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- PDB-5yjm: Human chymase in complex with 7-oxo-3-(phenoxyimino)-1,4-diazepan... -

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Basic information

Entry
Database: PDB / ID: 5yjm
TitleHuman chymase in complex with 7-oxo-3-(phenoxyimino)-1,4-diazepane derivative
Componentshuman chymase
KeywordsHYDROLASE / protease / inhibitor / complex
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule ...chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / 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 / intracellular membrane-bounded organelle / serine-type endopeptidase activity / extracellular space / extracellular region / cytoplasm / cytosol
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSugawara, H.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Structure-based design, synthesis, and binding mode analysis of novel and potent chymase inhibitors
Authors: Futamura-Takahashi, J. / Tanaka, T. / Sugawara, H. / Iwashita, S. / Imajo, S. / Oyama, Y. / Muto, T.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: human chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1355
Polymers25,0331
Non-polymers1,1024
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-15 kcal/mol
Surface area10650 Å2
Unit cell
Length a, b, c (Å)75.089, 75.089, 49.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein human chymase


Mass: 25032.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris (fungus) / References: UniProt: P23946*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-8W3 / 2-amino-4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-7-oxo-3-(phenoxyimino)-1,4-diazepane-1-carboxamido)propyl)benzoic acid / 2-azanyl-4-[(1R)-1-[[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-7-oxidanylidene-3-phenoxyimino-1,4-diazepan-1-yl] carbonylamino]propyl]benzoic acid


Mass: 594.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H32ClN5O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 22% PEG8000, 5mM zinc chloride, 100mM MES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 21174 / % possible obs: 95.9 % / Redundancy: 4.1 % / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementResolution: 1.9→29.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.633 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18562 1090 5.1 %RANDOM
Rwork0.14701 ---
obs0.14899 20076 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.745 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 71 88 1854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191817
X-RAY DIFFRACTIONr_bond_other_d0.0060.021692
X-RAY DIFFRACTIONr_angle_refined_deg2.4941.9972463
X-RAY DIFFRACTIONr_angle_other_deg2.83633924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6185218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61122.572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48815298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2061514
X-RAY DIFFRACTIONr_chiral_restr0.1640.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211982
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02379
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_it1.6051.67872
X-RAY DIFFRACTIONr_mcbond_other1.6061.667871
X-RAY DIFFRACTIONr_mcangle_it2.4572.4881087
X-RAY DIFFRACTIONr_mcangle_other2.4572.4921088
X-RAY DIFFRACTIONr_scbond_it2.7042.162945
X-RAY DIFFRACTIONr_scbond_other2.6722.154942
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3063.0851373
X-RAY DIFFRACTIONr_long_range_B_refined6.07820.4861950
X-RAY DIFFRACTIONr_long_range_B_other6.07420.3321939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 76 -
Rwork0.234 1395 -
obs--90.3 %
Refinement TLS params.Method: refined / Origin x: -13.298 Å / Origin y: -24.776 Å / Origin z: -0.257 Å
111213212223313233
T0.005 Å2-0.0065 Å2-0.0007 Å2-0.0341 Å2-0.0016 Å2--0.0036 Å2
L1.4559 °2-1.1702 °20.256 °2-2.3767 °2-0.2735 °2--0.7857 °2
S-0.0321 Å °-0.0503 Å °-0.0065 Å °0.0295 Å °0.0109 Å °0.061 Å °-0.0272 Å °-0.0712 Å °0.0212 Å °

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