[English] 日本語
Yorodumi
- PDB-5e80: The crystal structure of PDEd in complex with inhibitor-2a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5.0E+80
TitleThe crystal structure of PDEd in complex with inhibitor-2a
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsLIPID BINDING PROTEIN / Prenyl binding Protein /inhibitor / Immunoglobulin-like beta-sandwich / GDI-like solubilizing factor
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / cytoplasmic vesicle / cytoskeleton ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / small GTPase binding / cilium / RAS processing / cytoplasmic vesicle / cytoskeleton / cytoplasm / cytosol
Similarity search - Function
GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
Chem-5KP / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIsmail, S. / Fansa, E.K. / Murarka, S. / Wittinghofer, A.
CitationJournal: Nat Commun / Year: 2016
Title: Identification of pyrazolopyridazinones as PDE delta inhibitors.
Authors: Papke, B. / Murarka, S. / Vogel, H.A. / Martin-Gago, P. / Kovacevic, M. / Truxius, D.C. / Fansa, E.K. / Ismail, S. / Zimmermann, G. / Heinelt, K. / Schultz-Fademrecht, C. / Al Saabi, A. / ...Authors: Papke, B. / Murarka, S. / Vogel, H.A. / Martin-Gago, P. / Kovacevic, M. / Truxius, D.C. / Fansa, E.K. / Ismail, S. / Zimmermann, G. / Heinelt, K. / Schultz-Fademrecht, C. / Al Saabi, A. / Baumann, M. / Nussbaumer, P. / Wittinghofer, A. / Waldmann, H. / Bastiaens, P.I.
History
DepositionOct 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4034
Polymers34,5042
Non-polymers9002
Water27015
1
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7022
Polymers17,2521
Non-polymers4501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7022
Polymers17,2521
Non-polymers4501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.760, 40.900, 68.800
Angle α, β, γ (deg.)97.700, 102.380, 89.310
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17


Mass: 17251.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli (E. coli) / References: UniProt: O43924
#2: Chemical ChemComp-5KP / N-(3-chloro-2-methylphenyl)-4-(3,4-dimethyl-7-oxo-2-phenyl-2,7-dihydro-6H-pyrazolo[3,4-d]pyridazin-6-yl)butanamide


Mass: 449.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24ClN5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Calcium acetate, 20% (w/v) PEG 3350 / PH range: 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.6→26.06 Å / Num. obs: 9570 / % possible obs: 97.7 % / Redundancy: 3.45 % / Rsym value: 0.113 / Net I/σ(I): 9.54
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.26 / Rsym value: 0.466 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALE5.7.0032data scaling
MOLREP3.15phasing
REFMAC5.7.0032refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5G

3t5g


Resolution: 2.6→26.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.048 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 504 5 %RANDOM
Rwork0.1853 ---
obs0.1884 9570 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.75 Å2 / Biso mean: 35.365 Å2 / Biso min: 21.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.04 Å2-0.02 Å2
2---0.04 Å20.04 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.6→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 64 15 2503
Biso mean--41.53 34.02 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022546
X-RAY DIFFRACTIONr_bond_other_d0.0030.022427
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9813439
X-RAY DIFFRACTIONr_angle_other_deg0.8213.0065576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3825296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73323.95119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23915456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4171518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_mcbond_it1.6693.4131190
X-RAY DIFFRACTIONr_mcbond_other1.6633.4131189
X-RAY DIFFRACTIONr_mcangle_it2.6495.1191484
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 36 -
Rwork0.32 689 -
all-725 -
obs--96.54 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more