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- PDB-8y9s: Crystal structure of nanobody MY6321 bound to human serum albumin... -

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Basic information

Entry
Database: PDB / ID: 8y9s
TitleCrystal structure of nanobody MY6321 bound to human serum albumin (HSA)
Components
  • Albumin
  • nanobody MY6321
KeywordsPROTEIN BINDING / antibody / human serum albumin
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
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsDing, Y. / Zhong, P.Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070939 China
National Science Foundation (NSF, China)82030106 China
Ministry of Science and Technology (MoST, China)2021YFA0805200 China
CitationJournal: To Be Published
Title: Crystal structure of nanobody MY6321 bound to human serum albumin (HSA)
Authors: Ding, Y. / Zhong, P.Y.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
B: nanobody MY6321
C: Albumin
D: nanobody MY6321


Theoretical massNumber of molelcules
Total (without water)160,9704
Polymers160,9704
Non-polymers00
Water00
1
A: Albumin
B: nanobody MY6321


Theoretical massNumber of molelcules
Total (without water)80,4852
Polymers80,4852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-8 kcal/mol
Surface area33430 Å2
MethodPISA
2
C: Albumin
D: nanobody MY6321


Theoretical massNumber of molelcules
Total (without water)80,4852
Polymers80,4852
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-8 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.260, 143.900, 93.670
Angle α, β, γ (deg.)90.00, 100.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Albumin / HSA


Mass: 67346.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALB / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: P02768
#2: Antibody nanobody MY6321


Mass: 13138.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Saccharomyces cerevisiae (brewer's yeast)
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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.15 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.88→46.25 Å / Num. obs: 38264 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.983 / Rmerge(I) obs: 0.286 / Rpim(I) all: 0.12 / Rrim(I) all: 0.31 / Χ2: 1.05 / Net I/σ(I): 5.5
Reflection shellResolution: 2.88→2.95 Å / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 2.018 / Num. measured all: 19122 / Num. unique obs: 2819 / CC1/2: 0.436 / Rpim(I) all: 0.825 / Rrim(I) all: 2.183 / Χ2: 1.04 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS0.7.7data scaling
XDS0.7.7data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→46.25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 30.159 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29265 1808 4.7 %RANDOM
Rwork0.23008 ---
obs0.23313 36434 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.932 Å2
Baniso -1Baniso -2Baniso -3
1-6.6 Å2-0 Å22.23 Å2
2---5.73 Å20 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 2.88→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10903 0 0 0 10903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01211342
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610688
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.86515310
X-RAY DIFFRACTIONr_angle_other_deg0.5561.77724774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.84451406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.568560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.284102046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1570.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213170
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022490
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_it6.2287.0925636
X-RAY DIFFRACTIONr_mcbond_other6.2277.0925636
X-RAY DIFFRACTIONr_mcangle_it9.97612.747038
X-RAY DIFFRACTIONr_mcangle_other9.97612.747039
X-RAY DIFFRACTIONr_scbond_it6.2347.5925706
X-RAY DIFFRACTIONr_scbond_other6.2337.5925707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.09913.7638273
X-RAY DIFFRACTIONr_long_range_B_refined15.58868.4613165
X-RAY DIFFRACTIONr_long_range_B_other15.58968.4613166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.88→2.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 133 -
Rwork0.387 2675 -
obs--99.26 %

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