9JTQ | pdb_00009jtq

Deposited: 2024-10-06 Released: 2025-04-02
Deposition Author(s): Matsuzaki, Y., Tzlil, G., Del Carmen Marin, M., Shihoya, W., Beja, O., Nureki, O.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	254	Candidatus Heimdallarchaeota archaeon	Mutation(s): 0 Gene Names: CME83_04245
UniProt
Find proteins for A0A2E9CEV6 (Candidatus Heimdallarchaeota archaeon) Explore A0A2E9CEV6 Go to UniProtKB: A0A2E9CEV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2E9CEV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], F [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A]
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A]	E [auth A], G [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A]