[English] 日本語
Yorodumi
- PDB-1bma: BENZYL METHYL AMINIMIDE INHIBITOR COMPLEXED TO PORCINE PANCREATIC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bma
TitleBENZYL METHYL AMINIMIDE INHIBITOR COMPLEXED TO PORCINE PANCREATIC ELASTASE
ComponentsChymotrypsin-like elastase family member 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / Metal-binding / Protease / Secreted / Zymogen / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
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
(1R)-1-benzyl-1-methyl-1-(2-{[4-(1-methylethyl)phenyl]amino}-2-oxoethyl)-2-{(2S)-4-methyl-2-[(trifluoroacetyl) amino]pentanoyl}diazanium / Chem-0QH / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsPeisach, E. / Casebier, D. / Gallion, S.L. / Furth, P. / Petsko, G.A. / Hogan Jr., J.C. / Ringe, D.
Citation
Journal: Science / Year: 1995
Title: Interaction of a peptidomimetic aminimide inhibitor with elastase.
Authors: Peisach, E. / Casebier, D. / Gallion, S.L. / Furth, P. / Petsko, G.A. / Hogan Jr., J.C. / Ringe, D.
#1: Journal: Biochemistry / Year: 1995
Title: Structural Analysis of the Active Site of Porcine Pancreatic Elastase Based on the X-Ray Crystal Structures of Complexes with Trifluoroacetyl-Dipeptide-Anilide Inhibitors
Authors: Mattos, C. / Giammona, D.A. / Petsko, G.A. / Ringe, D.
#2: Journal: J.Mol.Recog. / Year: 1990
Title: Interaction of the Peptide Cf3-Leu-Ala-Nh-C6H4-Cf3 (Tfla) with Porcine Pancreatic Elastase. X-Ray Studies at 1.8 Angstroms
Authors: Li De La Sierra, I. / Papamichael, E. / Sakarelos, C. / Dimicoli, J.-L. / Prange, T.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of Native Porcine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
#4: Journal: J.Mol.Biol. / Year: 1986
Title: Structure of the Product Complex of Acetyl-Ala-Pro-Ala with Porcine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyer, E. / Radhakrishnan, R. / Cole, G. / Presta, L.G.
#5: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic Study of the Binding of a Tri-Fluoroacetyl Dipeptide Anilide Inhibitor with Elastase
Authors: Hughes, D.L. / Diecker, L.C. / Bieth, L.C. / Dimicoli, J.-L.
#6: Journal: Eur.J.Biochem. / Year: 1980
Title: The Indirect Mechanism of Action of the Trifluoroacetyl Peptides on Elastase
Authors: Dimicoli, J.-L. / Renaud, A. / Bieth, J.
#7: Journal: J.Mol.Biol. / Year: 1978
Title: The Atomic Structure of Crystalline Porcine Pancreatic Elastase at 2.5 Angstroms Resolution. Comparisons with the Structure of Alpha-Chymotrypsin
Authors: Sawyer, L. / Shotton, C.M. / Campbell, J.W. / Wendell, P.L. / Muirhead, H. / Watson, H.C. / Diamond, R. / Ladner, R.C.
History
DepositionMay 1, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEETS PRESENTED AS *S1* AND *S2* IN SHEET RECORDS BELOW ARE ACTUALLY TWO SIX-STRANDED ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* IN SHEET RECORDS BELOW ARE ACTUALLY TWO SIX-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY TWO SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS OF EACH SHEET ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chymotrypsin-like elastase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5864
Polymers25,9281
Non-polymers6583
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.160, 57.680, 75.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Chymotrypsin-like elastase family member 1 / Elastase-1


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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-0QH / (1R)-1-benzyl-1-methyl-1-(2-{[4-(1-methylethyl)phenyl]amino}-2-oxoethyl)-2-{(2S)-4-methyl-2-[(trifluoroacetyl)amino]pentanoyl}diazanium


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 521.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36F3N4O3
References: (1R)-1-benzyl-1-methyl-1-(2-{[4-(1-methylethyl)phenyl]amino}-2-oxoethyl)-2-{(2S)-4-methyl-2-[(trifluoroacetyl) amino]pentanoyl}diazanium
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsNOTE THAT SUBCOMPONENT MBH IS REFERRED TO AS MBA IN THE PAPER CITED IN THE JRNL RECORDS ABOVE.
Sequence detailsTHE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL STARTING WITH VAL A 16 AND ENDING WITH ...THE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL STARTING WITH VAL A 16 AND ENDING WITH ASN A 255. THE IDENTITY OF ASN A 81 AGREES WITH THE SEQUENCES OF SEVERAL OTHER ELASTASE STRUCTURES. THE AUTHORS, THEREFORE, BELIEVE IT TO BE CORRECT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growDetails: THE INHIBITOR WAS SOAKED INTO THE GROWN CRYSTALS USING A 4 MM STOCK SOLUTION OF THE INHIBITOR IN 10% ACETONITRILE.
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 5 / Method: unknown / Details: or 20 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlelastase11
210 mMsodium sulfate11
31 Msodium sulfate12

-
Data collection

Diffraction sourceWavelength: 1.5148 Å
DetectorType: SIEMENS / Date: May 20, 1994
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5148 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 39545 / % possible obs: 58.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063
Reflection
*PLUS
Num. measured all: 44505 / Rmerge(I) obs: 0.063

-
Processing

Software
NameVersionClassification
XDSdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.192 --
obs0.192 44505 58.7 %
Displacement parametersBiso mean: 18.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 43 134 1999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.01
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.01

+
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