6NID | pdb_00006nid

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 (Depositor), 0.240 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (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

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
Modeled Residue Count: 277
Deposited Residue Count: 294
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(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] mmCIF 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 (Depositor), 0.240 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

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

View Full Validation Report

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 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.