[English] 日本語
Yorodumi
- PDB-1qb1: Bovine Trypsin with 1-[2-[5-[amino(imino)methyl]-2-hydroxyphenoxy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qb1
TitleBovine Trypsin with 1-[2-[5-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy]pyridin-4-yl]piperidine-3-carboxylic Acid (ZK-806974)
ComponentsPROTEIN (TRYPSIN)
KeywordsHYDROLASE / SERINE PROTEINASE / PROTEIN-INHIBITOR COMPLEX / S1 POCKET / 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 / 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-974 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.8 Å
AuthorsWhitlow, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin.
Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. ...Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. / Light, D.R. / Morrissey, M.M.
#1: Journal: FEBS Lett. / Year: 1978
Title: Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen
Authors: Bode, W. / Huber, R.
#2: Journal: J.Med.Chem. / Year: 1999
Title: Design, Synthesis, and Activity of 2,6-Diphenoxypyridine-Derived Factor Xa Inhibitors
Authors: Phillips, G. / Davey, D. / Eagen, K. / Ng, H.P. / Pinkerton, M. / Koovakkat, S.K. / Whitlow, M. / Liang, A. / Trinh, L. / Morrissey, M.M.
#3: Journal: J.Med.Chem. / Year: 1998
Title: Discovery of N-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-3,5- Difluoro-6-[3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy] Pyridin-4-Yl-N-Methylglycine (Zk-807834): A Potent, Selective and ...Title: Discovery of N-[2-[5-[Amino(Imino)Methyl]-2-Hydroxyphenoxy]-3,5- Difluoro-6-[3-(4,5-Dihydro-1-Methyl-1H-Imidazol-2-Yl)Phenoxy] Pyridin-4-Yl-N-Methylglycine (Zk-807834): A Potent, Selective and Orally Active Inhibitor of the Blood Coagulation Enzyme Factor Xa
Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J. / Smith, D. / ...Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J. / Smith, D. / Subramanyam, B. / Sullivan, M.E. / Trinh, L. / Vergona, R. / Walters, J. / White, K. / Whitlow, M. / Wu, S. / Xu, W. / Morrissey, M.M.
#4: Journal: FEBS Lett. / Year: 1995
Title: Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin
Authors: Stubbs, M.T. / Huber, R. / Bode, W.
#5: Journal: J.Biol.Chem. / Year: 1996
Title: X-Ray Structure of Active Site-Inhibited Clotting Factor Xa. Implications for Drug Design and Substrate Recognition
Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / Von Der Saal, W. / Wirthensohn, K. / Engh, R.A.
#6: Journal: J.Mol.Biol. / Year: 1993
Title: Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution
Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W.
#7: Journal: Eur.J.Biochem. / Year: 1990
Title: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N Alpha-(3-Methyl- ...Title: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)- L-Arginyl]-2-Piperidine to Carboxylic Acid (Mqpa) Human Alpha-Thrombin. X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin
Authors: Bode, W. / Turk, D. / Sturzebecher, J.
#8: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Bovine Beta-Trypsin at 1.5 A Resolution in a Crystal Form with Low Molecular Packing Density. Active Site Geometry, Ion Pairs and Solvent Structure
Authors: Bartunik, H.D. / Summers, L.J. / Bartsch, H.H.
History
DepositionApr 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (TRYPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9303
Polymers23,3241
Non-polymers6062
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.16, 63.78, 69.35
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a monomer.

-
Components

#1: Protein PROTEIN (TRYPSIN) / EC 3.4.21.4


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: BOVINE TRYPSIN / Source method: isolated from a natural source / Details: BOEHRINGER MANNHEIM CATALOG NUMBER 109,827 / Source: (natural) Bos taurus (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-974 / 1-[2-[5-[AMINO(IMINO)METHYL]-2-HYDROXYPHENOXY]-6-[3-(4,5-DIHYDRO-1-METHYL-1H-IMIDAZOL-2-YL)PHENOXY] PYRIDIN-4-YL]PIPERIDINE-3-CARBOXYLIC ACID / ZK-806974


Mass: 565.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27F2N6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3 Å3/Da / Density % sol: 58.4 %
Description: STARTING FROM THE TRYPSIN 2-AMINOBENZIMIDAZOLE STRUCTURE
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MICROCRYSTALS WERE INITIALLY GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. REFERENCES 7 (BODE, TURK & STURZEBACHER) AND 8 (BARTUNIK, SUMMERS & BARTSH) HAVE DESCRIBED THE ...Details: MICROCRYSTALS WERE INITIALLY GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. REFERENCES 7 (BODE, TURK & STURZEBACHER) AND 8 (BARTUNIK, SUMMERS & BARTSH) HAVE DESCRIBED THE CRYSTALLIZATION OF THE ORTHORHOMBIC FORM OF BOVINE TRYPSIN. CRYSTALS WERE SEEDING INTO DROPS CONTAINING 40 MG/ML BOVINE TRYPSIN, 0.0125 M BENZAMIDINE, 0.7 TO 0.9 M AS, 0.05 M MES PH 6.0, 0.0025 M CACL2 AFTER EQUILIBRATION AGAINST THE CRYSTALLIZATION RESERVOIR FOR 1 DAY. THE CRYSTALLIZATION RESERVOIRS CONTAINED 1.4 TO 1.8 M AS, 0.1 M MES PH 6.0, 0.005 M CACL2., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8-2.0 Mammonium sulfate1reservoir
250 mMTris-HCl1reservoir
310 mM1reservoirCaCl2
415 mg/mltrypsin1drop
520 mM2-aminobenzimidazole1drop

-
Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 1995 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 26263 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.078 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.11 % / Mean I/σ(I) obs: 3.11 / Rsym value: 0.222 / % possible all: 99.9
Reflection
*PLUS
Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.222

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PROFFTrefinement
RefinementMethod to determine structure: DIRECT REPLACEMENT / Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: W.A.Hendrickson (1985) Methods in Enzymology, Volume 115, pages 370-381.
RfactorNum. reflection% reflection
Rfree0.237 890 4 %
Rwork0.183 --
all-22476 -
obs-21586 99 %
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 42 218 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6282
X-RAY DIFFRACTIONp_mcangle_it2.4293
X-RAY DIFFRACTIONp_scbond_it3.1353
X-RAY DIFFRACTIONp_scangle_it4.5524
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1650.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.5
X-RAY DIFFRACTIONp_multtor_nbd0.2140.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.2280.5
X-RAY DIFFRACTIONp_planar_tor33
X-RAY DIFFRACTIONp_staggered_tor16.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.320
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 4 % / Rfactor obs: 0.183 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it4

+
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