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- PDB-3n7o: X-ray structure of human chymase in complex with small molecule i... -

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Basic information

Entry
Database: PDB / ID: 3n7o
TitleX-ray structure of human chymase in complex with small molecule inhibitor.
ComponentsChymase
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / angiotensin maturation / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule ...chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / angiotensin maturation / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule / cellular response to glucose stimulus / peptide binding / protein catabolic process / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / extracellular space / extracellular region / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-N7O / Unknown ligand / Chymase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAbad, M.C. / Kervinen, J. / Crysler, C. / Bayoumy, S. / Spurlino, J. / Deckman, I. / Greco, M.N. / Maryanoff, B.E. / Degaravilla, L.
CitationJournal: Biochem. Pharmacol. / Year: 2010
Title: Potency variation of small-molecule chymase inhibitors across species.
Authors: Kervinen, J. / Crysler, C. / Bayoumy, S. / Abad, M.C. / Spurlino, J. / Deckman, I. / Greco, M.N. / Maryanoff, B.E. / de Garavilla, L.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: citation / pdbx_unobs_or_zero_occ_atoms ...citation / pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3006
Polymers25,0101
Non-polymers1,2915
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.475, 124.475, 124.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

Details1

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Components

#1: Protein Chymase / / Alpha-chymase / Mast cell protease I


Mass: 25009.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: chymase (16-245), CMA1, CYH, CYM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23946, chymase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-N7O / (S)-[(1S)-1-(5-chloro-1-benzothiophen-3-yl)-2-{[(E)-2-(3,4-difluorophenyl)ethenyl]amino}-2-oxoethyl]methylphosphinic acid


Mass: 441.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15ClF2NO3PS
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 45% Methanol and 0.1M sodium malonate pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 9, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 29831 / Num. obs: 29810 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Rsym value: 0.047 / Net I/σ(I): 37.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 7.5 / Num. unique all: 2929 / Rsym value: 0.256

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PJP

1pjp


Resolution: 1.8→39.362 Å / SU ML: 0.21 / Isotropic thermal model: anisotropic / σ(F): 0.06 / σ(I): 0 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1941 6.76 %random
Rwork0.1827 ---
obs0.1846 28721 96.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.302 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 98 162 1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081877
X-RAY DIFFRACTIONf_angle_d1.2192537
X-RAY DIFFRACTIONf_dihedral_angle_d20.582709
X-RAY DIFFRACTIONf_chiral_restr0.083281
X-RAY DIFFRACTIONf_plane_restr0.007321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.28581250.20161737X-RAY DIFFRACTION88
1.845-1.89490.23141310.21131761X-RAY DIFFRACTION90
1.8949-1.95070.23471320.19741809X-RAY DIFFRACTION92
1.9507-2.01360.24481340.19281860X-RAY DIFFRACTION95
2.0136-2.08560.23551420.19311939X-RAY DIFFRACTION98
2.0856-2.16910.22891420.18551942X-RAY DIFFRACTION98
2.1691-2.26780.26951390.18741929X-RAY DIFFRACTION98
2.2678-2.38740.17571360.18081907X-RAY DIFFRACTION97
2.3874-2.53690.21251370.17371942X-RAY DIFFRACTION98
2.5369-2.73270.22551360.19151933X-RAY DIFFRACTION98
2.7327-3.00770.22471410.19391977X-RAY DIFFRACTION99
3.0077-3.44270.17841450.16971987X-RAY DIFFRACTION99
3.4427-4.33650.15891490.15222004X-RAY DIFFRACTION100
4.3365-39.37180.22391520.18532053X-RAY DIFFRACTION99

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