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- PDB-9q8u: Complex of Caprine Serum Albumin with Cefaclor -

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Basic information

Entry
Database: PDB / ID: 9q8u
TitleComplex of Caprine Serum Albumin with Cefaclor
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / serum albumin / cefaclor
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
Cefaclor / CITRIC ACID / Albumin
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDuszynski, K. / Talaj, 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: 2026
Title: Structural Interactions of beta-Lactam Antibiotics with Mammalian Serum Albumins.
Authors: Duszynski, K. / Sekula, B. / Talaj, J. / Bujacz, A.
History
DepositionFeb 25, 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: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1074
Polymers66,3551
Non-polymers7523
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint4 kcal/mol
Surface area27300 Å2
Unit cell
Length a, b, c (Å)42.846, 67.580, 214.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Albumin


Mass: 66354.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: B3VHM9
#2: Chemical ChemComp-8XI / Cefaclor / (6R,7R)-7-[[(2R)-2-azanyl-2-phenyl-ethanoyl]amino]-3-chloranyl-8-oxidanylidene-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid


Mass: 367.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14ClN3O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O
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: 1.85 Å3/Da / Density % sol: 33.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Jeffamine ED-2001, Ba2+, Na2+, Cl-, Citrate buffer

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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: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.7→42.04 Å / Num. obs: 60997 / % possible obs: 98 % / Redundancy: 3.2 % / Biso Wilson estimate: 41.246 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.049 / Net I/σ(I): 18.61
Reflection shellResolution: 1.77→1.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 9378 / CC1/2: 0.635 / Rrim(I) all: 0.707 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→42.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.408 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22758 2101 3.4 %RANDOM
Rwork0.17999 ---
obs0.18163 59485 98.01 %-
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: 41.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.22 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.76→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 50 571 5260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0141.9876827
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7175638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05624.873236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73315933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0891525
X-RAY DIFFRACTIONr_chiral_restr0.1370.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213808
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_it1.2662.3012392
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.993.4393004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8942.52621
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.95421.1318587
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: 1.762→1.808 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 146 -
Rwork0.291 4115 -
obs--93.55 %
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)
11.96820.33320.65452.88390.62172.0447-0.17360.36680.4262-0.7327-0.1850.6327-0.5915-0.11210.35860.32240.0631-0.2380.11340.02740.24232.377520.1121-36.1089
23.1937-0.3122-1.28261.65540.53462.8395-0.170.4875-0.0952-0.6895-0.04290.44670.0752-0.09670.21280.3837-0.0049-0.13630.2695-0.00520.15858.73381.7272-42.9618
32.84420.7661-0.71812.16850.13822.1736-0.07140.3204-0.2656-0.5034-0.05430.16530.18190.21490.12570.22470.0603-0.01710.2072-0.00690.088815.2808-2.0418-35.5351
40.4541-0.03560.71990.50010.03231.3463-0.0489-0.04740.1148-0.007-0.04830.0959-0.05440.01030.09720.0824-0.00260.00080.14040.00290.20467.9428.1122-13.7133
51.0241-0.45050.62792.5247-0.40381.11880.02810.00960.0978-0.2045-0.0042-0.0781-0.08310.1486-0.02390.0624-0.00870.00020.10720.02140.125121.88967.7637-18.6843
62.8644-1.4281-1.2551.47030.55662.7644-0.05-0.03550.00010.13460.0110.0558-0.10510.12040.03890.0627-0.005-0.00140.10820.0010.11929.80862.68855.1431
71.6314-0.2009-1.34851.56830.68723.0673-0.0673-0.0167-0.10680.0776-0.00250.2586-0.0253-0.10020.06980.0510.03230.0130.11180.00580.13351.4214-2.99873.2133
80.0749-0.2062-0.22772.80113.35545.3042-0.0483-0.0332-0.09890.12660.05290.09210.20550.0108-0.00450.10.02480.02810.11120.00950.18043.9007-17.0222-4.5402
92.96980.0580.19340.82540.42441.5093-0.04060.00450.0626-0.0090.0063-0.02050.1162-0.08120.03430.1159-0.02220.02210.1475-0.03720.1098-6.5251-20.3599-23.6292
102.1185-0.18550.2220.6040.23450.65130.04340.14380.1165-0.14990.0011-0.07310.03940.0327-0.04450.0734-0.00580.03030.1174-0.00510.13930.694-11.4776-22.0056
111.77010.15060.67661.0192-0.01340.97580.0649-0.01180.02010.1113-0.088-0.01910.0475-0.09110.02310.0536-0.01410.00690.1433-0.00280.1683-11.5334-10.7836-14.8458
122.1852-0.8895-0.69191.295-0.40413.94360.11750.4337-0.0768-0.29020.03180.24820.1733-0.1591-0.14930.2479-0.018-0.04730.2169-0.01540.0839-10.7925-23.7066-36.0213
132.60851.2873-1.36540.90810.2246.0394-0.02150.3336-0.1293-0.08870.0809-0.06370.5575-0.2753-0.05950.29580.0737-0.04470.1105-0.01780.0159-11.0015-33.884-38.1194
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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