7WDB | pdb_00007wdb

Human TRPC5 channel in complex with riluzole

PDB DOI: https://doi.org/10.2210/pdb7WDB/pdb
EM Map EMD-32436: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2021-12-21 Released: 2022-04-13
Deposition Author(s): Chen, L., Wei, M., Yang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC), National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structural identification of riluzole-binding site on human TRPC5.

Yang, Y., Wei, M., Chen, L.

(2022) Cell Discov 8: 67-67

PubMed: 35821012 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-022-00410-5
Primary Citation of Related Structures:
7WDB

Organizational Affiliation

Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.

Macromolecule Content

Total Structure Weight: 366.77 kDa
Atom Count: 22,400
Modeled Residue Count: 2,660
Deposited Residue Count: 3,056
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short transient receptor potential channel 5	A, B, C, D	764	Homo sapiens	Mutation(s): 0 Gene Names: TRPC5, TRP5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL62 (Homo sapiens) Explore Q9UL62 Go to UniProtKB: Q9UL62
PHAROS: Q9UL62 GTEx: ENSG00000072315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UL62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain S [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth D]	E [auth A], L [auth B], S [auth C], Z [auth D]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Z [auth D]
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain EA [auth D] SDF format, chain Q [auth B] SDF format, chain X [auth C] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C]	EA [auth D], J [auth A], Q [auth B], X [auth C]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain EA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C]
A1L8M Query on A1L8M Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain Y [auth C] MOL2 format, chain R [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain R [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain Y [auth C]	FA [auth D], K [auth A], R [auth B], Y [auth C]	[(2S)-1-oxidanyl-3-[(E)-tetradec-9-enoyl]oxy-propan-2-yl] (Z)-pentadec-9-enoate C₃₂ H₅₈ O₅ BXDNXAULBWUASM-MBCKKLRHSA-N		Interactions Focus chain FA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Y [auth C]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain T [auth C]	AA [auth D], F [auth A], M [auth B], T [auth C]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain M [auth B] Focus chain T [auth C]
657 (Subject of Investigation/LOI) Query on 657 Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	DA [auth D], I [auth A], P [auth B], W [auth C]	6-(trifluoromethoxy)-1,3-benzothiazol-2-amine C₈ H₅ F₃ N₂ O S FTALBRSUTCGOEG-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain W [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain BA [auth D]	BA [auth D], G [auth A], N [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain U [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain CA [auth D] SDF format, chain V [auth C] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain V [auth C] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain V [auth C]	CA [auth D], H [auth A], O [auth B], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain H [auth A] Focus chain O [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-13

Deposition Author(s):

Chen, L.

Wei, M.

Yang, Y.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91957201
National Natural Science Foundation of China (NSFC)	China	31870833
National Science Foundation (NSF, China)	China	31821091
National Science Foundation (NSF, China)	China	11902021

Revision History (Full details and data files)

Version 1.0: 2022-04-13
Type: Initial release
Version 1.1: 2022-08-03
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Structure summary
Version 2.0: 2025-03-26
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary