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- PDB-1ppf: X-RAY CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN LEUKOCYTE ELASTAS... -

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Basic information

Entry
Database: PDB / ID: 1ppf
TitleX-RAY CRYSTAL STRUCTURE OF THE COMPLEX OF HUMAN LEUKOCYTE ELASTASE (PMN ELASTASE) AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR
Components
  • HUMAN LEUKOCYTE ELASTASENeutrophil elastase
  • TURKEY OVOMUCOID INHIBITOR (OMTKY3)
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 / 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 / molecular function inhibitor activity / 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 / phagocytic vesicle / transcription repressor complex / 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 / serine-type endopeptidase inhibitor activity / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / positive regulation of immune response / azurophil granule lumen / heparin binding / peptidase activity / 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 / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site ...Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ovomucoid / Neutrophil elastase / Ovomucoid
Similarity search - Component
Biological speciesHomo sapiens (human)
Meleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBode, W. / Wei, A-Z.
Citation
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.
#2: Journal: Biochemistry / Year: 1989
Title: Human Leukocyte and Porcine Pancreatic Elastase: X-Ray Crystal Structure, Mechanism, Substrate Specificity, and Mechanism-Based Inhibitors
Authors: Bode, W. / Meyer, E. / Powers, J.C.
#3: Journal: FEBS Lett. / Year: 1988
Title: The Refined 2.3 Angstroms Crystal Structure of Human Leukocyte Elastase in a Complex with a Valine Chloromethyl Ketone Inhibitor
Authors: Wei, A.Z. / Mayr, I. / Bode, W.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Primary Structure of Human Neutrophil Elastase
Authors: Sinha, S. / Watorek, W. / Karr, S. / Giles, J. / Bode, W. / Travis, J.
#1: Journal: To be Published
Authors: Bode, W. / Wei, A.Z. / Stubbs, M. / Laskowski, M.
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: Non-polymer description / Version format compliance
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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
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

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Assembly

Deposited unit
E: HUMAN LEUKOCYTE ELASTASE
I: TURKEY OVOMUCOID INHIBITOR (OMTKY3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1904
Polymers29,3462
Non-polymers2,8452
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint30 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.050, 72.550, 52.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO I 12 IS A CIS PROLINE.

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Components

#1: Protein HUMAN LEUKOCYTE ELASTASE / Neutrophil elastase


Mass: 23318.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P08246, leukocyte elastase
#2: Protein TURKEY OVOMUCOID INHIBITOR (OMTKY3)


Mass: 6026.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / References: UniProt: P01004, UniProt: P68390*PLUS
#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-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1- ...alpha-D-glucopyranose-(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
DGlcpa1-4DGlcpNAcb1-2DManpa1-6[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][a2122h-1a_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)][a-L-TalpNAc]{[(4+1)][a-D-Allp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsASN 109 AND ASN 159 ARE GLYCOSYLATED; AT BOTH SITES AN ASN-LINKED N-ACETYLGLUCOSAMINE, AN ALPHA-1, ...ASN 109 AND ASN 159 ARE GLYCOSYLATED; AT BOTH SITES AN ASN-LINKED N-ACETYLGLUCOSAMINE, AN ALPHA-1, 6-BOUND L-FUCOPYRANOSE AND A BETA-1, 4-LINKED N-ACETYLGLUCOSAMINE ARE WELL DEFINED, A BRANCHING MANNOSE SUGAR IN PART.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal grow
*PLUS
pH: 10 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 0.45-0.5 M / Common name: sodium citrate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 21000 / % possible obs: 75 % / Observed criterion σ(I): 1 / Num. measured all: 62000 / Rmerge(I) obs: 0.083

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.8→8 Å / Rfactor Rwork: 0.166
Details: THE SER 195 OG - LEU 18I C INTERACTION HAS NOT BEEN CONSTRAINED ("FREE APPROACH"). HLE: 218 RESIDUES FROM ILE E 16 TO GLN E 243 ARE DEFINED BY ELECTRON DENSITY; THERE MIGHT BE ONE OR MORE ...Details: THE SER 195 OG - LEU 18I C INTERACTION HAS NOT BEEN CONSTRAINED ("FREE APPROACH"). HLE: 218 RESIDUES FROM ILE E 16 TO GLN E 243 ARE DEFINED BY ELECTRON DENSITY; THERE MIGHT BE ONE OR MORE ADDITIONAL RESIDUES PRESENT AT THE C-TERMINUS (WHERE POSTTRANSLATIONAL TRIMMING OCCURS).
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 192 272 2518
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS

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