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- PDB-6hn0: Complex of Ovine Serum Albumin with diclofenac -

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Basic information

Entry
Database: PDB / ID: 6hn0
TitleComplex of Ovine Serum Albumin with diclofenac
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Ovine serum albumin / Sheep serum albumin / diclofenac / nonsteroidal anti-inflammatory drugs
Function / homology
Function and homology information


enterobactin binding / blood microparticle / lipid binding / 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
ACETATE ION / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / FORMIC ACID / (2S)-2-hydroxybutanedioic acid / MALONATE ION / Albumin
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsTalaj, J.A. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/11/B/ST5/02271 Poland
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Investigation of Diclofenac Binding to Ovine, Caprine, and Leporine Serum Albumins.
Authors: Talaj, J.A. / Zielinski, K. / Bujacz, A.
History
DepositionSep 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / database_2 / diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / entity / entity_src_nat / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _diffrn_detector.details / _diffrn_radiation.monochromator / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity_src_nat.common_name / _pdbx_audit_support.funding_organization / _pdbx_contact_author.address_1 / _pdbx_contact_author.id / _pdbx_contact_author.postal_code / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.label_alt_id_1 / _pdbx_validate_rmsd_angle.label_alt_id_2 / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_work / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand identity
Details: Removing one DIF (diclofenac) molecule and replacing it by LMR - ligand from crystallization solution.
Provider: author / Type: Coordinate replacement
Revision 2.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,26827
Polymers66,4281
Non-polymers2,84026
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-86 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.680, 121.680, 121.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1186-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serum albumin


Mass: 66427.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P14639

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Non-polymers , 7 types, 592 molecules

#2: Chemical
ChemComp-DIF / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / DICLOFENAC


Mass: 296.149 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H11Cl2NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, medication*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: CH2O2
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.9 Å3/Da / Density % sol: 68.8 % / Description: needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: Tacsimate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 58784 / % possible obs: 98.9 % / Redundancy: 9.1 % / Biso Wilson estimate: 45.095 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.59
Reflection shellResolution: 2.12→2.22 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.427 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 7388 / CC1/2: 0.706 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LUF

4luf


Resolution: 2.12→48.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.672 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21377 2941 5 %RANDOM
Rwork0.16476 ---
obs0.16721 55842 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.176 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å20 Å2
2--0.87 Å2-0 Å2
3----2.82 Å2
Refinement stepCycle: 1 / Resolution: 2.12→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 182 566 5393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.9596781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14225.065231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83115897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2531523
X-RAY DIFFRACTIONr_chiral_restr0.1390.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213813
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0213.1092361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9874.652954
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9343.672652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.03729.3358568
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: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 212 -
Rwork0.32 3997 -
obs--95.92 %
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)
11.0369-0.79610.28821.60390.01650.13740.0899-0.0905-0.06210.3351-0.0730.03150.1182-0.0631-0.01690.1865-0.044-0.0320.0611-0.01090.071163.936917.38547.8493
20.18950.0612-0.01080.61150.53720.5858-0.0121-0.17170.0916-0.1261-0.0190.0114-0.14180.03460.03110.1401-0.0084-0.0340.1628-0.07490.126268.686235.086437.4402
32.550.79930.22280.79140.34750.3613-0.0450.3492-0.0238-0.12880.0882-0.0255-0.10220.048-0.04330.1264-0.0309-0.00440.08090.0210.0569.628531.966627.4143
40.44520.2404-0.58430.40080.20191.75710.0360.070.00140.03410.0154-0.02380.004-0.1386-0.05150.09750.0215-0.03140.0627-0.00960.092955.561111.567824.1426
50.25580.30770.48780.50690.67071.3604-0.04490.048-0.1166-0.01260.1077-0.1696-0.09020.1594-0.06280.08370.0076-0.00640.056-0.03130.152669.798412.575520.3614
60.7478-0.3534-0.17110.17770.05820.3814-0.0591-0.0747-0.01460.00020.06320.01540.11050.0135-0.00410.1148-0.04410.00050.07920.00620.087347.03443.7646.8442
72.88911.8188-0.28732.4716-0.03720.2536-0.04550.05650.07680.1490.12810.0925-0.0899-0.1125-0.08260.09660.05330.03950.11920.05040.059339.808110.78739.0966
81.15772.62610.27316.58460.98270.27910.00480.02070.0453-0.1388-0.01460.1252-0.0736-0.03890.00980.0910.0026-0.02010.09430.00490.074642.88926.06165.1802
95.16662.6676-3.75152.0762-1.4853.05110.09880.0620.1383-0.2811-0.03630.214-0.3405-0.1002-0.06250.21870.048-0.01020.0625-0.00980.09843.012541.834720.2947
100.8281-0.4175-0.93960.96760.4951.0941-0.007-0.03710.0051-0.06160.0442-0.0204-0.05270.0314-0.03720.0970.01440.00360.0858-0.01190.073749.892532.670421.1782
110.7967-1.2406-0.29342.40921.20921.3618-0.01150.0504-0.1774-0.0067-0.13510.3104-0.0207-0.03890.14660.03680.01260.02830.0957-0.02070.123235.737829.830923.1708
120.21170.073-0.01850.83910.48460.29880.1098-0.0766-0.0545-0.2047-0.0736-0.0689-0.1591-0.017-0.03610.1599-0.0003-0.00850.0864-0.00920.070544.631252.633428.6961
135.41143.4952.18475.21923.78564.5841-0.20350.3920.2025-0.43820.0910.2455-0.32220.1390.11250.22380.050.00320.06730.02480.033243.402162.184224.5003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 106
2X-RAY DIFFRACTION2A107 - 147
3X-RAY DIFFRACTION3A148 - 198
4X-RAY DIFFRACTION4A199 - 250
5X-RAY DIFFRACTION5A251 - 295
6X-RAY DIFFRACTION6A296 - 336
7X-RAY DIFFRACTION7A337 - 366
8X-RAY DIFFRACTION8A367 - 398
9X-RAY DIFFRACTION9A399 - 417
10X-RAY DIFFRACTION10A418 - 468
11X-RAY DIFFRACTION11A469 - 497
12X-RAY DIFFRACTION12A498 - 537
13X-RAY DIFFRACTION13A538 - 583

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