[English] 日本語
Yorodumi
- PDB-2vdb: Structure of human serum albumin with S-naproxen and the GA module -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vdb
TitleStructure of human serum albumin with S-naproxen and the GA module
Components
  • PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN
  • SERUM ALBUMIN
KeywordsPROTEIN BINDING / LIPID-BINDING / METAL-BINDING / PEPTIDOGLYCAN-ANCHOR / BACTERIAL ALBUMIN-BINDING / DISEASE MUTATION / THREE-HELIX BUNDLE / GA MODULE / DRUG BINDING / GLYCOPROTEIN / CLEAVAGE ON PAIR OF BASIC RESIDUES / HUMAN SERUM ALBUMIN / SECRETED / NAPROXEN / CELL WALL / GLYCATION
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / platelet alpha granule lumen / cellular response to starvation / 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
Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / GA-like domain / GA-like domain / Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site ...Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / GA-like domain / GA-like domain / 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 / Immunoglobulin/albumin-binding domain superfamily / Serum Albumin; Chain A, Domain 1 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DECANOIC ACID / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / Albumin / Peptostreptococcal albumin-binding protein
Similarity search - Component
Biological speciesPEPTOSTREPTOCOCCUS MAGNUS (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsLejon, S. / Cramer, J.F. / Nordberg, P.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structural Basis for the Binding of Naproxen to Human Serum Albumin in the Presence of Fatty Acids and the Ga Module.
Authors: Lejon, S. / Cramer, J.F. / Nordberg, P.A.
History
DepositionOct 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERUM ALBUMIN
B: PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3909
Polymers72,1272
Non-polymers1,2647
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-15.6 kcal/mol
Surface area36130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)190.507, 49.462, 79.933
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein SERUM ALBUMIN / HUMAN SERUM ALBUMIN


Mass: 65917.484 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-608 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: SERUM / References: UniProt: P02768
#2: Protein PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN / GA MODULE


Mass: 6209.128 Da / Num. of mol.: 1 / Fragment: RESIDUES 213-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PEPTOSTREPTOCOCCUS MAGNUS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q51911
#3: Chemical
ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H20O2
#4: Chemical ChemComp-NPS / (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid / NAPROXEN


Mass: 230.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14O3 / Comment: antiinflammatory*YM
Has protein modificationY
Nonpolymer details(NPX): S-NAPROXEN.
Sequence detailsSTRUCTURE CONTAINS RESIDUES 30 TO 608 OF THE UNIPROT ENTRY, CORRESPONDING TO RESIDUES 6 TO 584 IN ...STRUCTURE CONTAINS RESIDUES 30 TO 608 OF THE UNIPROT ENTRY, CORRESPONDING TO RESIDUES 6 TO 584 IN THE BIOLOGICAL MOLECULE. THE GA MODULE IS RESIDUES 213 TO 265 OF THE UNIPROT ENTRY. THE STRUCTURE ALSO CONTAINS 2 N-TERMINAL TAG RESIDUES.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 26-32% PEG 3350, 50 MM POTASSIUM PHOSPHATE, 0.1 M AMMONIUM PHOSPHATE/POTASSIUM PHOSPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 17, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→80.32 Å / Num. obs: 24847 / % possible obs: 99 % / Observed criterion σ(I): 3.7 / Redundancy: 6.33 % / Biso Wilson estimate: 58.71 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.22
Reflection shellResolution: 2.5→2.52 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.95 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1E7E AND 1TF0

1e7e

1tf0


Resolution: 2.52→94.92 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.905 / SU B: 24.495 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.661 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1273 5.14 %RANDOM
Rwork0.234 ---
obs0.236 24846 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.891 Å20 Å20.198 Å2
2--2.076 Å20 Å2
3----0.164 Å2
Refinement stepCycle: LAST / Resolution: 2.52→94.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 89 0 4872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224977
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9746742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13324.502211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69215792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9051523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023732
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2650.22553
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23461
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2210
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0330.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.86323230
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38535024
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.86521949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.27731718
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: 11.17→94.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 17
Rwork0.293 264
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)
16.4372-0.4552-1.28253.2271-1.22288.1325-0.13091.6769-0.8563-0.18770.00160.4563-0.097-1.45550.1293-0.14150.0693-0.11210.5611-0.40950.227910.335-10.88316.489
27.1002-0.3121-2.01750.9258-0.01022.4077-0.01730.54640.06410.062-0.13790.4003-0.0172-0.60880.1553-0.1340.034-0.0567-0.1739-0.1208-0.265332.281-5.63820.257
36.9941-0.53070.58483.52970.90632.9487-0.0637-0.0170.3423-0.0756-0.1392-0.4597-0.16410.12180.203-0.25380.0603-0.0426-0.3336-0.0263-0.397949.043-1.17521.346
410.4763-3.7031-8.04931.31312.77467.3764-0.1985-0.3060.36330.10540.0528-0.02550.23160.00740.1456-0.13140.0078-0.0958-0.2486-0.1444-0.067835.4279.45335.941
59.8225-0.1534-4.16282.45880.58724.57480.4977-0.58240.05860.2891-0.35940.2859-0.0886-0.551-0.1382-0.0968-0.066-0.02590.0395-0.1285-0.04715.15614.4350.049
65.1466-1.3985-0.88529.50341.08715.41940.17281.35790.296-0.5846-0.1146-0.4366-0.03450.2623-0.0581-0.13610.03490.03230.13130.0484-0.368153.256-5.0865.25
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 170
2X-RAY DIFFRACTION2A174 - 280
3X-RAY DIFFRACTION3A283 - 336
4X-RAY DIFFRACTION4A343 - 466
5X-RAY DIFFRACTION5A471 - 584
6X-RAY DIFFRACTION6B1 - 53

+
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