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- PDB-1o5e: Dissecting and Designing Inhibitor Selectivity Determinants at th... -

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Entry
Database: PDB / ID: 1o5e
TitleDissecting and Designing Inhibitor Selectivity Determinants at the S1 site Using an Artificial Ala190 Protease (Ala190 uPA)
Components(Serine protease hepsin) x 2
Keywordsserine protease / hydrolase / srcr / scavenger receptor cysteine-rich domain / serine protease Ala190 uPA / S1 site / selectivity / conserved water displacement hydrogen bond deficit / trypsin / thrombin / hepsin / factor VIIa
Function / homology
Function and homology information


hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation ...hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation / response to thyroid hormone / negative regulation of epithelial to mesenchymal transition / positive regulation by host of viral transcription / positive regulation of hepatocyte proliferation / potassium ion transmembrane transport / serine-type peptidase activity / negative regulation of epithelial cell proliferation / cell-cell junction / peptidase activity / regulation of cell shape / positive regulation of cell growth / apical plasma membrane / serine-type endopeptidase activity / neuronal cell body / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / cell surface / proteolysis / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Hepsin, SRCR domain / Hepsin, SRCR domain / Mac-2 Binding Protein / SRCR-like domain / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Hepsin, SRCR domain / Hepsin, SRCR domain / Mac-2 Binding Protein / SRCR-like domain / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-132 / Serine protease hepsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsKatz, B.A. / Luong, C. / Ho, J.D. / Somoza, J.R. / Gjerstad, E. / Tang, J. / Williams, S.R. / Verner, E. / Mackman, R.L. / Young, W.B. ...Katz, B.A. / Luong, C. / Ho, J.D. / Somoza, J.R. / Gjerstad, E. / Tang, J. / Williams, S.R. / Verner, E. / Mackman, R.L. / Young, W.B. / Sprengeler, P.A. / Chan, H. / Mortara, K. / Janc, J.W. / McGrath, M.E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA).
Authors: Katz, B.A. / Luong, C. / Ho, J.D. / Somoza, J.R. / Gjerstad, E. / Tang, J. / Williams, S.R. / Verner, E. / Mackman, R.L. / Young, W.B. / Sprengeler, P.A. / Chan, H. / Mortara, K. / Janc, J.W. / McGrath, M.E.
History
DepositionSep 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Serine protease hepsin
H: Serine protease hepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4583
Polymers40,0952
Non-polymers3631
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.77, 47.88, 63.33
Angle α, β, γ (deg.)90.0, 104.77, 90.0
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Serine protease hepsin / E.C.3.4.21.- / Transmembrane protease / serine 1


Mass: 12522.299 Da / Num. of mol.: 1 / Fragment: light chain / Mutation: N67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPN OR TMPRSS1 / Production host: Pichia pastoris (fungus) / Variant (production host): KM71
References: UniProt: P05981, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Serine protease hepsin / E.C.3.4.21.- / Transmembrane protease / serine 1


Mass: 27573.111 Da / Num. of mol.: 1 / Fragment: heavy chain (catalytic domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPN OR TMPRSS1 / Production host: Pichia pastoris (fungus) / Variant (production host): KM71
References: UniProt: P05981, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical ChemComp-132 / 6-CHLORO-2-(2-HYDROXY-BIPHENYL-3-YL)-1H-INDOLE-5-CARBOXAMIDINE


Mass: 362.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17ClN3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M ammonium fluoride, 20-25% PEG 3350, pH 7.6, vapor diffusion at 290 K Soak in synthetic mother liquor - CRA-10302 at pH 6.9., pH 6.5

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→25.8 Å / Num. all: 34620 / Num. obs: 29472 / % possible obs: 85.13 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 5.3
Reflection shellResolution: 1.75→1.83 Å / % possible obs: 30.7 % / Rmerge(I) obs: 0.435 / Num. unique all: 4235

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Processing

Software
NameVersionClassification
CrystalClear1.3data collection
CrystalClear1.3data reduction
X-PLOR3.851refinement
CrystalClear(MSC/RIGAKU)data scaling
Quantamodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: X-PLOR force field
Details: The first four residues of the light chain are not visible and are not included in the model. The loop comprising the sequence "RDPNSEE" between Phe_H97 and Asn_H99 is not visible and is not ...Details: The first four residues of the light chain are not visible and are not included in the model. The loop comprising the sequence "RDPNSEE" between Phe_H97 and Asn_H99 is not visible and is not included in the model. Residues simultaneously refined in two or more conformations are: Arg_L35, Val_L75, Arg_L79, Lys_L112, Leu_H41, Leu_H46, Gln_H73, Ser_H109, Pro_H185, Thr_H208, Lys_H224, Ser_H246, Gln_H254. Discretely disordered waters are HOH_212 and HOH_323. His_H40, HIS_H57, and His_H107 are doubly protonated. HIS_H91 is monoprotonated on the epsilon nitrogen No energy terms are included Og_Ser_H195, HOH_383, and O6' of the inhibitor. These atoms form a short hydrogen-bonding network.
RfactorNum. reflection% reflection
Rfree0.227 2935 10 %
Rwork0.198 --
obs0.2 28791 84.59 %
all-34037 -
Refinement stepCycle: LAST / Resolution: 1.75→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 42 534 6102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_angle_deg4

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