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- PDB-5ce1: Crystal Structure of Serine protease Hepsin in complex with Inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ce1
TitleCrystal Structure of Serine protease Hepsin in complex with Inhibitor
ComponentsSerine protease hepsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HEPSIN / PROSTATE CANCER / HYDROLASE-HYDROLASE INHIBITOR complex
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 / endoplasmic reticulum membrane / positive regulation of gene expression / 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-50K / Serine protease hepsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRao, K.N. / Anita, R.C. / Sangeetha, R. / Anirudha, L. / Subramnay, H.
CitationJournal: To Be Published
Title: Crystal Structure of Serine protease Hepsin in complex with Inhibitor
Authors: Rao, K.N. / Anita, R.C. / Sangeetha, R. / Anirudha, L. / Subramnay, H.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.plasmid_name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease hepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8262
Polymers40,4921
Non-polymers3341
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14440 Å2
Unit cell
Length a, b, c (Å)59.583, 47.678, 60.784
Angle α, β, γ (deg.)90.00, 105.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine protease hepsin / Transmembrane protease serine 1


Mass: 40491.793 Da / Num. of mol.: 1 / Fragment: UNP residues 46-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPN, TMPRSS1 / Plasmid: pFastBac1 / Cell line (production host): sf9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P05981, hepsin
#2: Chemical ChemComp-50K / 2-[6-(1-hydroxycyclohexyl)pyridin-2-yl]-1H-indole-5-carboximidamide


Mass: 334.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.19 % / Description: Crystals were grown as long rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Activated hepsin was incubated with 10 mM Benzamidine at 4 oC for 2 hours and concentrated to7 mg/ml using 10 KDa cut off centricon [Millipore]. 1microlit of protein was mixed with 1 ...Details: Activated hepsin was incubated with 10 mM Benzamidine at 4 oC for 2 hours and concentrated to7 mg/ml using 10 KDa cut off centricon [Millipore]. 1microlit of protein was mixed with 1 microlit of reservoir buffer containing 100 mM sodium Cacodylate (6.0), 22% PEG 3350, and 200 mM ammonium fluoride. Plate clusters with a dimension of 50 micron m x 100 micron m were observed after 2 days of crystallization set up.
PH range: 5.8 - 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2012
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 26276 / Num. obs: 10137 / % possible obs: 87.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 2.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.229 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z8G

1z8g


Resolution: 2.5→58.63 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.859 / SU B: 10.623 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE REASON FOR POOR ELECTRON DENSITY IS THAT THE REGION BETWEEN A LEU 158 AND RESIDUE A ILE 163 HIGHLY DISORDERED AND HENCE THE ATOMS POSITIONS ARE NOT STABILIZED IN THE CRYSTAL. HYDROGENS ...Details: THE REASON FOR POOR ELECTRON DENSITY IS THAT THE REGION BETWEEN A LEU 158 AND RESIDUE A ILE 163 HIGHLY DISORDERED AND HENCE THE ATOMS POSITIONS ARE NOT STABILIZED IN THE CRYSTAL. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 485 4.8 %RANDOM
Rwork0.18714 ---
obs0.19165 9554 86.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0.09 Å2
2---0.03 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 25 46 2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192721
X-RAY DIFFRACTIONr_bond_other_d0.0010.022471
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9523715
X-RAY DIFFRACTIONr_angle_other_deg0.8873.0065621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8875356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37323.01103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35815369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4881517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 41 -
Rwork0.23 701 -
obs--88.97 %

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