8C1T | pdb_00008c1t

Crystal structure of Trichoplax Dlg PDZ1 domain in complex with Trichoplax Vangl peptide

• PDB DOI: https://doi.org/10.2210/pdb8C1T/pdb

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


• Deposited: 2022-12-21 Released: 2024-01-10 
• Deposition Author(s): Maddumage, J.C., Kvansakul, M.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Trichoplax Dlg PDZ1 domain in complex with Trichoplax Vangl peptide

Maddumage, J.C., Kvansakul, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.45 kDa 
• Atom Count: 3,037 
• Modeled Residue Count: 388 
• Deposited Residue Count: 408 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large-like protein 1	A [auth D], B [auth A], C [auth B], D [auth C]	94	Trichoplax sp. H2	Mutation(s): 0  Gene Names: TrispH2_000924

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vang-like protein 1	E, F, G, H	8	Trichoplax sp. H2	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA (Subject of Investigation/LOI)	I [auth B], J [auth B], K [auth C]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.696	α = 85.25
b = 47.953	β = 72.08
c = 50.83	γ = 69.17

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-10 
Deposition Author(s): Maddumage, J.C., Kvansakul, M.

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

Revision History  

• Version 1.0: 2024-01-10
  Type: Initial release