5E8F: Fully modified geranylgeranylated PDE6C Peptide

Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D. Determined by X-ray diffraction at 2.1 Å resolution. Released 18 Nov 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,651
Mol. weight: 36.33 kDa
Ligands: GER
Released: 18 Nov 2015

Explore 5E8F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E8F 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 A: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	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
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 C: 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

Chains D and E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	852	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A, C	protein	149	Homo sapiens	O43924 (AlphaFold model)
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'	D, E	protein	5	Homo sapiens	P51160 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5E8F_1 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (chains A, C)
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSR
ELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPAS
VLTGNVIIETKFFDDDLLVSTSRVRLFYV

Sequence of entity 2 (D, E), FASTA

>5E8F_2 Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' (chains D, E)
KSKTC

Ligands and cofactors

ID	Name	Formula	Copies
GER	Geran-8-yl geran	C20 H34	2

Primary citation

The N- and C-terminal ends of RPGR can bind to PDE6 delta. Fansa, E.K., O'Reilly, N.J., Ismail, S. et al. EMBO Rep (2015) 16:1583-1585. DOI 10.15252/embr.201541404 · 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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