[English] 日本語
Yorodumi
- PDB-1fle: CRYSTAL STRUCTURE OF ELAFIN COMPLEXED WITH PORCINE PANCREATIC ELASTASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fle
TitleCRYSTAL STRUCTURE OF ELAFIN COMPLEXED WITH PORCINE PANCREATIC ELASTASE
Components
  • ELAFIN
  • ELASTASE
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / HYDROLASE / SERINE PROTEASE / ZYMOGEN / PANCREAS / COMPLEX (SERINE PROTEASE-INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


structural constituent of skin epidermis / copulation / pancreatic elastase / peptide cross-linking / Formation of the cornified envelope / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity ...structural constituent of skin epidermis / copulation / pancreatic elastase / peptide cross-linking / Formation of the cornified envelope / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity / antibacterial humoral response / innate immune response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding / cytosol
Similarity search - Function
Seminal vesicle protein I / Trappin protein transglutaminase-binding repeat / Trappin protein transglutaminase binding domain / Seminal vesicle protein I repeats signature. / : / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' ...Seminal vesicle protein I / Trappin protein transglutaminase-binding repeat / Trappin protein transglutaminase binding domain / Seminal vesicle protein I repeats signature. / : / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / : / Few Secondary Structures / Irregular / 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
Chymotrypsin-like elastase family member 1 / Elafin
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsTsunemi, M. / Matsuura, Y. / Sakakibara, S. / Katsube, Y.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of an elastase-specific inhibitor elafin complexed with porcine pancreatic elastase determined at 1.9 A resolution.
Authors: Tsunemi, M. / Matsuura, Y. / Sakakibara, S. / Katsube, Y.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of a Complex between an Elastase-Specific Inhibitor Elafin and Porcine Pancreatic Elastase
Authors: Tsunemi, M. / Matsuura, Y. / Sakakibara, S. / Katsube, Y.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1992
Title: Synthesis and Structure-Activity Relationships of Elafin, an Elastase-Specific Inhibitor
Authors: Tsunemi, M. / Kato, H. / Nishiuchi, Y. / Kumagaye, S. / Sakakibara, S.
History
DepositionJul 4, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: ELASTASE
I: ELAFIN


Theoretical massNumber of molelcules
Total (without water)31,9422
Polymers31,9422
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-12 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.910, 73.320, 48.920
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ELASTASE


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Protein ELAFIN / SKIN-DERIVED ANTILEUKOPROTEINASE (SKALP)


Mass: 6014.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: SKIN / References: UniProt: P19957
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.9 / Details: pH 5.9
Crystal
*PLUS
Crystal grow
*PLUS
Method: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
168-74 %(v/v)MPD11
210 mMphosphate11

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15809 / % possible obs: 76.8 % / Observed criterion σ(I): 1 / Redundancy: 1.7 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 20575

-
Processing

Software
NameClassification
RAXISdata collection
PROFFTrefinement
R-AXISdata reduction
RefinementResolution: 1.9→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.197 --
obs-15809 76.8 %
Displacement parametersBiso mean: 24.81 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 0 157 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9241
X-RAY DIFFRACTIONp_mcangle_it1.6611.5
X-RAY DIFFRACTIONp_scbond_it1.5031.5
X-RAY DIFFRACTIONp_scangle_it2.4382
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1670.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.5
X-RAY DIFFRACTIONp_multtor_nbd0.240.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1920.5
X-RAY DIFFRACTIONp_planar_tor2.73
X-RAY DIFFRACTIONp_staggered_tor20.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 15659 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more