7A9B | pdb_00007a9b

Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide

PDB DOI: https://doi.org/10.2210/pdb7A9B/pdb

Classification: PROTEIN BINDING
Organism(s): Rattus norvegicus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-01 Released: 2020-10-21
Deposition Author(s): Mariam McAuley, M., Ali, M., Ivarsson, Y., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (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 Shank1 PDZ domain with ARAP3-derived peptide

Mariam McAuley, M., Ali, M., Ivarsson, Y., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 30.18 kDa
Atom Count: 1,992
Modeled Residue Count: 253
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SH3 and multiple ankyrin repeat domains protein 1,Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3	A, B	140	Rattus norvegicus, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: Shank1, ARAP3, CENTD3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWN8 (Homo sapiens) Explore Q8WWN8 Go to UniProtKB: Q8WWN8
PHAROS: Q8WWN8 GTEx: ENSG00000120318
Find proteins for Q9WV48 (Rattus norvegicus) Explore Q9WV48 Go to UniProtKB: Q9WV48
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q8WWN8Q9WV48
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.201 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.799	α = 90
b = 67.799	β = 90
c = 248.967	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-21

Deposition Author(s):

Mariam McAuley, M.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission		675341

Revision History (Full details and data files)

Version 1.0: 2020-10-21
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description

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.