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), 0.251 (DCC)
R-Value Work:
0.201 (Depositor), 0.203 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q8WWN8 Q9WV48
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), 0.251 (DCC)
R-Value Work: 0.201 (Depositor), 0.203 (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

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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

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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.