9KGL | pdb_00009kgl

Structure of KATP channel in complex with centipede toxin SpTx1

PDB DOI: https://doi.org/10.2210/pdb9KGL/pdb
EM Map EMD-62322: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Mesocricetus auratus, Scolopendra polymorpha
Expression System: Homo sapiens, Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-08 Released: 2025-11-12
Deposition Author(s): Chen, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of KATP in complex with SpTx1

Chen, L., Wang, M.

To be published.

Macromolecule Content

Total Structure Weight: 896.13 kDa
Atom Count: 55,831
Modeled Residue Count: 7,074
Deposited Residue Count: 7,944
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-sensitive inward rectifier potassium channel 11	A, C, E, G	390	Homo sapiens	Mutation(s): 2 Gene Names: KCNJ11
UniProt & NIH Common Fund Data Resources
Find proteins for Q14654 (Homo sapiens) Explore Q14654 Go to UniProtKB: Q14654
PHAROS: Q14654 GTEx: ENSG00000187486
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14654
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-binding cassette sub-family C member 8 isoform X2	B, D, F, H	1,582	Mesocricetus auratus	Mutation(s): 0 Gene Names: Abcc8
UniProt
Find proteins for A0A1U7R319 (Mesocricetus auratus) Explore A0A1U7R319 Go to UniProtKB: A0A1U7R319
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1U7R319
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SpTx1	I	56	Scolopendra polymorpha	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain U [auth H] SDF format, chain S [auth G] SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain U [auth H] MOL2 format, chain S [auth G] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain U [auth H] mmCIF format, chain S [auth G] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A] L [auth B] M [auth C] O [auth D] P [auth E] J [auth A], L [auth B], M [auth C], O [auth D], P [auth E], R [auth F], S [auth G], U [auth H]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain U [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain U [auth H]
GBM Query on GBM Download Ideal Coordinates CCD File SDF format, chain T [auth H] SDF format, chain Q [auth F] SDF format, chain N [auth D] SDF format, chain K [auth B] MOL2 format, chain T [auth H] MOL2 format, chain Q [auth F] MOL2 format, chain N [auth D] MOL2 format, chain K [auth B] mmCIF format, chain T [auth H] mmCIF format, chain Q [auth F] mmCIF format, chain N [auth D] mmCIF format, chain K [auth B]	K [auth B], N [auth D], Q [auth F], T [auth H]	5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide C₂₃ H₂₈ Cl N₃ O₅ S ZNNLBTZKUZBEKO-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain N [auth D] Focus chain Q [auth F] Focus chain T [auth H] Interactions & Density Focus chain K [auth B] Focus chain N [auth D] Focus chain Q [auth F] Focus chain T [auth H]