+Open data
-Basic information
Entry | Database: PDB / ID: 7u5b | ||||||
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Title | Structure of Human KLK5 bound to anti-KLK5 Fab | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / Protease / Kallikrien / KLK5 / HYDROLASE / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information cornification / positive regulation of antibacterial peptide production / epidermal lamellar body / amelogenesis / positive regulation of G protein-coupled receptor signaling pathway / Formation of the cornified envelope / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / epidermis development / serine-type peptidase activity ...cornification / positive regulation of antibacterial peptide production / epidermal lamellar body / amelogenesis / positive regulation of G protein-coupled receptor signaling pathway / Formation of the cornified envelope / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / epidermis development / serine-type peptidase activity / secretory granule / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | synthetic construct (others) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.371 Å | ||||||
Authors | Yin, J. / Sudhamsu, J. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: Dual antibody inhibition of KLK5 and KLK7 for Netherton syndrome and atopic dermatitis. Authors: Chavarria-Smith, J. / Chiu, C.P.C. / Jackman, J.K. / Yin, J. / Zhang, J. / Hackney, J.A. / Lin, W.Y. / Tyagi, T. / Sun, Y. / Tao, J. / Dunlap, D. / Morton, W.D. / Ghodge, S.V. / Maun, H.R. / ...Authors: Chavarria-Smith, J. / Chiu, C.P.C. / Jackman, J.K. / Yin, J. / Zhang, J. / Hackney, J.A. / Lin, W.Y. / Tyagi, T. / Sun, Y. / Tao, J. / Dunlap, D. / Morton, W.D. / Ghodge, S.V. / Maun, H.R. / Li, H. / Hernandez-Barry, H. / Loyet, K.M. / Chen, E. / Liu, J. / Tam, C. / Yaspan, B.L. / Cai, H. / Balazs, M. / Arron, J.R. / Li, J. / Wittwer, A.J. / Pappu, R. / Austin, C.D. / Lee, W.P. / Lazarus, R.A. / Sudhamsu, J. / Koerber, J.T. / Yi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u5b.cif.gz | 243.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u5b.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 7u5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u5b_validation.pdf.gz | 496.8 KB | Display | wwPDB validaton report |
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Full document | 7u5b_full_validation.pdf.gz | 530.3 KB | Display | |
Data in XML | 7u5b_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 7u5b_validation.cif.gz | 62.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/7u5b ftp://data.pdbj.org/pub/pdb/validation_reports/u5/7u5b | HTTPS FTP |
-Related structure data
Related structure data | 2psxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23659.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 23363.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster) #3: Protein | Mass: 25192.920 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK5, SCTE, UNQ570/PRO1132 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q9Y337, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 15% PEG4K, 0.1 M MgSO4 and 0.1 M sodium citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9876 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9876 Å / Relative weight: 1 |
Reflection | Resolution: 2.371→52.875 Å / Num. obs: 806688 / % possible obs: 99.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 56.31 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.371→2.379 Å / Redundancy: 9.8 % / Num. unique obs: 2797 / CC1/2: 0.866 / % possible all: 97 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PSX Resolution: 2.371→52.875 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.87 Å2 / Biso mean: 75.722 Å2 / Biso min: 32.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.371→52.875 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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