9CXH

Structure of PDE6C in complex with the rod inhibitory p gamma subunit in the presence of cGMP

PDB DOI: https://doi.org/10.2210/pdb9CXH/pdb
EM Map EMD-45991: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens, Bos taurus
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): No

Deposited: 2024-07-31 Released: 2024-12-18
Deposition Author(s): Srivastava, D., Singh, S., Artemyev, N.
Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 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

Structural and functional dynamics of human cone cGMP-phosphodiesterase important for photopic vision

Singh, S., Srivastava, D., Boyd, K., Artemyev, N.

(2025) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 219.16 kDa
Atom Count: 13,877
Modelled Residue Count: 1,692
Deposited Residue Count: 1,884
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'	A, B	843	Homo sapiens	Mutation(s): 0 Gene Names: PDE6C, PDEA2 EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for P51160 (Homo sapiens) Explore P51160 Go to UniProtKB: P51160
PHAROS: P51160 GTEx: ENSG00000095464
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51160
Sequence AnnotationsExpand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma	C [auth D], D [auth C]	99	Bos taurus	Mutation(s): 0 Gene Names: PDE6G, PDEG EC: 3.1.4.35
UniProt
Find proteins for P04972 (Bos taurus) Explore P04972 Go to UniProtKB: P04972
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04972
Sequence AnnotationsExpand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP (Subject of Investigation/LOI) Query on 5GP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
PCG (Subject of Investigation/LOI) Query on PCG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	CYCLIC GUANOSINE MONOPHOSPHATE C₁₀ H₁₂ N₅ O₇ P ZOOGRGPOEVQQDX-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]