9UC2 | pdb_00009uc2

Crystal structure of voltage-gated sodium channel NavAb N49K/S178A mutant

PDB DOI: https://doi.org/10.2210/pdb9UC2/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Aliarcobacter butzleri
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-03 Released: 2026-02-18
Deposition Author(s): Irie, K., Maeda, Y., Kojima, K.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.294 (Depositor), 0.294 (DCC)
R-Value Work:
0.256 (Depositor), 0.260 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure-function analysis of lithium-ion selectivity of voltage-gated sodium channel

Maeda, Y., Kojima, K., Nakamura, T., Nakatsu, T., Irie, K.

(2026) J Gen Physiol

DOI: https://doi.org/10.1085/jgp.202513855

Macromolecule Content

Total Structure Weight: 38.08 kDa
Atom Count: 2,346
Modeled Residue Count: 229
Deposited Residue Count: 271
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein	A	271	Aliarcobacter butzleri	Mutation(s): 2 Gene Names: Abu_1752
UniProt
Find proteins for A8EVM5 (Aliarcobacter butzleri (strain RM4018)) Explore A8EVM5 Go to UniProtKB: A8EVM5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8EVM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX4 Query on PX4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
1N7 Query on 1N7 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHAPSO C₃₂ H₅₉ N₂ O₈ S GUQQBLRVXOUDTN-XOHPMCGNSA-O		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]