[English] 日本語
Yorodumi
- PDB-2heo: General Structure-Based Approach to the Design of Protein Ligands... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2heo
TitleGeneral Structure-Based Approach to the Design of Protein Ligands: Application to the Design of Kv1.2 Potassium Channel Blockers.
Components
  • 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
  • Z-DNA binding protein 1
KeywordsImmune System/DNA / PROTEIN DLM1-Z-DNA COMPLEX / Immune System-DNA COMPLEX
Function / homology
Function and homology information


left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / antiviral innate immune response / defense response to fungus / activation of innate immune response / positive regulation of inflammatory response ...left-handed Z-DNA binding / regulation of interleukin-1-mediated signaling pathway / double-stranded RNA adenosine deaminase activity / positive regulation of necroptotic process / positive regulation of type I interferon-mediated signaling pathway / pyroptotic inflammatory response / antiviral innate immune response / defense response to fungus / activation of innate immune response / positive regulation of inflammatory response / double-stranded RNA binding / regulation of inflammatory response / defense response to virus / positive regulation of apoptotic process / apoptotic process / DNA binding / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Z-DNA-binding protein 1 / RHIM domain / RIP homotypic interaction motif / Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Z-DNA-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMagis, C. / Gasparini, S. / Charbonnier, J.B. / Stura, E. / Le Du, M.H. / Menez, A. / Cuniasse, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Structure-based secondary structure-independent approach to design protein ligands: Application to the design of Kv1.2 potassium channel blockers.
Authors: Magis, C. / Gasparini, D. / Lecoq, A. / Le Du, M.H. / Stura, E. / Charbonnier, J.B. / Mourier, G. / Boulain, J.C. / Pardo, L. / Caruana, A. / Joly, A. / Lefranc, M. / Masella, M. / Menez, A. / Cuniasse, P.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
E: 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'
A: Z-DNA binding protein 1
D: Z-DNA binding protein 1


Theoretical massNumber of molelcules
Total (without water)19,1064
Polymers19,1064
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.910, 79.910, 55.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Detailsthe biological assembly is dimer present in the asymmetric unit, no need to symmetry operations

-
Components

#1: DNA chain 5'-D(*TP*CP*GP*CP*GP*CP*G)-3'


Mass: 2114.398 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Z-DNA binding protein 1 / Tumor stroma and activated macrophage protein DLM-1


Mass: 7438.605 Da / Num. of mol.: 2 / Fragment: N-TERMINAL WINGED-HELIX DOMAIN ZALPHA / Mutation: K130A, G132F, E162S, A164K, T165Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zbp1 / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9QY24
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG 4000, 0.2M Na/K phosphate, 0.1M MES, 5mM Bmercapto-ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Na/K phosphate11
3MES11
4Bmercapto-ethanol11
5H2O11
6PEG 400012
7Na/K phosphate12
8MES12
9Bmercapto-ethanol12

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorDate: Nov 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→65 Å / Num. obs: 22226 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 16.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3227 / Rsym value: 0.417 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J75

1j75


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.88 / SU B: 7.467 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30507 1129 5.1 %RANDOM
Rwork0.241 ---
all0.2414 22241 --
obs0.248 21057 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 246 0 228 1398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221235
X-RAY DIFFRACTIONr_angle_refined_deg2.0072.2531712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1985114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.54325.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33215195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.039155
X-RAY DIFFRACTIONr_chiral_restr0.1580.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02813
X-RAY DIFFRACTIONr_nbd_refined0.2770.2730
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.222
X-RAY DIFFRACTIONr_mcbond_it0.851.5604
X-RAY DIFFRACTIONr_mcangle_it1.3142958
X-RAY DIFFRACTIONr_scbond_it2.0023807
X-RAY DIFFRACTIONr_scangle_it2.6954.5754
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 98 -
Rwork0.315 1525 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5439-2.432-1.22044.8850.36173.13760.30270.28390.1433-0.4773-0.23080.0914-0.1511-0.1384-0.0718-0.03330.01950.0263-0.15070.0108-0.2056-10.94569.801-2.523
21.59241.6171-1.64886.0612.79186.2215-0.00110.1437-0.14770.10390.1599-0.14070.25940.1657-0.1589-0.0643-0.0439-0.0364-0.1165-0.049-0.1568-14.96458.66.441
33.91110.4782-0.0853.3464-0.52644.7423-0.0644-0.2480.17760.13880.05430.2042-0.2691-0.23350.0101-0.0769-0.00130.003-0.06860.0026-0.1955-24.48946.63320.963
41.5671.45941.91476.19473.568710.161-0.1990.11950.09650.3590.1872-0.11130.26780.12070.0118-0.0289-0.0258-0.0303-0.1289-0.0443-0.1689-16.88255.3811.524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC113 - 17010 - 67
2X-RAY DIFFRACTION2BA201 - 2062 - 7
3X-RAY DIFFRACTION3DD113 - 16910 - 66
4X-RAY DIFFRACTION4EB201 - 2062 - 7

+
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://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