7Q9S: PDE6D KRas peptide complex with Compound-1

Crystal structure of PDE6D KRas peptide complex with Compound-1. Determined by X-ray diffraction at 1.85 Å resolution. Released 19 Jan 2022.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,967
Mol. weight: 39.36 kDa
Ligands: 9TI, FAR
Released: 19 Jan 2022

Explore 7Q9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q9S contains 12 α-helices and 22 β-strands across 4 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	15-24	10	4
β-strand	30-34	5	4
β-strand	44-49	6	5
α-helix	51-55	5
β-strand	58-67	10	4
β-strand	71-82	12	5
β-strand	85-97	13	5
β-strand	101-110	10	4
β-strand	111	1	6
α-helix	112-113	2
α-helix	114-116	3
α-helix	118-119	2
α-helix	120-123	4
β-strand	127-135	9	5
β-strand	138-149	12	5

Chain BBB: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
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
β-strand	111	1	3
α-helix	112-113	2
α-helix	114-116	3
α-helix	117-119	3
α-helix	120-123	4
β-strand	127-135	9	2
β-strand	138-149	12	2

Chain CCC: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	22	1	6

Chain DDD: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	AAA, BBB	protein	150	Homo sapiens	O43924 (AlphaFold model)
KRas	CCC, DDD	protein	13	Homo sapiens

Sequence of entity 1 (AAA, BBB), FASTA

>7Q9S_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains AAA, BBB)
MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVS
RELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPA
SVLTGNVIIETKFFDDDLLVSTSRVRLFYV

Sequence of entity 2 (CCC, DDD), FASTA

>7Q9S_2 KRas (chains CCC, DDD)
DGKKKKKKSKTKC

Ligands and cofactors

ID	Name	Formula	Copies
9TI	2-methyl-3-(1~{H}-pyrazol-5-yl)imidazo[1,2-a]pyridine	C11 H10 N4	2
FAR	Farnesyl	C15 H26	2

Water and common crystallization additives (SO4, EDO, DMS) 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

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