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- PDB-7wz9: HSA-In agent complex -

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Basic information

Entry
Database: PDB / ID: 7wz9
TitleHSA-In agent complex
ComponentsSerum albumin
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / 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 / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / 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
Chem-7Q8 / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsZhang, Z.L. / Yang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077021 China
CitationJournal: To Be Published
Title: Structure of HSA-In agent complex
Authors: Zhang, Z.L. / Yang, F.
History
DepositionFeb 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1618
Polymers66,2151
Non-polymers1,9467
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.900, 38.530, 95.620
Angle α, β, γ (deg.)90.000, 105.400, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
/ NCS domain segments: (Refine code: 4 )
NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2given(1), (1), (1)

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Components

#1: Protein Serum albumin /


Mass: 66214.844 Da / Num. of mol.: 1
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: Escherichia coli (E. coli) / References: UniProt: P02768
#2: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-7Q8 / 16-chloranyl-~{N},~{N}-dimethyl-15-thia-1$l^{4},12$l^{4},13-triaza-16$l^{4}-indatetracyclo[8.6.0.0^{2,7}.0^{12,16}]hexadeca-1,3,5,7,9,11,13-heptaen-14-amine


Mass: 407.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13ClInN4S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG3350, 50 mM potassium phosphate (pH 7.5), 5% glycerol, 4% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 8, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 16176 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.5
Reflection shellResolution: 2.83→2.88 Å / Rmerge(I) obs: 0.035 / Num. unique obs: 717

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJ5

1bj5


Resolution: 2.83→92.19 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 28.259 / SU ML: 0.514 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.286 773 4.8 %RANDOM
Rwork0.2231 ---
obs0.2279 15391 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.08 Å2 / Biso mean: 18.811 Å2 / Biso min: 54.56 Å2
Baniso -1Baniso -2Baniso -3
1-10.21 Å20 Å25.23 Å2
2---3.9 Å2-0 Å2
3----7.98 Å2
Refinement stepCycle: final / Resolution: 2.83→92.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 121 0 4564
Biso mean--114.19 --
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194667
X-RAY DIFFRACTIONr_bond_other_d0.0020.024276
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9866313
X-RAY DIFFRACTIONr_angle_other_deg1.03539929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2595580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62824.596198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.51715748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9581521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215149
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02912
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 8538 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

TypeWeight position
MEDIUM POSITIONAL0.5
MEDIUM THERMAL2
LS refinement shellResolution: 2.83→2.903 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.519 75 -
Rwork0.321 1114 -
all-1189 -
obs--99.41 %

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