[English] 日本語
Yorodumi
- PDB-1o3p: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Bindin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o3p
TitleElaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Components(Urokinase-type plasminogen activatorUrokinase) x 2
KeywordsBLOOD CLOTTING / hydrolase / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / tertiary granule membrane / regulation of cell adhesion mediated by integrin / negative regulation of fibrinolysis / specific granule membrane / regulation of cell adhesion / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. ...Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / 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-655 / CITRIC ACID / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.81 Å
AuthorsKatz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...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. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W.
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. / Hui, H.C. / Breitenbucher, J.G. ...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. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 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 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urokinase-type plasminogen activator
B: Urokinase-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8645
Polymers31,1442
Non-polymers7213
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-2 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.54, 50.17, 66.44
Angle α, β, γ (deg.)90.0, 113.49, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-455-

HOH

21B-582-

HOH

31B-582-

HOH

-
Components

#1: Protein/peptide Urokinase-type plasminogen activator / Urokinase / UPA / U-PLASMINOGEN ACTIVATOR / UROKINASE-PLASMINOGEN ACTIVATOR


Mass: 2708.183 Da / Num. of mol.: 1 / Fragment: SHORT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: PPIC9LMWUPA / Production host: Pichia pastoris (fungus) / References: UniProt: P00749, u-plasminogen activator
#2: Protein Urokinase-type plasminogen activator / Urokinase / E.C.3.4.21.73 / UPA / U-PLASMINOGEN ACTIVATOR / UROKINASE-PLASMINOGEN ACTIVATOR


Mass: 28435.428 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: N145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: PPIC9LMWUPA / Production host: Pichia pastoris (fungus) / References: UniProt: P00749, u-plasminogen activator
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#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 / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→41.66 Å / Num. all: 22960 / Num. obs: 15430 / % possible obs: 67.2 % / Observed criterion σ(I): 0.8 / Redundancy: 2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.1
Reflection shellResolution: 1.81→1.89 Å / % possible obs: 36.6 % / Rmerge(I) obs: 0.215 / Num. unique all: 2749

-
Processing

Software
NameVersionClassification
bioteX1.2data collection
bioteX1.2data reduction
X-PLOR3.851refinement
bioteXdata scaling
Quantamodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.81→7 Å / Cross valid method: THROUGHOUT / σ(F): 1.6 / Stereochemistry target values: X-PLOR force field
Details: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues ...Details: Only Leu_A9 to Lys_A16 are included for the A-chain. Residues prior and after these residues are not visible (disordered). Residues after Lys_B243 are not visible (disordered). Residues simultaneously refined in two or more conformations are: Lys_A10, Met_B47, Glu_B84, Glu_B86, Leu_B123, Thr_B139, Gln_B192, Arg_B217, Leu_B235. HIS_H57 IS doubly protonated. HIS_H91 and His_H119 are MONOPROTONATED ON the epsilon nitrogen Disordered waters are: HOH382 which is close to conformation 1 of Arg_B217; HOH582 which is close to a symmetry-related equivalent of itself; HOH721 which is close to conformation 1 of Lys_A10; HOH1010 which is close to a symmetry-related equivalent of itself; Some of the waters may correspond to the disordered or mobile termini of the light chain. No energy terms between citrate 1 and 2 are included because they are hydrogen-bonded to one another via an unusually short hydrogen bond between carboxylate / hydroxyl groups. No energy terms are included among HOH_849, and OgSer195, and O6' of the inhibitor. These atoms form a very short multi-centered hydrogen-bonding network.
RfactorNum. reflection% reflection
Rfree0.249 1531 10 %
Rwork0.191 --
obs0.195 15319 69.02 %
all-22196 -
Refinement stepCycle: LAST / Resolution: 1.81→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 81 1029 5194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg4.2

+
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