7QF9: PDE6D

Crystal structure of PDE6D bound to HRas peptide. Determined by X-ray diffraction at 1.95 Å resolution. Released 9 Feb 2022.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,705
Mol. weight: 36.47 kDa
Ligands: FAR, CMT
Released: 9 Feb 2022

Explore 7QF9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QF9 contains 11 α-helices and 19 β-strands across 3 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 AAA: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10
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	101-111	11	3
α-helix	112	1
α-helix	114-116	3
α-helix	118-119	2
α-helix	120-123	4
β-strand	127-135	9	4
β-strand	138-149	12	4

Chain BBB: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
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	111-113	3
α-helix	118-119	2
α-helix	120-123	4
β-strand	127-135	9	2
β-strand	138-149	12	2

Chain EEE: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	15-17	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	AAA, BBB	protein	149	Homo sapiens	O43924 (AlphaFold model)
HRas peptide	EEE	protein	10	Homo sapiens

Sequence of entity 1 (AAA, BBB), FASTA

>7QF9_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains AAA, BBB)
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSR
ELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPAS
VLTGNVIIETKFFDDDLLVSTSRVRLFYV

Sequence of entity 2 (EEE), FASTA

>7QF9_2 HRas peptide (chains EEE)
SGPGCMSCKC

Ligands and cofactors

ID	Name	Formula	Copies
FAR	Farnesyl	C15 H26	2
CMT	O-methylcysteine	C4 H9 N O2 S	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling. Yelland, T., Garcia, E., Parry, C. et al. J Med Chem (2022) 65:1898-1914. DOI 10.1021/acs.jmedchem.1c01265 · 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
9HMC 1.65 Å, Crystal structure of PDE6D in complex with compound 5e
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

Browse structure collections

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