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- PDB-7u5b: Structure of Human KLK5 bound to anti-KLK5 Fab -

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Basic information

Entry
Database: PDB / ID: 7u5b
TitleStructure of Human KLK5 bound to anti-KLK5 Fab
Components
  • Kallikrein-5
  • anti-KLK5 Fab Heavy Chain
  • anti-KLK5 Fab Light Chain
KeywordsHYDROLASE/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 / Formation of the cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / epidermis development ...cornification / positive regulation of antibacterial peptide production / epidermal lamellar body / amelogenesis / Formation of the cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / epidermis development / serine-type peptidase activity / secretory granule / protein maturation / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.371 Å
AuthorsYin, J. / Sudhamsu, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: 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
DepositionMar 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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: anti-KLK5 Fab Heavy Chain
B: anti-KLK5 Fab Light Chain
H: anti-KLK5 Fab Heavy Chain
J: Kallikrein-5
L: anti-KLK5 Fab Light Chain
I: Kallikrein-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,87321
Polymers144,4326
Non-polymers1,44115
Water2,198122
1
A: anti-KLK5 Fab Heavy Chain
B: anti-KLK5 Fab Light Chain
J: Kallikrein-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,88810
Polymers72,2163
Non-polymers6727
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: anti-KLK5 Fab Heavy Chain
L: anti-KLK5 Fab Light Chain
I: Kallikrein-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,98511
Polymers72,2163
Non-polymers7698
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.686, 283.624, 295.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Antibody anti-KLK5 Fab Heavy Chain


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 anti-KLK5 Fab Light Chain


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 Kallikrein-5 / Kallikrein-like protein 2 / KLK-L2 / Stratum corneum tryptic enzyme


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 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 15% PEG4K, 0.1 M MgSO4 and 0.1 M sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9876 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.371→2.379 Å / Redundancy: 9.8 % / Num. unique obs: 2797 / CC1/2: 0.866 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.12-2829_finalrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSX

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
RfactorNum. reflection% reflection
Rfree0.2704 3498 4.96 %
Rwork0.2216 66989 -
obs0.224 70487 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.87 Å2 / Biso mean: 75.722 Å2 / Biso min: 32.12 Å2
Refinement stepCycle: final / Resolution: 2.371→52.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 75 122 9101
Biso mean--108.22 59.84 -
Num. residues----1174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019213
X-RAY DIFFRACTIONf_angle_d1.2212521
X-RAY DIFFRACTIONf_chiral_restr0.0651402
X-RAY DIFFRACTIONf_plane_restr0.0071581
X-RAY DIFFRACTIONf_dihedral_angle_d9.2526520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3711-2.40360.36531470.3167265099
2.4036-2.43790.33821450.30142669100
2.4379-2.47430.34791420.2787262099
2.4743-2.5130.27741210.2675268799
2.513-2.55420.31161050.2664269499
2.5542-2.59820.29991290.2638268799
2.5982-2.64550.35841300.2719266399
2.6455-2.69630.29251470.2537267499
2.6963-2.75140.33921210.2416265599
2.7514-2.81120.25391340.2369267599
2.8112-2.87660.28391560.24112669100
2.8766-2.94850.31381550.24352652100
2.9485-3.02820.26921340.2432267299
3.0282-3.11730.29251450.2484265398
3.1173-3.21790.33321370.2451250393
3.2179-3.33290.26321450.24432678100
3.3329-3.46640.29211350.23712712100
3.4664-3.62410.27461350.23232710100
3.6241-3.81510.28351420.23252726100
3.8151-4.0540.29461450.22032689100
4.054-4.36690.24341590.18692707100
4.3669-4.80610.25981470.17842731100
4.8061-5.50090.22251600.18942724100
5.5009-6.92820.26731600.2179260495
6.9282-52.8750.22111220.2114288599

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