8BP4 | pdb_00008bp4

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

PDB DOI: https://doi.org/10.2210/pdb8BP4/pdb

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

Deposited: 2022-11-16 Released: 2023-11-29
Deposition Author(s): Maddumage, 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: 1.15 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 32.85 kDa
Atom Count: 2,383
Modeled Residue Count: 286
Deposited Residue Count: 303
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat-containing protein 1	A, B, C	93	Trichoplax sp. H2	Mutation(s): 0 Gene Names: TrispH2_005790
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	D, E, F	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

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File 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 F] 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 F] 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 F]	I [auth A] J [auth A] K [auth A] L [auth B] M [auth B] I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions 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 F] Interactions & Density 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 F]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]