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

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] 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 E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	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]