8YCP | pdb_00008ycp

structure of human trpv1 in complex with BC5

PDB DOI: https://doi.org/10.2210/pdb8YCP/pdb
EM Map EMD-39151: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-02-18 Released: 2025-01-29
Deposition Author(s): Ke, B.W., Hu, S.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8YCP

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

Literature

Sequential multitarget modulation: Developing Ultra-long-acting sensory-specific local anesthetics for postoperative pain

Hu, S.L., Wenrui, G.

To be published.

Macromolecule Content

Total Structure Weight: 306.49 kDa
Atom Count: 20,462
Modeled Residue Count: 2,486
Deposited Residue Count: 2,624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	656	Homo sapiens	Mutation(s): 0 Gene Names: TRPV1, VR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NER1 (Homo sapiens) Explore Q8NER1 Go to UniProtKB: Q8NER1
PHAROS: Q8NER1 GTEx: ENSG00000196689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NER1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6OU (Subject of Investigation/LOI) Query on 6OU Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], J [auth B], M [auth D]	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate C₃₉ H₇₆ N O₈ P FHQVHHIBKUMWTI-OTMQOFQLSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth D]
A1LZ2 Query on A1LZ2 Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], L [auth D]	(1~{R},2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)-1-[5-[(2~{S})-2-[(2,6-dimethylphenyl)carbamoyl]piperidin-1-yl]pentyl]piperidin-1-ium-2-carboxamide C₃₇ H₅₇ N₄ O₂ LDTYQAIXDFBLCF-JHWKUKDKSA-O		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release
Version 1.1: 2025-06-18
Changes: Data collection

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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.