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- PDB-5fuo: Extending the half-life of a Fab fragment through generation of a... -

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Basic information

Entry
Database: PDB / ID: 5fuo
TitleExtending the half-life of a Fab fragment through generation of a humanised anti-Human Serum Albumin (HSA) Fv domain: an investigation into the correlation between affinity and serum half-life
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
  • SERUM ALBUMIN
KeywordsIMMUNE SYSTEM / ANTI-ALBUMIN / FAB FRAGMENT / SERUM HALF-LIFE / FCRN / HUMAN SERUM ALBUMIN
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / 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 / 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; Chain A, Domain 1 - #10 / 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 ...Serum Albumin; Chain A, Domain 1 - #10 / 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 / Serum Albumin; Chain A, Domain 1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsAdams, R. / Ceska, T.
CitationJournal: Mabs / Year: 2016
Title: Extending the Half-Life of a Fab Fragment Through Generation of a Humanized Anti-Human Serum Albumin Fv Domain: An Investigation Into the Correlation between Affinity and Serum Half-Life.
Authors: Adams, R. / Griffin, L. / Compson, J.E. / Jairaj, M. / Baker, T. / Ceska, T. / West, S. / Zaccheo, O. / Dave, E. / Lawson, A.D.G. / Humphreys, D.P. / Heywood, S.
History
DepositionJan 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: SERUM ALBUMIN
H: FAB HEAVY CHAIN
L: FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)114,8923
Polymers114,8923
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-43.7 kcal/mol
Surface area55800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)217.640, 217.640, 78.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SERUM ALBUMIN / FAB645-HSA


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: TESTIS / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P02768
#2: Antibody FAB HEAVY CHAIN


Mass: 24900.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: TESTIS / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster)
#3: Antibody FAB LIGHT CHAIN


Mass: 23419.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: TESTIS / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster)
Has protein modificationY
Sequence detailsIN-HOUSE DISCOVERED FAB

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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: 4.72 Å3/Da / Density % sol: 73.94 % / Description: NONE
Crystal growpH: 1
Details: 0.1 M CITRIC ACID PH 4.4, 0.1 M DI-SODIUM HYDROGEN PHOSPHATE, 38% V/V ETHANOL, 5% V/V POLYETHYLENE GLYCOL 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9713
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9713 Å / Relative weight: 1
ReflectionResolution: 3.58→30 Å / Num. obs: 46115 / % possible obs: 93.9 % / Observed criterion σ(I): 1.6 / Redundancy: 2.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 7.57
Reflection shellResolution: 3.58→3.79 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 1.64 / % possible all: 86.1

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Processing

Software
NameVersionClassification
CNS1.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G03 AND FAB WWPDB SUBMISSION CODE 62161

4g03


Resolution: 3.6→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CHAIN A RESIDUES 1-4, 583-585 AND CHAIN H RESIDUES 136-142, 224-233 ARE TOO DISORDERED TO MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 2405 9.6 %RANDOM
Rwork0.2151 ---
obs0.2151 24409 97.6 %-
Solvent computationBsol: 64.83 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.946 Å20 Å20 Å2
2--13.946 Å20 Å2
3----27.892 Å2
Refinement stepCycle: LAST / Resolution: 3.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7869 0 0 0 7869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.010461
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.44231
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 3.6→3.73 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3713 2405 9.6 %
Rwork0.3256 2209 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR PROTEIN_REP.PARAMA
X-RAY DIFFRACTION2CNS_TOPPAR DNA-RNA_REP.PARAMA
X-RAY DIFFRACTION3CNS_TOPPAR WATER_REP.PARAMA
X-RAY DIFFRACTION4CNS_TOPPAR ION.PARAMA
X-RAY DIFFRACTION5CNS_TOPPAR CARBOHYDRATE.PARAMA

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