6NID

Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide

PDB DOI: https://doi.org/10.2210/pdb6NID/pdb

Classification: protein binding/peptide
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-27 Released: 2020-01-01
Deposition Author(s): Sun, Y.J., Gakhar, L., Fuentes, E.J.
Funding Organization(s): American Heart Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.240
R-Value Work: 0.192
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

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

Literature

CASK PDZ domain specificity

Sun, Y.J., Hou, T., Fuentes, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 34.37 kDa
Atom Count: 2,472
Modelled Residue Count: 277
Deposited Residue Count: 294
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peripheral plasma membrane protein CASK	A, B, C	88	Homo sapiens	Mutation(s): 0 Gene Names: CASK, LIN2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14936 (Homo sapiens) Explore O14936 Go to UniProtKB: O14936
PHAROS: O14936 GTEx: ENSG00000147044
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14936
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurexin-1	D, E, F	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULB1 (Homo sapiens) Explore Q9ULB1 Go to UniProtKB: Q9ULB1
PHAROS: Q9ULB1 GTEx: ENSG00000179915
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ULB1
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 G [auth B] MOL2 format, chain G [auth B]	G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.240
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.328	α = 90
b = 51.177	β = 97.72
c = 72.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
pointless	data scaling
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-01-01

Deposition Author(s):

Funding Organization	Location	Grant Number
American Heart Association	United States	15GRNT25740021

Revision History (Full details and data files)

Version 1.0: 2020-01-01
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.