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), 0.290 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 129
Deposited Residue Count: 131
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95166
Sequence Annotations Expand
Reference Sequence LOADING

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IZQ1
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.296 (Depositor), 0.290 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (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

View Full Validation Report

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

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.