Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.274 (Depositor), 0.277 (DCC)
R-Value Work:
0.205 (Depositor), 0.212 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5B1Z

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Bcl-xL in complex with HBx-BH3 motif

Yuan, Y.A.

To be published.

Macromolecule Content

Total Structure Weight: 40.53 kDa
Atom Count: 2,765
Modeled Residue Count: 322
Deposited Residue Count: 352
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A, B	153	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
Peptide from Protein X	C, D	23	Hepatitis B virus	Mutation(s): 0
UniProt
Find proteins for I3XMW8 (Hepatitis B virus) Explore I3XMW8 Go to UniProtKB: I3XMW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3XMW8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.274 (Depositor), 0.277 (DCC)
R-Value Work: 0.205 (Depositor), 0.212 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.708	α = 90
b = 135.317	β = 90
c = 97.593	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology	China	--

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2017-10-04
Changes: Data collection
Version 1.2: 2024-03-20
Changes: Data collection, Database references

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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.