[English] 日本語
Yorodumi
- PDB-1o2i: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Bindin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o2i
TitleElaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / 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
Chem-655 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsKatz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, W.F. / Hui, H. / Breitenbucher, G. / Allen, D. / Janc, J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, ...Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7974
Polymers23,3241
Non-polymers4733
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.67, 63.39, 69.21
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein BETA-TRYPSIN / E.C.3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#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-655 / 2-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}-6-(CYCLOPENTYLOXY)BENZENOLATE / CRA_10655


Mass: 336.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.1
Details: magnesium sulfate soak at target pH (6.54). vapor diffusion at 298 K, pH 8.10
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Katz, B.A., (2001) J.Mol.Biol., 307, 1451.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.10 MHEPES1reservoirpH7.5 or 8.2
30.30 M1reservoirNaCl
422 %(v/v)PEG5000 MME1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→28.92 Å / Num. all: 45626 / Num. obs: 34199 / % possible obs: 75 % / Observed criterion σ(I): 0.6 / Redundancy: 2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.8
Reflection shellResolution: 1.5→1.57 Å / % possible obs: 43.3 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 1.2 / Num. unique all: 5764
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. obs: 35909 / Num. measured all: 70117
Reflection shell
*PLUS
Mean I/σ(I) obs: 1.3

-
Processing

Software
NameVersionClassification
bioteX1.2data collection
bioteX1.2data reduction
X-PLOR3.851refinement
bioteXdata scaling
Quantamodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→7 Å / Cross valid method: THROUGHOUT / σ(F): 1.2
Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Ser110, Ser113, Ser130, Lys159, Asp165, Lys169, Ser170, Gln175, Lys230, Ser236, Ser244 Note that HOH383 ...Details: Residues simultaneously refined in two or more conformations are: Val53, Leu66, Ser86, Ser110, Ser113, Ser130, Lys159, Asp165, Lys169, Ser170, Gln175, Lys230, Ser236, Ser244 Note that HOH383 makes short H-bonds to OgSer195 and O6' of the inhibitor Disordered waters are: HOH276 which is close to conformation #2 of Lys230; HOH301 which is close to conformation #1 of Asp165 His40 and HIS91 are MONOPROTONATED ON THE EPSILON NITROGEN. His57 is doubly protonated.
RfactorNum. reflection% reflection
Rfree0.211 3390 10 %
Rwork0.19 --
obs0.192 33675 74.77 %
all-45038 -
Refinement stepCycle: LAST / Resolution: 1.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 51 894 4299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg3.5
Refinement
*PLUS
Highest resolution: 1.5 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rfree: 0.211

+
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