8BQ8 | pdb_00008bq8

Crystal structure of Trichoplax Dlg PDZ2 domain in complex with Trichoplax Vangl peptide

PDB DOI: https://doi.org/10.2210/pdb8BQ8/pdb

Classification: PROTEIN BINDING
Organism(s): Trichoplax sp. H2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-11-20 Released: 2023-11-29
Deposition Author(s): Madduamge, J.C., Kvansakul, M.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.272 (Depositor), 0.260 (DCC)
R-Value Work:
0.222 (Depositor), 0.230 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Trichoplax Dlg PDZ2 domain in complex with Trichoplax Vangl peptide

Madduamge, J.C., Kvansakul, M., Humbert, P.O.

To be published.

Macromolecule Content

Total Structure Weight: 32.27 kDa
Atom Count: 2,171
Modeled Residue Count: 288
Deposited Residue Count: 306
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large-like protein 1	A, B, C	94	Trichoplax sp. H2	Mutation(s): 0 Gene Names: TrispH2_000924
UniProt
Find proteins for A0ACD6BAH5 (Trichoplax sp. H2) Explore A0ACD6BAH5 Go to UniProtKB: A0ACD6BAH5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0ACD6BAH5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vang-like protein 1	D, E [auth F], F [auth E]	8	Trichoplax sp. H2	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAH3 (Trichoplax sp. H2) Explore A0ACD6BAH3 Go to UniProtKB: A0ACD6BAH3
Entity Groups
UniProt Group	A0ACD6BAH3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.272 (Depositor), 0.260 (DCC)
R-Value Work: 0.222 (Depositor), 0.230 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.673	α = 90
b = 101.98	β = 90
c = 106.063	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Madduamge, J.C.

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1103871
Australian Research Council (ARC)	Australia	FT130101349

Revision History (Full details and data files)

Version 1.0: 2023-11-29
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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.