8ESF | pdb_00008esf

Crystal structure of human Nischarin PX and LRR domains with engineered mutations

PDB DOI: https://doi.org/10.2210/pdb8ESF/pdb

Classification: ENDOCYTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-10-13 Released: 2023-10-25
Deposition Author(s): Eldershaw, D.E., Collins, B.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.243 (Depositor), 0.241 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of human Nischarin PX and LRR domains with engineered mutations

Eldershaw, D.E., Collins, B.M.

To be published.

Macromolecule Content

Total Structure Weight: 112.86 kDa
Atom Count: 6,808
Modeled Residue Count: 847
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nischarin	A, B	502	Homo sapiens	Mutation(s): 1 Gene Names: NISCH, IRAS, KIAA0975
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2I1 (Homo sapiens) Explore Q9Y2I1 Go to UniProtKB: Q9Y2I1
PHAROS: Q9Y2I1 GTEx: ENSG00000010322
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2I1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD (Subject of Investigation/LOI) Query on IMD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.243 (Depositor), 0.241 (DCC)
R-Value Work: 0.215 (Depositor), 0.215 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.173	α = 90
b = 83.307	β = 94.36
c = 90.83	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Eldershaw, D.E.

Funding Organization	Location	Grant Number
Not funded	Australia	--

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.