9P3E | pdb_00009p3e

LC3B bound to BLM peptide

PDB DOI: https://doi.org/10.2210/pdb9P3E/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-06-13 Released: 2026-06-24
Deposition Author(s): Kosmatka, J., Lim, D., Keating, A., Davis, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.263 (Depositor), 0.264 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9P3E

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

Literature

A proteome-wide screen defines binding determinants of the core autophagy protein LC3B

Kosmatka, J., Halpin, J., Liu, C., Lim, D.C., Davis, J., Keating, A.

To be published.

Macromolecule Content

Total Structure Weight: 17.12 kDa
Atom Count: 1,183
Modeled Residue Count: 135
Deposited Residue Count: 145
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RecQ-like DNA helicase BLM,Microtubule-associated protein 1 light chain 3 beta	A	145	Homo sapiens	Mutation(s): 0 Gene Names: BLM, RECQ2, RECQL3, MAP1LC3B, MAP1ALC3 EC: 5.6.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for P54132 (Homo sapiens) Explore P54132 Go to UniProtKB: P54132
PHAROS: P54132 GTEx: ENSG00000197299
Find proteins for Q9GZQ8 (Homo sapiens) Explore Q9GZQ8 Go to UniProtKB: Q9GZQ8
PHAROS: Q9GZQ8 GTEx: ENSG00000140941
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9GZQ8 P54132
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.263 (Depositor), 0.264 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.09	α = 90
b = 46.74	β = 102.2
c = 45.48	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM149227

Revision History (Full details and data files)

Version 1.0: 2026-06-24
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.