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- PDB-1h1b: Crystal structure of human neutrophil elastase complexed with an ... -

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Basic information

Entry
Database: PDB / ID: 1h1b
TitleCrystal structure of human neutrophil elastase complexed with an inhibitor (GW475151)
ComponentsLEUKOCYTE ELASTASE
KeywordsHYDROLASE / SERINE PROTEASE
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
Chem-151 / Neutrophil elastase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMacdonald, S.J.F. / Dowle, M.D. / Harrison, L.A. / Clarke, G.D.E. / Inglis, G.G.A. / Johnson, M.R. / Smith, R.A. / Amour, A. / Fleetwood, G. / Humphreys, D.C. ...Macdonald, S.J.F. / Dowle, M.D. / Harrison, L.A. / Clarke, G.D.E. / Inglis, G.G.A. / Johnson, M.R. / Smith, R.A. / Amour, A. / Fleetwood, G. / Humphreys, D.C. / Molloy, C.R. / Dixon, M. / Godward, R.E. / Wonacott, A.J. / Singh, O.M.P. / Hodgson, S.T. / Hardy, G.W.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Discovery of Further Pyrrolidine Trans-Lactams as Inhibitors of Human Neutrophil Elastase (Hne) with Potential as Development Candidates and the Crystal Structure of Hne Complexed with an Inhibitor (Gw475151)
Authors: Macdonald, S.J.F. / Dowle, M.D. / Harrison, L.A. / Clarke, G.D.E. / Inglis, G.G.A. / Johnson, M.R. / Shah, P. / Smith, R.A. / Amour, A. / Fleetwood, G. / Humphreys, D.C. / Molloy, C.R. / ...Authors: Macdonald, S.J.F. / Dowle, M.D. / Harrison, L.A. / Clarke, G.D.E. / Inglis, G.G.A. / Johnson, M.R. / Shah, P. / Smith, R.A. / Amour, A. / Fleetwood, G. / Humphreys, D.C. / Molloy, C.R. / Dixon, M. / Godward, R.E. / Wonacott, A.J. / Singh, O.M.P. / Hodgson, S.T. / Hardy, G.W.
History
DepositionJul 5, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUKOCYTE ELASTASE
B: LEUKOCYTE ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9928
Polymers46,6382
Non-polymers2,3546
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-19 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.880, 68.880, 241.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99452, 0.00393, -0.10444), (-0.00423, -0.99999, 0.00268), (-0.10443, 0.00311, 0.99453)
Vector: 39.038, -8.041, 2.095)

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Components

#1: Protein LEUKOCYTE ELASTASE / ELASTASE / NEUTROPHIL ELASTASE / PMN ELASTASE / BONE MARROW SERINE PROTEASE / MEDULLASIN


Mass: 23318.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: LEUKOCYTE / References: UniProt: P08246, leukocyte elastase
#2: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-151 / (2S)-3-METHYL-2-((2R,3S)-3-[(METHYLSULFONYL)AMINO]-1-{[2-(PYRROLIDIN-1-YLMETHYL)-1,3-OXAZOL-4-YL]CARBONYL}PYRROLIDIN-2-YL)BUTANOIC ACID


Mass: 442.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30N4O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4
Details: HNE/GW475151 COMPLEX 10MG/ML IN 10MM NA CITRATE PH 5.0. HANGING DROPS OF EQUAL VOLUMES OF PROTEIN AND PRECIPITANT. PRECIPITANT 1.1-1.2M AMMONIUM SULPHATE, 100MM CITRATE PH 3.8-4.0, ROOM TEMP.
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMsodium acetate1droppH5.0
210 mg/mlprotein1drop
31.1-1.2 Mammonium sulfate1reservoir
4100 mMcitrate1reservoirpH3.8-4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 38930 / % possible obs: 96.1 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 83

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HNE

1hne


Resolution: 2→20 Å / SU B: 6.5 / SU ML: 0.179 / ESU R: 0.21 / ESU R Free: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1948 5 %RANDOM
Rwork0.251 ---
obs0.254 36959 96 %-
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 154 244 3670

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