9HMD | pdb_00009hmd

Crystal structure of PDE6D in complex with DeltaTag (6a)

PDB DOI: https://doi.org/10.2210/pdb9HMD/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-09 Released: 2025-12-24
Deposition Author(s): Zhang, R., Waldmann, H., Gasper, R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.283 (Depositor), 0.283 (DCC)
R-Value Work:
0.240 (Depositor), 0.239 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of PDE6D in complex with DeltaTag (6a)

Zhang, R.

To be published.

Macromolecule Content

Total Structure Weight: 37.78 kDa
Atom Count: 2,491
Modeled Residue Count: 292
Deposited Residue Count: 312
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A, B	156	Homo sapiens	Mutation(s): 0 Gene Names: PDE6D, PDED
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens) Explore O43924 Go to UniProtKB: O43924
PHAROS: O43924 GTEx: ENSG00000156973
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43924
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IWD (Subject of Investigation/LOI) Query on A1IWD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	4-[3,4-dimethyl-2-(4-methylphenyl)-7-oxidanylidene-pyrazolo[3,4-d]pyridazin-6-yl]-~{N}-[2-(3-ethylphenyl)ethyl]-~{N}-(piperidin-4-ylmethyl)butane-1-sulfonamide C₃₄ H₄₆ N₆ O₃ S QHFTYTSBWBJCGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.283 (Depositor), 0.283 (DCC)
R-Value Work: 0.240 (Depositor), 0.239 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.47	α = 90
b = 75.22	β = 90
c = 81.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-12-24
Type: Initial release

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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.