[English] 日本語
Yorodumi
- PDB-5dqf: Horse Serum Albumin (ESA) in complex with Cetirizine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dqf
TitleHorse Serum Albumin (ESA) in complex with Cetirizine
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / albumin / cetirizine / ESA / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space / metal ion binding / cytoplasm
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CZE / Chem-LCR / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHanding, K.B. / Shabalin, I.G. / Majorek, K.A. / Chruszcz, M. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-5U54GM094662-05 United States
CitationJournal: Mol.Immunol. / Year: 2016
Title: Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site.
Authors: Handing, K.B. / Shabalin, I.G. / Szlachta, K. / Majorek, K.A. / Minor, W.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Other
Revision 1.2Mar 9, 2016Group: Data collection / Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.5Sep 12, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.details / _pdbx_related_exp_data_set.metadata_reference
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Sep 27, 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
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,07718
Polymers65,4141
Non-polymers2,66317
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.234, 94.234, 141.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Serum albumin /


Mass: 65413.746 Da / Num. of mol.: 1 / Mutation: R561A / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747

-
Non-polymers , 6 types, 265 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-LCR / (2-{4-[(R)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}ethoxy)acetic acid / R-levocetirizine / Levocetirizine


Mass: 388.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25ClN2O3
#5: Chemical ChemComp-CZE / (2-{4-[(S)-(4-chlorophenyl)(phenyl)methyl]piperazin-1-yl}ethoxy)acetic acid / (S)-dextrocetirizine


Mass: 388.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25ClN2O3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 ul of 30 mg/mL protein in 10 mM Tris pH 7.5, 150 mM NaCl was mixed with 1ul of the well condition: 100 mM Tris pH 7.5, 1800 mM (NH4)2SO4, 87.5 mM NaBr, 2.5% w/v PEG 8K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2011 / Details: Bimorph K-B pair
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→80 Å / Num. obs: 38645 / % possible obs: 99.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Rsym value: 0.07 / Χ2: 1.399 / Net I/av σ(I): 35.6 / Net I/σ(I): 9.7 / Num. measured all: 297500
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.15-2.197.70.94719230.7850.3630.894100
2.19-2.237.70.75919290.8240.2910.9331000.813
2.23-2.277.70.69219160.8460.2660.9341000.742
2.27-2.327.70.55919260.9080.2140.9561000.599
2.32-2.377.70.47219380.9230.1810.9771000.506
2.37-2.427.70.39419320.9430.1510.9811000.422
2.42-2.487.70.31919390.9650.1231.0131000.342
2.48-2.557.70.27919310.970.1071.0771000.299
2.55-2.627.70.22319320.9810.0861.0971000.239
2.62-2.717.70.19419310.9830.0751.12899.90.208
2.71-2.817.70.16919260.9860.0651.31199.90.182
2.81-2.927.70.14519150.9890.0561.46999.90.155
2.92-3.057.70.11319460.9920.0441.67199.90.121
3.05-3.217.70.08919320.9940.0341.73899.90.095
3.21-3.417.80.06419340.9970.0251.65399.70.069
3.41-3.687.80.05319310.9980.021.68299.70.057
3.68-4.057.60.05719390.9970.0222.53199.70.061
4.05-4.637.60.05119320.9980.022.61599.50.055
4.63-5.847.80.04119520.9990.0161.77499.30.044
5.84-807.50.0319410.9990.0121.54597.80.033

-
Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
Cootmodel building
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V08

3v08


Resolution: 2.15→80 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2345 / WRfactor Rwork: 0.1886 / FOM work R set: 0.8091 / SU B: 12.309 / SU ML: 0.159 / SU R Cruickshank DPI: 0.2189 / SU Rfree: 0.1915 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 1879 4.9 %RANDOM
Rwork0.1888 ---
obs0.1912 36754 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.14 Å2 / Biso mean: 55.868 Å2 / Biso min: 28.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.78 Å20 Å2
2--1.55 Å2-0 Å2
3----5.04 Å2
Refinement stepCycle: final / Resolution: 2.15→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 124 248 4860
Biso mean--70.03 57.29 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194714
X-RAY DIFFRACTIONr_bond_other_d0.0040.024384
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9956372
X-RAY DIFFRACTIONr_angle_other_deg1.0143.00210174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0215579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70124.877203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55115787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9211519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02993
X-RAY DIFFRACTIONr_mcbond_it1.3253.4452319
X-RAY DIFFRACTIONr_mcbond_other1.3253.4452318
X-RAY DIFFRACTIONr_mcangle_it2.1015.1622897
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 117 -
Rwork0.259 2710 -
all-2827 -
obs--98.95 %
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)
12.501-0.20860.87461.3088-0.18922.41040.16830.12170.2110.13830.0701-0.1697-0.14880.2098-0.23830.08030.0437-0.02970.0794-0.09650.3362-41.33541.489-0.111
24.8692-1.7974-2.23212.32470.4592.3829-0.3698-0.2284-0.27740.62790.23220.17080.0832-0.22570.13750.180.07610.03070.1605-0.00060.2661-51.51124.7818.078
31.5867-0.54140.82444.8630.16171.53040.11470.17040.2222-0.3433-0.1649-0.08410.0818-0.14360.05010.09860.0345-0.07050.07710.00530.268-45.90521.156-15.593
42.5089-1.2686-0.88442.18720.93912.0568-0.01790.1594-0.0391-0.16730.00450.0420.0543-0.00880.01340.1448-0.0239-0.09250.0170.01510.25-39.0015.551-20.21
50.6733-0.30621.0711.0167-0.33922.99850.0287-0.01040.0682-0.1612-0.1034-0.01650.1401-0.03580.07470.21660.02650.05430.02530.03390.286-37.0332.30310.323
61.78250.01371.00391.0626-0.72722.02390.1332-0.16680.09520.1063-0.15260.02290.1709-0.01040.01940.11370.002-0.02960.0562-0.01370.2666-30.5497.8513.864
72.0164-0.4749-1.58052.59410.7694.4040.0997-0.0550.11280.3377-0.11780.065-0.07340.14120.0180.2471-0.05090.03030.0170.00040.277-34.732.75329.229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 110
2X-RAY DIFFRACTION2A111 - 205
3X-RAY DIFFRACTION3A206 - 270
4X-RAY DIFFRACTION4A271 - 383
5X-RAY DIFFRACTION5A384 - 435
6X-RAY DIFFRACTION6A436 - 501
7X-RAY DIFFRACTION7A502 - 583

+
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