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- PDB-2vdb: Structure of human serum albumin with S-naproxen and the GA module -

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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


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / 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 / 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
Albumin-binding domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Serum Albumin; Chain A, Domain 1 - #10 / GA-like domain / GA-like domain / 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) / Serum Albumin; Chain A, Domain 1 - #10 / GA-like domain / GA-like domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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.

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Experimental details

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Experiment

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

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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

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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

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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

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