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- PDB-8j8e: Human serum albumin-palladium(II) agent complex -

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Basic information

Entry
Database: PDB / ID: 8j8e
TitleHuman serum albumin-palladium(II) agent complex
ComponentsSerum albumin
KeywordsHORMONE / Complex
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 / copper ion binding / endoplasmic reticulum lumen / endoplasmic reticulum / Golgi apparatus / 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
PALMITIC ACID / : / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, Z.L. / Zhang, J.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077021 China
CitationJournal: To Be Published
Title: Structure of human serum albumin palladium(II) agent complex
Authors: Zhang, Z.L. / Zhang, J.Z.
History
DepositionMay 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
I: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,99916
Polymers133,1422
Non-polymers3,85714
Water3,171176
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5008
Polymers66,5711
Non-polymers1,9287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5008
Polymers66,5711
Non-polymers1,9287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.356, 92.706, 95.345
Angle α, β, γ (deg.)74.89, 89.73, 79.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serum albumin


Mass: 66571.219 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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02768
#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-U5U / ~{N},~{N}-dimethyl-7-phenyl-3-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-palladatricyclo[6.4.0.0^{2,6}]dodeca-1(12),4,6,8,10-pentaen-4-amine


Mass: 389.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N4PdS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 3350, 0.05M PB 7.0, 5% G, 5% 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: Jan 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→91.96 Å / Num. obs: 42319 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 4.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.177 / Num. unique obs: 3143

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata scaling
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→91.96 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.86 / SU B: 18.748 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R: 1.136 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31619 2130 5 %RANDOM
Rwork0.24973 ---
obs0.2531 40171 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.276 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-0.26 Å2-0.17 Å2
2--2.82 Å2-1.45 Å2
3----2.06 Å2
Refinement stepCycle: 1 / Resolution: 2.5→91.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8886 0 244 176 9306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199336
X-RAY DIFFRACTIONr_bond_other_d0.0020.028552
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.98612624
X-RAY DIFFRACTIONr_angle_other_deg1.016319856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74851160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83224.596396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.165151496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8781542
X-RAY DIFFRACTIONr_chiral_restr0.0780.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110302
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021824
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_it2.634.7544646
X-RAY DIFFRACTIONr_mcbond_other2.6294.7534645
X-RAY DIFFRACTIONr_mcangle_it4.2447.1265804
X-RAY DIFFRACTIONr_mcangle_other4.2447.1275805
X-RAY DIFFRACTIONr_scbond_it2.6344.9534690
X-RAY DIFFRACTIONr_scbond_other2.6344.9534691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2417.3386821
X-RAY DIFFRACTIONr_long_range_B_refined7.24658.07910587
X-RAY DIFFRACTIONr_long_range_B_other7.24158.0810571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 140 -
Rwork0.337 3000 -
obs--97.79 %

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