3WIM | pdb_00003wim

GABARAP-LIR peptide complex

PDB DOI: https://doi.org/10.2210/pdb3WIM/pdb

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

Deposited: 2013-09-19 Released: 2014-03-12
Deposition Author(s): Lystad, A., Ichimura, Y., Takagi, K., Yang, Y., Pankiv, S., Mizushima, T., Komatsu, M., Simonsen, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.296 (Depositor), 0.291 (DCC)
R-Value Work:
0.210 (Depositor), 0.206 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

GABARAP-LIR peptide complex

Lystad, A., Ichimura, Y., Takagi, K., Yang, Y., Pankiv, S., Mizushima, T., Komatsu, M., Simonsen, A.

To be published.

Macromolecule Content

Total Structure Weight: 15.56 kDa
Atom Count: 1,099
Modeled Residue Count: 129
Deposited Residue Count: 131
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor-associated protein	A	117	Homo sapiens	Mutation(s): 0 Gene Names: GABARAP, FLC3B, HT004
UniProt & NIH Common Fund Data Resources
Find proteins for O95166 (Homo sapiens) Explore O95166 Go to UniProtKB: O95166
PHAROS: O95166 GTEx: ENSG00000170296
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95166
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat and FYVE domain-containing protein 3	B	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZQ1 (Homo sapiens) Explore Q8IZQ1 Go to UniProtKB: Q8IZQ1
PHAROS: Q8IZQ1 GTEx: ENSG00000163625
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IZQ1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.296 (Depositor), 0.291 (DCC)
R-Value Work: 0.210 (Depositor), 0.206 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.491	α = 90
b = 53.491	β = 90
c = 83.193	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-12
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.