4ROF | pdb_00004rof

Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide

PDB DOI: https://doi.org/10.2210/pdb4ROF/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-10-28 Released: 2014-12-10
Deposition Author(s): Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.297 (Depositor), 0.276 (DCC)
R-Value Work:
0.239 (Depositor)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4ROF

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide

Liu, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 13.54 kDa
Atom Count: 768
Modeled Residue Count: 94
Deposited Residue Count: 122
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Itchy homolog	A, B	47	Homo sapiens	Mutation(s): 0 Gene Names: ITCH EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96J02 (Homo sapiens) Explore Q96J02 Go to UniProtKB: Q96J02
PHAROS: Q96J02 GTEx: ENSG00000078747
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96J02
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-interacting protein	C, D	14	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3M7 (Homo sapiens) Explore Q9H3M7 Go to UniProtKB: Q9H3M7
PHAROS: Q9H3M7 GTEx: ENSG00000265972
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H3M7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.297 (Depositor), 0.276 (DCC)
R-Value Work: 0.239 (Depositor)
R-Value Observed: 0.246 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.171	α = 90
b = 55.312	β = 90
c = 59.796	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-12-10

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-12-10
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

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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.