[English] 日本語
Yorodumi
- PDB-2xnt: Acetylcholine binding protein (AChBP) as template for hierarchica... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xnt
TitleAcetylcholine binding protein (AChBP) as template for hierarchical in silico screening procedures to identify structurally novel ligands for the nicotinic receptors
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / CHOLINE-BINDING PROTEIN / IN-SILICO SCREENING / LIGAND-GATED ION CHANNELS / ELECTROPHYSIOLOGY / CYS-LOOP RECEPTORS
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / 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
BROMIDE ION / (2S)-2-[(4-CHLOROBENZYL)OXY]-2-PHENYLETHANAMINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsRucktooa, P. / Akdemir, A. / deEsch, I. / Sixma, T.K.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Acetylcholine Binding Protein (Achbp) as Template for Hierarchical in Silico Screening Procedures to Identify Structurally Novel Ligands for the Nicotinic Receptors.
Authors: Akdemir, A. / Rucktooa, P. / Jongejan, A. / Elk, R.V. / Bertrand, S. / Sixma, T.K. / Bertrand, D. / Smit, A.B. / Leurs, R. / De Graaf, C. / De Esch, I.J.
History
DepositionAug 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 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

-
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
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,87630
Polymers266,46010
Non-polymers3,41720
Water00
1
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,93815
Polymers133,2305
Non-polymers1,70810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint-63.2 kcal/mol
Surface area42400 Å2
MethodPISA
2
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)134,93815
Polymers133,2305
Non-polymers1,70810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-63.2 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.111, 144.867, 145.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR


Mass: 26645.967 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: COMPOUND 6 FROM IN SILICO SCREEN
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-VU2 / (2S)-2-[(4-CHLOROBENZYL)OXY]-2-PHENYLETHANAMINE


Mass: 261.747 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C15H16ClNO
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.22 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M SODIUM BROMIDE, 0.1M BIS-TRIS PROPANE PH 7.5, 20% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.21→48.37 Å / Num. obs: 43483 / % possible obs: 96.4 % / Observed criterion σ(I): 1.4 / Redundancy: 3.9 % / Biso Wilson estimate: 85.39 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.1
Reflection shellResolution: 3.21→3.39 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.4 / % possible all: 84.9

-
Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR7

2br7


Resolution: 3.21→45.76 Å / Cor.coef. Fo:Fc: 0.8924 / Cor.coef. Fo:Fc free: 0.8771 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2195 5.08 %RANDOM
Rwork0.2159 ---
obs0.2167 43238 --
Displacement parametersBiso mean: 60.33 Å2
Baniso -1Baniso -2Baniso -3
1-10.479 Å20 Å20 Å2
2---5.8176 Å20 Å2
3----4.6614 Å2
Refine analyzeLuzzati coordinate error obs: 0.707 Å
Refinement stepCycle: LAST / Resolution: 3.21→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16360 0 190 0 16550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00716970HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8423150HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7610SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes450HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2400HARMONIC5
X-RAY DIFFRACTIONt_it16780HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2240SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17787SEMIHARMONIC4
LS refinement shellResolution: 3.21→3.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 115 5.09 %
Rwork0.3174 2143 -
all0.3192 2258 -
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)
11.5194-0.63990.40662.0428-0.13522.1063-0.0210.17830.102-0.1599-0.04580.0385-0.2533-0.00340.0668-0.13180.01020.0209-0.0441-0.0046-0.099159.57890.356314.3045
21.5413-0.09370.39592.8431-0.28431.74580.03570.1589-0.0876-0.206-0.07730.20510.2472-0.06550.0416-0.04210.07910.0317-0.0296-0.0242-0.169957.334165.25185.2852
32.96440.5497-0.12021.5819-0.44242.1301-0.0173-0.083-0.0007-0.1034-0.01380.08280.3179-0.14550.0311-0.00830.048-0.0095-0.097-0.0355-0.089458.648448.618626.5707
42.2469-0.0108-0.22631.6265-0.29921.86280.0385-0.2232-0.07890.1489-0.08720.0399-0.00990.10660.0486-0.1294-0.0098-0.0165-0.01260.0105-0.1562.005863.176248.9876
51.7674-0.0937-0.57352.272-0.52392.19440.00820.03110.02170.092-0.0541-0.023-0.307-0.010.0459-0.0794-0.0775-0.0275-0.066-0.0744-0.134562.073889.103741.166
63.150.4845-0.00942.0247-0.2041.80770.0032-0.0247-0.0752-0.0709-0.06610.06960.2165-0.09690.0629-0.0656-0.02440.0204-0.1171-0.0335-0.1037124.27634.240527.5167
71.85930.26630.11651.6806-0.17262.10670.0167-0.2513-0.01740.2967-0.04730.03610.0782-0.00290.0306-0.1182-0.04480.0084-0.07460.002-0.1487126.75550.362248.927
81.9122-0.3755-0.38671.6667-0.00932.13480.0090.08890.07290.0797-0.0999-0.0538-0.2922-0.04410.0909-0.0882-0.0654-0.0095-0.061-0.0431-0.1044125.49875.692439.7986
91.87830.13280.34652.98520.14462.05470.01760.16-0.0351-0.2614-0.06760.2010.1068-0.07790.050.01110.03150.0226-0.0236-0.0095-0.18121.73649.66465.4503
101.8646-0.09510.29421.81730.23572.2753-0.01590.16540.1997-0.12-0.0879-0.0224-0.2155-0.12740.1038-0.02420.01050.0448-0.06340.0323-0.1098122.68275.386712.9062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A1 - A205, A301 - A301)
2X-RAY DIFFRACTION2(B1 - B205, B301 - B301)
3X-RAY DIFFRACTION3(C1 - C205, C301 - C301)
4X-RAY DIFFRACTION4(D1 - D205, D301 - D301)
5X-RAY DIFFRACTION5(E1 - E205, E301 - E301)
6X-RAY DIFFRACTION6(F1 - F205, F301 - F301)
7X-RAY DIFFRACTION7(G1 - G205, G301 - G301)
8X-RAY DIFFRACTION8(H1 - H205, H301 - H301)
9X-RAY DIFFRACTION9(I1 - I205, I301 - I301)
10X-RAY DIFFRACTION10(J1 - J205, J301 - J301)

+
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