5E8F

Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D

PDB DOI: https://doi.org/10.2210/pdb5E8F/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-10-14 Released: 2015-11-18
Deposition Author(s): Fansa, E.K., O'Reilly, N.J., Ismail, S.A., Wittinghofer, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.256
R-Value Work: 0.198
R-Value Observed: 0.201

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The N- and C-terminal ends of RPGR can bind to PDE6 delta.

Fansa, E.K., O'Reilly, N.J., Ismail, S., Wittinghofer, A.

(2015) EMBO Rep 16: 1583-1585

PubMed: 26553937 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.15252/embr.201541404
Primary Citation of Related Structures:
5E8F

PubMed Abstract:
This study shows that the prenylated C‐terminus of RPGR can bind to PDE6δ with high affinity, suggesting two distinct binding sites of the RPGR/PDE6δ complex. The serine residue at the ?3 position relative to the prenylated cysteine seems to play a key role in defining the selectivity of PDE6δ towards ciliary prenylated cargo. [Image: see text]

Organizational Affiliation

Max Planck Institute of Molecular Physiology, Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 36.33 kDa
Atom Count: 2,651
Modelled Residue Count: 306
Deposited Residue Count: 308
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A, B [auth C]	149	Homo sapiens	Mutation(s): 0 Gene Names: PDE6D, PDED EC: 3.1.4.35
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O43924
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'	C [auth D], D [auth E]	5	Homo sapiens	Mutation(s): 0 Gene Names: PDE6C, PDEA2 EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for P51160 (Homo sapiens) Explore P51160 Go to UniProtKB: P51160
PHAROS: P51160 GTEx: ENSG00000095464
Entity Groups
UniProt Group	P51160
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GER Query on GER Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain F [auth E] MOL2 format, chain E [auth D] MOL2 format, chain F [auth E] mmCIF format, chain E [auth D] mmCIF format, chain F [auth E]	E [auth D], F [auth E]	GERAN-8-YL GERAN C₂₀ H₃₄ HSOYJGBJQAKCNA-CAIKYXSQSA-N		Interactions Focus chain E [auth D] Focus chain F [auth E] Interactions & Density Focus chain E [auth D] Focus chain F [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMT Query on CMT	C [auth D], D [auth E]	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.256
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: C 2 2 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 77.71	α = 90
b = 81.43	β = 90
c = 118.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-11-18
Type: Initial release
Version 1.1: 2015-12-16
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description