[English] 日本語
Yorodumi
- PDB-2w8g: Aplysia californica AChBP bound to in silico compound 35 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w8g
TitleAplysia californica AChBP bound to in silico compound 35
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / ACETYLCHOLINE RECEPTOR INHIBITOR / POSTSYNAPTIC NEUROTOXIN / TOXIN / SECRETED / AMIDATION / CONOTOXIN / NEUROTOXIN / ACETYLCHOLINE BINDING PROTEIN / NICOTINIC ACETYLCHOLINE RECEPTOR-TOXIN COMPLEX / CLEAVAGE ON PAIR OF BASIC RESIDUES / CONFORMATIONAL FLEXIBILITY
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / identical protein binding / membrane / metal ion binding
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-BS2 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUlens, C. / Akdemir, A. / Jongejan, A. / van Elk, R. / Edink, E. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. ...Ulens, C. / Akdemir, A. / Jongejan, A. / van Elk, R. / Edink, E. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. / Bertrand, D. / de Esch, I.J.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Use of Acetylcholine Binding Protein in the Search for Novel Alpha7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X- Ray Analysis.
Authors: Ulens, C. / Akdemir, A. / Jongejan, A. / Van Elk, R. / Bertrand, S. / Perrakis, A. / Leurs, R. / Smit, A.B. / Sixma, T.K. / Bertrand, D. / De Esch, I.J.
History
DepositionJan 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Database references / Derived calculations
Revision 1.3Mar 18, 2015Group: Data collection
Revision 1.4Sep 4, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6758
Polymers123,4435
Non-polymers1,2323
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12840 Å2
ΔGint-67.3 kcal/mol
Surface area43840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.510, 173.628, 129.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE-BINDING PROTEIN


Mass: 24688.578 Da / Num. of mol.: 5 / Fragment: RESIDUES 20-236 / Source method: isolated from a natural source / Source: (natural) APLYSIA CALIFORNICA (California sea hare) / References: UniProt: Q8WSF8
#2: Chemical ChemComp-BS2 / (3-ENDO,8-ANTI)-8-BENZYL-3-(10,11-DIHYDRO-5H-DIBENZO[A,D][7]ANNULEN-5-YLOXY)-8-AZONIABICYCLO[3.2.1]OCTANE


Mass: 410.570 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H32NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCOMPOUND 35 IS 3ALPHA-[(10,11-DIHYDRO-5H-DIBENZO[A,D] CYCLOHEPTEN-5-YL)OXY]-8-BENZYL-8- ...COMPOUND 35 IS 3ALPHA-[(10,11-DIHYDRO-5H-DIBENZO[A,D] CYCLOHEPTEN-5-YL)OXY]-8-BENZYL-8-AZONIABICYCLO[3.2.1]OCTANE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.25 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9201
DetectorType: ADSC CCD / Detector: CCD / Date: May 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.6→106 Å / Num. obs: 40542 / % possible obs: 87.5 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.117 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.547 / % possible all: 87.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9T

2c9t


Resolution: 2.6→106.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.88 / SU B: 20.754 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.818 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2032 5 %RANDOM
Rwork0.2 ---
obs0.203 38507 87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2--1.92 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→106.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8281 0 93 259 8633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228602
X-RAY DIFFRACTIONr_bond_other_d0.0030.025731
X-RAY DIFFRACTIONr_angle_refined_deg1.651.96611747
X-RAY DIFFRACTIONr_angle_other_deg0.9093.00513821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22451032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04124.491403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.508151374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.751547
X-RAY DIFFRACTIONr_chiral_restr0.0860.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021715
X-RAY DIFFRACTIONr_nbd_refined0.2220.21638
X-RAY DIFFRACTIONr_nbd_other0.2130.25828
X-RAY DIFFRACTIONr_nbtor_refined0.1950.24281
X-RAY DIFFRACTIONr_nbtor_other0.0940.24674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2325
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3780.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7231.56541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88228516
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.53134100
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2514.53231
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 94 -
Rwork0.336 1694 -
obs--52.88 %
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)
11.0518-0.17320.14944.17410.38721.2695-0.0555-0.020.08510.02710.0739-0.4132-0.0680.2142-0.0184-0.05720.0201-0.032-0.0555-0.0217-0.163542.7485-26.579320.8661
21.2350.8456-0.22763.76720.30821.1843-0.05830.11310.0434-0.2180.1387-0.2095-0.08970.1591-0.0804-0.060.05750.0466-0.0572-0.0408-0.125245.3731-31.4364-5.1866
31.14460.3679-0.273.0514-1.00491.8264-0.03190.1813-0.0153-0.11450.0870.1418-0.0078-0.2239-0.0551-0.02040.02410.0004-0.0868-0.0404-0.197320.9061-33.8028-15.9868
41.259-0.29630.06242.0063-1.12242.1755-0.01330.06320.05670.00520.06360.1672-0.0598-0.1287-0.0503-0.1103-0.04190.0147-0.1059-0.0046-0.15333.3059-29.61623.4937
51.1587-0.60190.3882.7948-0.5111.3142-0.0536-0.12120.10980.17370.0716-0.0485-0.1191-0.0326-0.0181-0.0111-0.00620.0521-0.10470.0016-0.212116.7035-25.328126.2814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 205
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C1 - 205
4X-RAY DIFFRACTION4D1 - 205
5X-RAY DIFFRACTION5E1 - 205

+
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