9YDF | pdb_00009ydf

Structure of the cyclic nucleotide binding domain of SLC9C1

PDB DOI: https://doi.org/10.2210/pdb9YDF/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-22 Released: 2025-11-12
Deposition Author(s): Lyu, C., Dong, A., Chandrasekaran, R., Mamai, A., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Tredup, C., Harding, R.J., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.237 (Depositor), 0.251 (DCC)
R-Value Work:
0.203 (Depositor), 0.212 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Structure of the cyclic nucleotide binding domain of SLC9C1

Lyu, C., Dong, A., Chandrasekaran, R., Mamai, A., Arrowsmith, C.H., Edwards, A.M., Burgess-Brown, N., Tredup, C., Harding, R.J., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 20.11 kDa
Atom Count: 1,043
Modeled Residue Count: 131
Deposited Residue Count: 173
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 9 member C1	A	173	Homo sapiens	Mutation(s): 0 Gene Names: SLC9C1, SLC9A10
UniProt & NIH Common Fund Data Resources
Find proteins for Q4G0N8 (Homo sapiens) Explore Q4G0N8 Go to UniProtKB: Q4G0N8
PHAROS: Q4G0N8 GTEx: ENSG00000172139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4G0N8
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 A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.237 (Depositor), 0.251 (DCC)
R-Value Work: 0.203 (Depositor), 0.212 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.788	α = 90
b = 45.788	β = 90
c = 276.932	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-12

Deposition Author(s):

Chandrasekaran, R.

Arrowsmith, C.H.

Burgess-Brown, N.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History (Full details and data files)

Version 1.0: 2025-11-12
Type: Initial release

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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.