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- PDB-9jgf: Crystal structure of Human Serum Albumin (HSA) complexed with Ebselen -

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Basic information

Entry
Database: PDB / ID: 9jgf
TitleCrystal structure of Human Serum Albumin (HSA) complexed with Ebselen
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Human Serum Albumin / Ebselen / Drug Delivery / Pharmacodynamics
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / 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 / platelet alpha granule lumen / fatty acid binding / cellular response to starvation / 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 / endoplasmic reticulum lumen / copper ion binding / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / DNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / 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
N-phenyl-2-selanylbenzamide / MYRISTIC ACID / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaji, S. / Shukla, M. / Yadav, V.K. / Bhattacharyya, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)SRG/2020/001353 India
CitationJournal: To Be Published
Title: Crystal structure of Human Serum Albumin (HSA) complexed with Ebselen
Authors: Maji, S. / Shukla, M. / Yadav, V.K. / Bhattacharyya, S.
History
DepositionSep 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: 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
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,70628
Polymers138,9392
Non-polymers5,76626
Water7,512417
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,03012
Polymers69,4701
Non-polymers2,56011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30180 Å2
MethodPISA
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,67616
Polymers69,4701
Non-polymers3,20715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-8 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.276, 93.001, 95.059
Angle α, β, γ (deg.)74.670, 89.820, 79.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 316 or resid 318 through 584 or resid 601))
d_2ens_1(chain "B" and (resid 3 through 316 or resid 318 through 584 or resid 601))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISCYSCYSAA3 - 31627 - 340
d_12ASNASNGLYGLYAA318 - 584342 - 608
d_139JT9JT9JT9JTAC601
d_21HISHISCYSCYSBB3 - 31627 - 340
d_22ASNASNGLYGLYBB318 - 584342 - 608
d_239JT9JT9JT9JTBN601

NCS oper: (Code: givenMatrix: (0.9998360641, 0.0162115504708, 0.0080641525364), (0.0161406982121, -0.999831225182, 0.00877490806774), (0.00820504637554, -0.00864330849286, -0.999928982694)Vector: 18. ...NCS oper: (Code: given
Matrix: (0.9998360641, 0.0162115504708, 0.0080641525364), (0.0161406982121, -0.999831225182, 0.00877490806774), (0.00820504637554, -0.00864330849286, -0.999928982694)
Vector: 18.4245957748, 69.3945320105, -91.4211604832)

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Components

#1: Protein Albumin


Mass: 69469.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Covalent modification at Cys34 position by Ebselen.
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG 3350, Potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.2→45.79 Å / Num. obs: 59201 / % possible obs: 93.7 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.019 / Rrim(I) all: 0.037 / Net I/σ(I): 30.9 / Num. measured all: 226705
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 92.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.059 / Num. measured all: 32467 / Num. unique obs: 8520 / CC1/2: 0.996 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I) obs: 18.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→31.58 Å / Cross valid method: FREE R-VALUE / σ(F): 5.61 / Phase error: 32.2387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 2944 5.34 %RANDOM
Rwork0.2196 56034 --
obs0.2251 59198 93.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.72 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9260 0 394 417 10071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00389819
X-RAY DIFFRACTIONf_angle_d1.01113128
X-RAY DIFFRACTIONf_chiral_restr0.03871415
X-RAY DIFFRACTIONf_plane_restr0.0051687
X-RAY DIFFRACTIONf_dihedral_angle_d11.49771520
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.959666881996 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.37091440.28862815X-RAY DIFFRACTION88.16
2.24-2.280.33471740.27872715X-RAY DIFFRACTION85.51
2.28-2.320.31151280.28062777X-RAY DIFFRACTION88.58
2.32-2.370.30211390.27592784X-RAY DIFFRACTION87.71
2.37-2.420.28941500.26772761X-RAY DIFFRACTION88.07
2.42-2.480.331330.26072768X-RAY DIFFRACTION88.77
2.48-2.540.29631330.26212871X-RAY DIFFRACTION89.08
2.54-2.610.29911390.26332789X-RAY DIFFRACTION89.36
2.61-2.680.30591550.25432796X-RAY DIFFRACTION88.71
2.68-2.770.26111470.25122838X-RAY DIFFRACTION89.81
2.77-2.870.27321640.24812778X-RAY DIFFRACTION88.67
2.87-2.990.31181280.24672882X-RAY DIFFRACTION90.29
2.99-3.120.3211580.23892788X-RAY DIFFRACTION88.93
3.12-3.290.30081500.22872841X-RAY DIFFRACTION89.76
3.29-3.490.30291550.21612858X-RAY DIFFRACTION89.9
3.49-3.760.26121470.19832831X-RAY DIFFRACTION90.33
3.76-4.140.22681690.18082834X-RAY DIFFRACTION90.05
4.14-4.730.21381640.16552860X-RAY DIFFRACTION90.05
4.74-5.960.24161350.18532854X-RAY DIFFRACTION91.04
5.96-31.580.20981330.18442813X-RAY DIFFRACTION88.91
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)
10.1943616256420.224254690138-0.05511840076850.766102622977-0.3740334443350.43472724263-0.07481885455710.103611226974-0.00844152235325-0.2005342966290.0579195989725-0.01735744516030.106655600354-0.0466575066998-0.007651242260550.114778713374-0.01521326668390.0539078197190.249169828339-0.0831007415890.08600530781267.6557710311826.4931980686-19.7428419317
20.170465363631-0.2011683829170.09541285769320.721292402901-0.4338847467590.452564958267-0.0706833907951-0.0905632708410.011890483460.1747863296290.0273254238689-0.0362689354261-0.0957604965508-0.004286927005990.02234236548340.1152137877240.01018510317110.00535461963760.247900425353-0.07664001366790.10376608899926.344528098642.8637322089-71.8971336522
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 3 - 601 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain A and resseq 3:601)AA - B
22(chain B and resseq 3:601)BC - D

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