5DZD

Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide

PDB DOI: https://doi.org/10.2210/pdb5DZD/pdb
Entry: 5DZD supersedes: 4ROI

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

Deposited: 2015-09-25 Released: 2015-10-14
Deposition Author(s): Liu, Y., Tempel, W., Dong, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.206
R-Value Work: 0.175
R-Value Observed: 0.176

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide

Liu, Y., Tempel, W., Dong, A., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J.

To be published.

Macromolecule Content

Total Structure Weight: 13.73 kDa
Atom Count: 897
Modelled Residue Count: 101
Deposited Residue Count: 122
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H3M7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth C], S [auth C], T [auth C], U [auth D]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.206
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.668	α = 90
b = 52.668	β = 90
c = 82.476	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 4ROI

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary