[English] 日本語
Yorodumi
- PDB-2za5: Crystal Structure of human tryptase with potent non-peptide inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2za5
TitleCrystal Structure of human tryptase with potent non-peptide inhibitor
ComponentsTryptase beta 2
KeywordsHYDROLASE / Tryptase / serine protease / tetramer
Function / homology
Function and homology information


tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / defense response / collagen-containing extracellular matrix / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding
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-2FF / Tryptase beta-2 / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSpurlino, J.C. / Barnakov, S.A. / Lewandowski, F. / Milligan, C.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Potent, nonpeptide inhibitors of human mast cell tryptase. Synthesis and biological evaluation of novel spirocyclic piperidine amide derivatives
Authors: Costanzo, M.J. / Yabut, S.C. / Zhang, H.-C. / White, K.B. / de Garavilla, L. / Wang, Y. / Minor, L.K. / Tounge, B.A. / Barnakov, A.N. / Lewandowski, F. / Milligan, C. / Spurlino, J.C. / ...Authors: Costanzo, M.J. / Yabut, S.C. / Zhang, H.-C. / White, K.B. / de Garavilla, L. / Wang, Y. / Minor, L.K. / Tounge, B.A. / Barnakov, A.N. / Lewandowski, F. / Milligan, C. / Spurlino, J.C. / Abraham, W.M. / Boswell-Smith, V. / Page, C.P. / Maryanoff, B.E.
#1: Journal: J.Med.Chem. / Year: 2003
Title: Potent, small-molecule inhibitors of human mast cell tryptase. Antiasthmatic action of a dipeptide-based transition-state analogue containing a benzothiazole ketone
Authors: Costanzo, M.J. / Yabut, S.C. / Almond, H.R. / Andrade-Gordon, P. / Corcoran, T.W. / de Garavilla, L. / Kauffman, J.A. / Abraham, W.M. / Recacha, R. / Chattopadhyay, D. / Maryanoff, B.E.
History
DepositionOct 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptase beta 2
B: Tryptase beta 2
C: Tryptase beta 2
D: Tryptase beta 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6168
Polymers109,9664
Non-polymers1,6504
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-30.8 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.678, 82.678, 170.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein
Tryptase beta 2


Mass: 27491.426 Da / Num. of mol.: 4 / Fragment: UNP residues 31-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: Q6B052, UniProt: P20231*PLUS, tryptase
#2: Chemical
ChemComp-2FF / (5-(aminomethyl)-2H-spiro[benzofuran-3,4'-piperidine]-1'-yl)(5-(phenylethynyl)furan-2-yl)methanone


Mass: 412.480 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H24N2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.1 / Details: pH 6.1, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 51904

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A0L

1a0l


Resolution: 2.3→19.915 Å / FOM work R set: 0.839 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2464 4.98 %RANDOM
Rwork0.181 ---
obs0.184 50943 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.675 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 83.59 Å2 / Biso mean: 21.16 Å2 / Biso min: 5.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.406 Å20 Å2-0 Å2
2--0.406 Å20 Å2
3----0.811 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7647 0 124 431 8202
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.2641
X-RAY DIFFRACTIONf_bond_d0.0091
X-RAY DIFFRACTIONf_chiral_restr0.0851
X-RAY DIFFRACTIONf_dihedral_angle_d24.2091
X-RAY DIFFRACTIONf_plane_restr0.0091
X-RAY DIFFRACTIONf_nbd_refined4.1321

+
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