[English] 日本語
Yorodumi
- PDB-3o5n: Tetrahydroquinoline carboxylates are potent inhibitors of the Sha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o5n
TitleTetrahydroquinoline carboxylates are potent inhibitors of the Shank PDZ domain, a putative target in autism disorders
ComponentsSH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / PDZ domain / Protein-protein interaction / GKAP / postsynaptic density
Function / homology
Function and homology information


response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / embryonic epithelial tube formation / positive regulation of synapse structural plasticity / negative regulation of actin filament bundle assembly ...response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / embryonic epithelial tube formation / positive regulation of synapse structural plasticity / negative regulation of actin filament bundle assembly / negative regulation of cell volume / structural constituent of postsynaptic density / positive regulation of glutamate receptor signaling pathway / regulation of grooming behavior / positive regulation of long-term neuronal synaptic plasticity / NMDA glutamate receptor clustering / vocalization behavior / RET signaling / regulation of behavioral fear response / neuron spine / regulation of dendritic spine morphogenesis / AMPA glutamate receptor clustering / dendritic spine morphogenesis / neural precursor cell proliferation / brain morphogenesis / locomotion / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / long-term synaptic depression / ciliary membrane / exploration behavior / regulation of postsynapse organization / regulation of long-term synaptic depression / positive regulation of dendritic spine development / locomotory exploration behavior / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / excitatory synapse / postsynaptic density, intracellular component / glial cell proliferation / synapse assembly / positive regulation of synaptic transmission, glutamatergic / learning / positive regulation of long-term synaptic potentiation / locomotory behavior / G protein-coupled receptor binding / long-term synaptic potentiation / ionotropic glutamate receptor binding / modulation of chemical synaptic transmission / regulation of synaptic plasticity / memory / SH3 domain binding / : / MAPK cascade / actin binding / gene expression / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / learning or memory / neuron projection / glutamatergic synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Chem-BR0 / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsSaupe, J. / Roske, Y. / Schillinger, C. / Kamdem, N. / Radetzki, S. / Diehl, A. / Oschkinat, H. / Krause, G. / Heinemann, U. / Rademann, J.
CitationJournal: Chemmedchem / Year: 2011
Title: Discovery, structure-activity relationship studies, and crystal structure of nonpeptide inhibitors bound to the shank3 PDZ domain.
Authors: Saupe, J. / Roske, Y. / Schillinger, C. / Kamdem, N. / Radetzki, S. / Diehl, A. / Oschkinat, H. / Krause, G. / Heinemann, U. / Rademann, J.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 3
B: SH3 and multiple ankyrin repeat domains protein 3
C: SH3 and multiple ankyrin repeat domains protein 3
D: SH3 and multiple ankyrin repeat domains protein 3
E: SH3 and multiple ankyrin repeat domains protein 3
F: SH3 and multiple ankyrin repeat domains protein 3
G: SH3 and multiple ankyrin repeat domains protein 3
H: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9529
Polymers97,6478
Non-polymers3041
Water5,224290
1
H: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5102
Polymers12,2061
Non-polymers3041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
G: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
E: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules

H: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)24,7163
Polymers24,4122
Non-polymers3041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Unit cell
Length a, b, c (Å)55.954, 64.063, 101.924
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+2, y-1/2, -z+2.

-
Components

#1: Protein
SH3 and multiple ankyrin repeat domains protein 3 / Shank3 / Proline-rich synapse-associated protein 2 / ProSAP2 / SPANK-2


Mass: 12205.927 Da / Num. of mol.: 8 / Fragment: PDZ domain, residues 637-744
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shank3, Kiaa1650 / Plasmid: pLIC-His / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q4ACU6
#2: Chemical ChemComp-BR0 / (3aS,4R,9bR)-9-nitro-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-4,6-dicarboxylic acid


Mass: 304.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 1.87 Å3/Da / Density % sol: 34.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG4000, 2-Propanol, Sodium acetate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.072 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 25, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.514
11h,-k,-l20.486
ReflectionResolution: 1.83→33.97 Å / Num. all: 56826 / Num. obs: 119285 / % possible obs: 89 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Redundancy: 2.1 % / Rmerge(I) obs: 0.026
Reflection shellResolution: 1.83→1.88 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.36 / % possible all: 72.3

-
Processing

Software
NameVersionClassification
MD2data collection
PHASESphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→33.97 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.718 / SU ML: 0.11 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2852 5 %RANDOM
Rwork0.233 ---
all0.23562 56826 --
obs0.23562 119285 88.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.694 Å2
Baniso -1Baniso -2Baniso -3
1--21.29 Å20 Å2-2.1 Å2
2--29.47 Å20 Å2
3----8.18 Å2
Refinement stepCycle: LAST / Resolution: 1.83→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 0 22 290 6313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226160
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9578331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.135766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9823.227282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.298151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9551556
X-RAY DIFFRACTIONr_chiral_restr0.1170.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214611
X-RAY DIFFRACTIONr_mcbond_it0.6981.53807
X-RAY DIFFRACTIONr_mcangle_it1.15326146
X-RAY DIFFRACTIONr_scbond_it1.76432353
X-RAY DIFFRACTIONr_scangle_it2.4464.52180

+
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