[English] 日本語
Yorodumi
- PDB-4z69: Human serum albumin complexed with palmitic acid and diclofenac -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z69
TitleHuman serum albumin complexed with palmitic acid and diclofenac
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Diclofenac / Complex
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / 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
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / PENTADECANOIC ACID / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.187 Å
AuthorsZhang, Y. / Yang, F.
CitationJournal: Chem.Biol.Drug Des. / Year: 2015
Title: Structural basis of non-steroidal anti-inflammatory drug diclofenac binding to human serum albumin.
Authors: Zhang, Y. / Lee, P. / Liang, S. / Zhou, Z. / Wu, X. / Yang, F. / Liang, H.
History
DepositionApr 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serum albumin
I: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,80716
Polymers133,1422
Non-polymers3,66514
Water3,189177
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7009
Polymers66,5711
Non-polymers2,1288
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1077
Polymers66,5711
Non-polymers1,5366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.396, 95.003, 96.339
Angle α, β, γ (deg.)105.00, 101.45, 89.97
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Pichia kudriavzevii (yeast) / References: UniProt: P02768
#2: Chemical
ChemComp-F15 / PENTADECANOIC ACID


Mass: 242.397 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H30O2
#3: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical
ChemComp-DIF / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / DICLOFENAC


Mass: 296.149 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11Cl2NO2 / Comment: antiinflammatory, medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, potassium phosphate, glycerol, DMSO / PH range: 7.0-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.187→45.817 Å / % possible obs: 98 % / Redundancy: 3.2 % / Net I/σ(I): 2.1

-
Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data scaling
PHENIXphasing
PHENIX1.6_289refinement
RefinementResolution: 2.187→45.817 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 37.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 3159 5.1 %
Rwork0.2251 --
obs0.2287 61968 93.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.838 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4679 Å2-0.3871 Å2-0.0086 Å2
2---4.2655 Å20.3625 Å2
3---7.7334 Å2
Refinement stepCycle: LAST / Resolution: 2.187→45.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8896 0 242 177 9315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089344
X-RAY DIFFRACTIONf_angle_d1.22412573
X-RAY DIFFRACTIONf_dihedral_angle_d18.9123403
X-RAY DIFFRACTIONf_chiral_restr0.0781410
X-RAY DIFFRACTIONf_plane_restr0.0061629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1874-2.26560.39592340.31554754X-RAY DIFFRACTION74
2.2656-2.35630.37592950.29865126X-RAY DIFFRACTION83
2.3563-2.46350.3632870.28315719X-RAY DIFFRACTION90
2.4635-2.59340.37163260.28156074X-RAY DIFFRACTION96
2.5934-2.75590.38093050.30016244X-RAY DIFFRACTION98
2.7559-2.96860.36953480.28516161X-RAY DIFFRACTION98
2.9686-3.26730.33013490.26056152X-RAY DIFFRACTION98
3.2673-3.73990.31713360.22556223X-RAY DIFFRACTION98
3.7399-4.71110.22963360.17386211X-RAY DIFFRACTION98
4.7111-45.82680.23553430.1796145X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 10.1822 Å / Origin y: 23.0572 Å / Origin z: -15.7876 Å
111213212223313233
T0.2347 Å20.0057 Å20.0037 Å2-0.2475 Å2-0.0057 Å2--0.2907 Å2
L0.0097 °20.03 °2-0.0159 °2-0.1885 °2-0.0697 °2--0.1322 °2
S0.0046 Å °-0.0017 Å °-0.0329 Å °0.0057 Å °-0.025 Å °-0.1133 Å °0.0001 Å °-0.0224 Å °0.0177 Å °
Refinement TLS groupSelection details: ALL

+
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