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- PDB-9qch: Complex of Ovine Serum Albumin with Cephalosporin C -

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Basic information

Entry
Database: PDB / ID: 9qch
TitleComplex of Ovine Serum Albumin with Cephalosporin C
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / serum albumin / cephalosporin
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 / Chem-CSC / FORMIC ACID / MALONATE ION / MYRISTIC ACID / NITRIC OXIDE / SUCCINIC ACID / Albumin
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 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
DepositionMar 4, 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)68,53229
Polymers66,4281
Non-polymers2,10428
Water8,863492
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint1 kcal/mol
Surface area26480 Å2
Unit cell
Length a, b, c (Å)120.310, 120.310, 123.019
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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 , 8 types, 520 molecules

#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MLI / MALONATE ION


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


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#7: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#8: Chemical ChemComp-CSC / 4-(3-ACETOXYMETHYL-2-CARBOXY-8-OXO-5-THIA-1-AZA-BICYCLO[4.2.0]OCT-2-EN-7-YLCARBAMOYL)-1-CARBOXY-BUTYL-AMMONIUM / CEPHALOSPORIN C


Mass: 416.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N3O8S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 3.87 Å3/Da / Density % sol: 68.28 % / Description: Hexagonal 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: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2016
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.198→48 Å / Num. obs: 52635 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.113 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 8324 / CC1/2: 0.724 / Rrim(I) all: 0.935 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.198→47.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.862 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20868 1316 2.5 %RANDOM
Rwork0.15806 ---
obs0.15934 51319 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20.38 Å20 Å2
2--0.76 Å2-0 Å2
3----2.48 Å2
Refinement stepCycle: 1 / Resolution: 2.198→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 141 492 5263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124938
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.8676653
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.451528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07510890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023714
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_it4.5554.6012354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.7338.2392938
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.4795.2672584
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.275547780
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: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 94 -
Rwork0.275 3672 -
obs--98.18 %
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)
10.8863-0.84950.5722.6087-0.13580.4908-0.05-0.2189-0.04460.42430.0977-0.09590.024-0.1641-0.04770.1460.0062-0.04510.07380.01650.018763.900117.723547.6168
21.2714-0.476-0.87240.80630.37631.114-0.0181-0.10560.1219-0.020.12-0.2297-0.24010.0517-0.1020.15320.0152-0.0320.0353-0.05350.125768.405235.113537.1309
32.9062.09620.47042.11260.25060.712-0.20640.3236-0.0886-0.1510.1725-0.1187-0.240.08520.03390.1221-0.0362-0.01970.0503-0.01570.048369.607632.125326.9956
40.4966-0.03410.53950.40520.30781.41230.0238-0.1065-0.1212-0.04160.054-0.0519-0.0512-0.0889-0.07780.09780.0077-0.0190.03190.01170.075455.427111.540723.7384
51.23810.69061.89020.95221.11794.076-0.05070.1734-0.2848-0.10070.1989-0.2488-0.17060.3637-0.14830.0775-0.01780.01870.0509-0.03330.158369.695812.746819.824
63.8482-0.3698-1.3330.08080.09851.4222-0.18970.0329-0.12420.02840.06680.04210.1134-0.01090.12290.1335-0.00930.05170.08780.03690.042746.793.34896.6701
74.06712.08480.06553.0876-0.56481.2371-0.21260.2153-0.0470.16150.37650.0491-0.1787-0.2576-0.16390.07650.04760.05810.08010.04240.075439.325210.25518.8929
80.93811.94080.16465.59441.03580.3392-0.04310.07480.0672-0.13090.05830.1139-0.0351-0.0402-0.01520.10510.0032-0.01310.09560.02560.098141.994225.57234.8998
94.19850.8719-2.88742.1955-0.17432.10350.1789-0.016-0.0719-0.3135-0.1976-0.0106-0.2563-0.05670.01870.16540.09130.0240.0656-0.00090.040941.474741.397920.1388
100.6278-0.1809-0.56980.56540.14371.0225-0.0291-0.07090.0425-0.08980.0792-0.1453-0.0932-0.0021-0.05010.0830.0190.02620.0456-0.02350.039348.910432.540720.7701
111.4102-1.0218-0.86681.7320.431.7129-0.00670.0557-0.2103-0.0805-0.1640.2048-0.0553-0.02020.17070.0590.0333-0.00940.0736-0.04580.055635.089329.279723.1467
120.6560.96530.18422.51181.36651.4130.1216-0.112-0.2115-0.468-0.0215-0.3691-0.49480.0606-0.10010.3895-0.0551-0.01420.09180.00670.081943.220452.360228.399
132.7172.54883.09124.93815.71516.9559-0.29030.16820.3364-0.49080.04750.3462-0.57210.02320.24280.39880.0291-0.01660.02670.04810.131441.569462.126624.5805
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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