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- PDB-6e69: Ortho-substituted phenyl sulfonyl fluoride and fluorosulfate as p... -

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Basic information

Entry
Database: PDB / ID: 6.0E+69
TitleOrtho-substituted phenyl sulfonyl fluoride and fluorosulfate as potent elastase inhibitory fragments
ComponentsNeutrophil elastase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / neutrophil / elastase / fragment / inhibitor / sulfonyl fluoride / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / cytokine binding / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / transcription repressor complex / phagocytic vesicle / Degradation of the extracellular matrix / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / protein catabolic process / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / azurophil granule lumen / positive regulation of immune response / peptidase activity / heparin binding / collagen-containing extracellular matrix / endopeptidase activity / protease binding / response to lipopolysaccharide / defense response to bacterium / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / proteolysis / extracellular space / extracellular exosome / 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
2-(fluorosulfonyl)benzene-1-sulfonic acid / Neutrophil elastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsWolan, D.W. / Woehl, J.L. / Kitamura, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase.
Authors: Zheng, Q. / Woehl, J.L. / Kitamura, S. / Santos-Martins, D. / Smedley, C.J. / Li, G. / Forli, S. / Moses, J.E. / Wolan, D.W. / Sharpless, K.B.
History
DepositionJul 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_close_contact / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Neutrophil elastase
B: Neutrophil elastase
C: Neutrophil elastase
D: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,01316
Polymers93,2764
Non-polymers4,73712
Water4,810267
1
A: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5544
Polymers23,3191
Non-polymers1,2353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5544
Polymers23,3191
Non-polymers1,2353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3514
Polymers23,3191
Non-polymers1,0323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5544
Polymers23,3191
Non-polymers1,2353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.470, 124.590, 126.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Neutrophil elastase / Bone marrow serine protease / Elastase-2 / Human leukocyte elastase / HLE / Medullasin / PMN elastase


Mass: 23318.982 Da / Num. of mol.: 4 / Fragment: UNP residues 30-247 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08246, leukocyte elastase

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Sugars , 3 types, 8 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 3 / Source method: isolated from a natural 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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural 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

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Non-polymers , 2 types, 271 molecules

#4: Chemical
ChemComp-HVP / 2-(fluorosulfonyl)benzene-1-sulfonic acid


Mass: 240.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5FO5S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.3 M ammonium citrate, pH 5.0, 14% w/v PEG3350 / PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2018 / Details: Flat Si Rh coated M0
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.329→50 Å / Num. obs: 47826 / % possible obs: 94.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 37.32 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 6
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.438 / % possible all: 94.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.51 Å46.81 Å
Translation3.51 Å46.81 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5ABW

5abw


Resolution: 2.33→46.81 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 2386 5.16 %
Rwork0.193 --
obs0.195 46245 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.77 Å2
Refinement stepCycle: LAST / Resolution: 2.33→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6409 0 302 267 6978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066869
X-RAY DIFFRACTIONf_angle_d0.9039309
X-RAY DIFFRACTIONf_dihedral_angle_d12.8352381
X-RAY DIFFRACTIONf_chiral_restr0.0351117
X-RAY DIFFRACTIONf_plane_restr0.0041195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3288-2.37640.2847870.2132010X-RAY DIFFRACTION76
2.3764-2.4280.29751390.21792562X-RAY DIFFRACTION98
2.428-2.48450.31450.20912607X-RAY DIFFRACTION98
2.4845-2.54660.2861390.21082584X-RAY DIFFRACTION98
2.5466-2.61550.24631510.21162577X-RAY DIFFRACTION99
2.6155-2.69250.2781260.20622631X-RAY DIFFRACTION98
2.6925-2.77930.21681590.20842582X-RAY DIFFRACTION98
2.7793-2.87870.24781720.2012590X-RAY DIFFRACTION99
2.8787-2.99390.24981330.20542611X-RAY DIFFRACTION99
2.9939-3.13010.31261430.20332635X-RAY DIFFRACTION99
3.1301-3.29510.22281560.1992569X-RAY DIFFRACTION97
3.2951-3.50150.24321530.19252610X-RAY DIFFRACTION98
3.5015-3.77180.21511240.1752652X-RAY DIFFRACTION99
3.7718-4.15110.21380.17172654X-RAY DIFFRACTION98
4.1511-4.75130.22171120.16292588X-RAY DIFFRACTION95
4.7513-5.98420.22941440.18982649X-RAY DIFFRACTION97
5.9842-46.81980.24541650.21132748X-RAY DIFFRACTION96

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