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- PDB-9sc5: Complex of Ovine Serum Albumin with Oxacillin -

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Basic information

Entry
Database: PDB / ID: 9sc5
TitleComplex of Ovine Serum Albumin with Oxacillin
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / serum albumin / oxacillin
Function / homology
Function and homology information


enterobactin binding / blood microparticle / lipid binding / metal ion binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
: / ACETATE ION / FORMIC ACID / MALONATE ION / NITRIC OXIDE / SUCCINIC ACID / Albumin
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDuszynski, K. / Talaj, J.A. / Bujacz, A. / Bujacz, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2013/11/B/T5/02271 Poland
CitationJournal: Int J Mol Sci / Year: 2026
Title: Structural Interactions of beta-Lactam Antibiotics with Mammalian Serum Albumins.
Authors: Duszynski, K. / Sekula, B. / Talaj, J. / Bujacz, A.
History
DepositionAug 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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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)67,85518
Polymers66,4281
Non-polymers1,42717
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer assembly generated by PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint2 kcal/mol
Surface area26960 Å2
Unit cell
Length a, b, c (Å)121.450, 121.450, 122.229
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-889-

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, 264 molecules

#2: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#3: Chemical ChemComp-A1JLX / (2~{R},5~{R},6~{S})-3,3-dimethyl-6-[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonylamino]-7-oxidanylidene-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid


Mass: 401.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H6O4
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.94 Å3/Da / Density % sol: 68.77 % / Description: hexagonal needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25 / Details: 80% Tacsimate at pH 7.25 and 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 46557 / % possible obs: 99.5 % / Redundancy: 6.57 % / CC1/2: 0.998 / Net I/σ(I): 13.24
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 6.68 % / Mean I/σ(I) obs: 2.31 / Num. unique obs: 7387 / CC1/2: 0.787 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.31 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.296 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21369 1164 2.5 %RANDOM
Rwork0.16399 ---
obs0.16519 45393 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.988 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å2-0 Å2
2--0.82 Å2-0 Å2
3----2.65 Å2
Refinement stepCycle: 1 / Resolution: 2.3→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 97 247 4989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0124867
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0821.8726573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.099522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35810872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1410.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023671
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_it3.1283.5122344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2556.32922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.9254.1122523
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.15538.667302
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: 2.3→2.44 Å
RfactorNum. reflection% reflection
Rfree0.267 83 -
Rwork0.247 3272 -
obs--98.9 %
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)
10.8052-0.56780.18382.0981-0.38110.6851-0.0108-0.1672-0.06880.40370.068-0.05880.0462-0.0734-0.05730.1136-0.0122-0.03910.05070.00960.0364.21317.33347.8215
21.2485-0.3255-0.68261.38420.54011.384-0.0441-0.0590.2257-0.080.0859-0.1831-0.22630.0486-0.04190.064-0.0032-0.02710.0091-0.01970.068968.793235.046437.5201
31.72330.08630.56911.06980.27030.8329-0.15040.26630.0092-0.1470.1215-0.2252-0.19250.12820.02890.1072-0.0361-0.00110.0527-0.02050.062170.06532.040127.3183
41.0337-0.0012-0.01440.1739-0.21871.1469-0.0154-0.0446-0.15080.01360.0504-0.05360.1125-0.0501-0.0350.06860.0021-0.02490.0164-0.00950.052656.068311.547923.8979
50.95420.17651.18241.33090.57883.049-0.03240.113-0.1498-0.09110.1498-0.1588-0.05320.2262-0.11740.013-0.00530.00110.0349-0.04150.073270.212112.635320.1588
62.7969-0.7401-0.7590.3511-0.11621.1727-0.10660.0188-0.21740.02230.06970.07640.0856-0.06540.0370.079-0.0180.01460.05150.00650.020947.42213.58956.6804
73.60122.4652-0.43293.2077-0.26360.6165-0.06090.15690.01040.05320.12310.195-0.0629-0.1379-0.06220.01640.01280.02020.03580.01460.031340.104410.58049.0688
80.8992.25750.23766.77041.13970.3325-0.01160.04950.0501-0.14480.01670.1026-0.0558-0.047-0.0050.03660.0006-0.01980.05360.01610.023542.814925.9095.0191
93.86990.6068-2.92461.273-0.1962.27220.03790.10060.0286-0.2242-0.02190.0444-0.0964-0.093-0.01590.08790.0408-0.0150.0361-0.01280.0142.254541.552620.1325
100.2326-0.2233-0.53540.29380.38631.6294-0.0041-0.06120.0405-0.02330.0423-0.088-0.10310.1136-0.03810.0710.0080.01810.0483-0.00620.038249.617832.615920.9249
112.0812-1.5149-1.28382.59371.87891.8216-0.04940.0608-0.1617-0.056-0.15820.2677-0.1114-0.08630.20750.02320.0034-0.00880.0415-0.02690.032535.697129.535722.9671
120.48220.0316-0.08541.30610.82480.56540.07210.0371-0.0595-0.26120.0148-0.1566-0.2222-0.0013-0.08690.13930.010.02030.0316-0.01230.026544.051252.448428.4178
131.81480.92290.96941.54111.9362.6009-0.20640.23310.2896-0.4520.10930.1013-0.43610.19820.09710.30040.0386-0.01760.08040.05290.058242.518262.200124.4307
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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