9HMC: PDE6D

Crystal structure of PDE6D in complex with compound 5e. Determined by X-ray diffraction at 1.65 Å resolution. Released 24 Dec 2025.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,704
Mol. weight: 38 kDa
Ligands: A1IWC
Released: 24 Dec 2025

Explore 9HMC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HMC contains 7 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-13	10
β-strand	15-24	10	1
β-strand	30-34	5	1
β-strand	44-49	6	2
α-helix	51-55	5
β-strand	58-67	10	1
β-strand	71-82	12	2
β-strand	85-97	13	2
β-strand	101-110	10	1
α-helix	120-123	4
β-strand	127-135	9	2
β-strand	138-149	12	2

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	15-24	10	3
β-strand	30-34	5	3
β-strand	44-49	6	4
α-helix	51-55	5
β-strand	58-67	10	3
β-strand	71-82	12	4
β-strand	85-97	13	4
β-strand	101-110	10	3
α-helix	117-119	3
α-helix	120-123	4
β-strand	127-135	9	4
β-strand	138-149	12	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A, B	protein	156	Homo sapiens	O43924 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9HMC_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains A, B)
HHHHHHMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKIL
KCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPE
SQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

Ligands and cofactors

ID	Name	Formula	Copies
A1IWC	4-[3,4-dimethyl-2-(4-methylphenyl)-7-oxidanylidene-pyrazolo[3,4-d]pyridazin-6-y…	C31 H48 N6 O3 S	2

Water and common crystallization additives (PEG, GOL) are not listed.

Primary citation

Covalent modification of a glutamic acid inspired by HaloTag technology. Zhang, R., Liu, J., Gasper, R. et al. Nat Commun (2026) 17:1257-1257. DOI 10.1038/s41467-026-68999-9 · PubMed

Other PDB entries of the same protein (UniProt O43924 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5ML3 1.4 Å, The crystal structure of PDE6D in complex to Deltasonamide1
4JV8 1.45 Å, The crystal structure of PDE6D in complex with rac-S1
7Q9Q 1.45 Å, Crystal structure of PDE6D Geranylgeranylated cystein complex
7PAD 1.49 Å, The crystal structure of DW-0254 in complex with PDE6D
5ML2 1.6 Å, The crystal structure of PDE6D in complex with inhibitor-3
3T5G 1.7 Å, Structure of fully modified farnesylated Rheb in complex with PDE6D
4JVB 1.75 Å, Crystal structure of PDE6D in complex with the inhibitor rac-2
1KSH 1.8 Å, Complex of Arl2 and PDE delta, Crystal Form 2 (native)
9RP6 1.8 Å, Crystal structure of covalent PDE6delta adduct modified by compound 13b
5F2U 1.85 Å, Structure of Fully modified farnesylated INPP5E Peptide in complex with PDE6D
7PAE 1.85 Å, The crystal structure of Deltarasin in complex with PDE6D
7Q9S 1.85 Å, Crystal structure of PDE6D KRas peptide complex with Compound-1

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