5DWS | pdb_00005dws

Crystal Structure of ITCH WW3 domain in complex with TXNIP peptide

PDB DOI: https://doi.org/10.2210/pdb5DWS/pdb
Entry: 5DWS supersedes: 4RRE

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-22 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: 1.65 Å
R-Value Free:
0.257 (Depositor), 0.262 (DCC)
R-Value Work:
0.222 (Depositor), 0.233 (DCC)
R-Value Observed:
0.224 (Depositor)

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 ITCH WW3 domain 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: 27.09 kDa
Atom Count: 1,689
Modeled Residue Count: 194
Deposited Residue Count: 244
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Itchy homolog	A, C, E, G	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
txnip	B, D, F, H	14	Homo sapiens	Mutation(s): 0
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

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 BA [auth G] SDF format, chain FA [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth G] SDF format, chain X [auth G] SDF format, chain W [auth G] SDF format, chain V [auth G] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth H] SDF format, chain GA [auth G] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain CA [auth G] SDF format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth G] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth G] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth G] CA [auth G] DA [auth G] EA [auth G] AA [auth G], BA [auth G], CA [auth G], DA [auth G], EA [auth G], FA [auth G], GA [auth G], HA [auth H], I [auth A], J [auth A], K [auth A], L [auth A], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth E], R [auth E], S [auth E], T [auth F], U [auth G], V [auth G], W [auth G], X [auth G], Y [auth G], Z [auth G]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.257 (Depositor), 0.262 (DCC)
R-Value Work: 0.222 (Depositor), 0.233 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.733	α = 90
b = 30.142	β = 109.2
c = 60.755	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Structural Genomics Consortium (SGC)

This entry supersedes: 4RRE

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, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary