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- PDB-9kqk: Crystal structure of HSA in complex with AmpHecy -

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Basic information

Entry
Database: PDB / ID: 9kqk
TitleCrystal structure of HSA in complex with AmpHecy
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / fluorogen-activating / Plane conformation / Non-covalent bonding / Confinement effect
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 / cellular response to starvation / fatty acid binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsChen, X. / Shi, M.W. / Ge, Y.H. / Fang, B. / Li, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21807088 China
CitationJournal: Adv Mater / Year: 2025
Title: Fluorogen-Activating Human Serum Albumin for Mitochondrial Nanoscale Imaging.
Authors: Fang, B. / Bai, H. / Zhang, J. / Shi, M. / Ge, Y. / Wang, L. / Li, P. / Ding, Y. / Zhang, S. / Zhang, C. / Qu, Y. / Zhang, D. / Peng, B. / Chen, X. / Li, L. / Huang, W.
History
DepositionNov 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,4733
Polymers138,9392
Non-polymers5341
Water00
1
A: Albumin


Theoretical massNumber of molelcules
Total (without water)69,4701
Polymers69,4701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0032
Polymers69,4701
Non-polymers5341
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.163, 58.406, 95.479
Angle α, β, γ (deg.)74.45, 88.13, 76.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Albumin


Mass: 69469.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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-A1EGK / 2-[[6-[5-[(~{E})-2-[1-[2-[2-(2-methoxyethoxy)ethoxy]ethyl]pyridin-1-ium-4-yl]ethenyl]thiophen-2-yl]naphthalen-2-yl]-methyl-amino]ethanol


Mass: 533.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H37N2O4S / Feature type: SUBJECT OF INVESTIGATION
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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 0.05 M KH2PO4, pH 7.0, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.05→91.93 Å / Num. obs: 22166 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.09 / Rrim(I) all: 0.173 / Net I/σ(I): 5.7
Reflection shellResolution: 3.05→3.26 Å / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2 / Num. unique obs: 4016 / CC1/2: 0.863 / Rpim(I) all: 0.32 / Rrim(I) all: 0.603 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→91.93 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.812 / SU B: 46.173 / SU ML: 0.792 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3403 1150 5.2 %RANDOM
Rwork0.29006 ---
obs0.29252 20962 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.07 Å2
Baniso -1Baniso -2Baniso -3
1-6.63 Å2-3.35 Å2-5.51 Å2
2---3.76 Å23.49 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 3.05→91.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9096 0 38 0 9134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139345
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178683
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.65712621
X-RAY DIFFRACTIONr_angle_other_deg1.4131.58720273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11151140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98523.554484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.717151716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2821546
X-RAY DIFFRACTIONr_chiral_restr0.0580.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021854
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_it3.4076.4564572
X-RAY DIFFRACTIONr_mcbond_other3.4026.4554571
X-RAY DIFFRACTIONr_mcangle_it5.6419.6735708
X-RAY DIFFRACTIONr_mcangle_other5.6419.6745709
X-RAY DIFFRACTIONr_scbond_it2.8856.5734773
X-RAY DIFFRACTIONr_scbond_other2.8856.5744774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9689.7936914
X-RAY DIFFRACTIONr_long_range_B_refined8.41176.77510579
X-RAY DIFFRACTIONr_long_range_B_other8.4176.77910580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 88 -
Rwork0.392 1529 -
obs--98.24 %

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