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- PDB-1ppg: The refined 2.3 angstroms crystal structure of human leukocyte el... -

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Basic information

Entry
Database: PDB / ID: 1ppg
TitleThe refined 2.3 angstroms crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor
Components
  • HUMAN LEUKOCYTE ELASTASE
  • MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / Expression of NOTCH2NL genes / acute inflammatory response to antigenic stimulus / neutrophil-mediated killing of fungus / negative regulation of chemotaxis / 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 / pyroptotic inflammatory response / neutrophil-mediated killing of gram-negative bacterium / Activation of Matrix Metalloproteinases / cytokine binding / positive regulation of MAP kinase activity / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / positive regulation of smooth muscle cell proliferation / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / protein catabolic process / positive regulation of immune response / negative regulation of inflammatory response / specific granule lumen / intracellular calcium ion homeostasis / azurophil granule lumen / transcription corepressor activity / peptidase activity / heparin binding / : / protease binding / response to lipopolysaccharide / endopeptidase activity / defense response to bacterium / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / cell surface / negative regulation of transcription by RNA polymerase II / Golgi apparatus / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Meo-Suc-Ala-Ala-Pro-Val-chloromethyl ketone / Neutrophil elastase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBode, W. / Wei, A-Z.
Citation
Journal: FEBS Lett. / Year: 1988
Title: The refined 2.3 A crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor.
Authors: Wei, A.Z. / Mayr, I. / Bode, W.
#1: Journal: Embo J. / Year: 1986
Title: X-Ray Crystal Structure of the Complex of Human Leukocyte Elastase (Pmn Elastase) and the Third Domain of the Turkey Ovomucoid Inhibitor
Authors: Bode, W. / Wei, A.-Z. / Huber, R. / Meyer, E. / Travis, J. / Neumann, S.
History
DepositionOct 24, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_symm_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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Jul 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Polymer sequence / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can
Remark 700SHEET THE SHEETS PRESENTED AS *B1* AND *B2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *B1* AND *B2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY SEVEN-STRANDED SHEETS 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
E: HUMAN LEUKOCYTE ELASTASE
I: MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6714
Polymers23,8262
Non-polymers2,8452
Water3,459192
1
E: HUMAN LEUKOCYTE ELASTASE
I: MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE
hetero molecules

E: HUMAN LEUKOCYTE ELASTASE
I: MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE
hetero molecules

E: HUMAN LEUKOCYTE ELASTASE
I: MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,01212
Polymers71,4786
Non-polymers8,5346
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint54 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.200, 74.200, 70.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein HUMAN LEUKOCYTE ELASTASE


Mass: 23318.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P08246, leukocyte elastase
#2: Protein/peptide MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE


Type: Peptide-like / Class: Inhibitor / Mass: 507.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Meo-Suc-Ala-Ala-Pro-Val-chloromethyl ketone
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1- ...alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpNAca1-2DManpb1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-2-4-5-6/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{[(2+1)][a-D-AllpNAc]{[(4+1)][a-D-Allp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND FORM OF THE INHIBITOR IS MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE. UPON REACTION ...THE UNBOUND FORM OF THE INHIBITOR IS MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO OG SER 195 FORMING A HEMIKETAL VAI AND 2) A COVALENT BOND TO NE2 OF HIS 57

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.2 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 7390 / % possible obs: 75 % / Num. measured all: 20260 / Rmerge(I) obs: 0.081

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.145
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 192 192 2053
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 7104 / σ(I): 2 / Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_angle_deg2.79

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