8BV7 | pdb_00008bv7

Crystal structure of the Trichoplax Scribble PDZ1 domain in complex with the Trichoplax phosphorylated Vangl peptide

PDB DOI: https://doi.org/10.2210/pdb8BV7/pdb

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

Deposited: 2022-12-02 Released: 2023-12-13
Deposition Author(s): Maddumage, J.C., Kvansakul, M.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.217 (Depositor), 0.217 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BV7

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

Literature

Crystal structure of Trichoplax Scribble PDZ1 domain in complex with Trichoplax the phosphorylated Vangl peptide

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

To be published.

Macromolecule Content

Total Structure Weight: 10.94 kDa
Atom Count: 812
Modeled Residue Count: 103
Deposited Residue Count: 104
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat-containing protein 1	A	96	Trichoplax sp. H2	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAH4 (Trichoplax sp. H2) Explore A0ACD6BAH4 Go to UniProtKB: A0ACD6BAH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BAH4
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	B	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

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.217 (Depositor), 0.217 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.092	α = 90
b = 45.236	β = 90
c = 70.87	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Maddumage, J.C.

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

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 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.