[English] 日本語
Yorodumi
- PDB-6t0m: Cationic Trypsin in Complex with a D-Phe-Pro-diaminopyridine deri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t0m
TitleCationic Trypsin in Complex with a D-Phe-Pro-diaminopyridine derivative
ComponentsCationic trypsin
KeywordsHYDROLASE / PROTEASE / SERINE PROTEASE / DIGESTION / METAL ION BINDING
Function / homology
Function and homology information


cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Trypsin
Similarity search - Domain/homology
Chem-GOZ / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsNgo, K. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Authors: Ngo, K. / Collins-Kautz, C. / Gerstenecker, S. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4816
Polymers25,8061
Non-polymers6755
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-25 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.454, 56.756, 66.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cationic trypsin


Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

-
Non-polymers , 5 types, 176 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOZ / (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[[2,6-bis(azanyl)pyridin-4-yl]methyl]pyrrolidine-2-carboxamide


Mass: 382.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M imidazole, 0.1% (w/v) sodium azide, 25-27% (w/v) PEG8000
PH range: 7-8

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.507→43.223 Å / Num. obs: 33113 / % possible obs: 99.4 % / Redundancy: 5.75 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.06 / Rsym value: 0.055 / Net I/σ(I): 17.54
Reflection shellResolution: 1.51→1.6 Å / Mean I/σ(I) obs: 3.12 / Num. unique obs: 5172 / CC1/2: 0.858 / Rrim(I) all: 0.537 / Rsym value: 0.487

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNK
Resolution: 1.51→43.22 Å / SU ML: 0.1201 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.4187
RfactorNum. reflection% reflection
Rfree0.1709 1655 5 %
Rwork0.1482 --
obs0.1494 33111 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.5 Å2
Refinement stepCycle: LAST / Resolution: 1.51→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 42 171 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731749
X-RAY DIFFRACTIONf_angle_d0.93492387
X-RAY DIFFRACTIONf_chiral_restr0.0647265
X-RAY DIFFRACTIONf_plane_restr0.0067324
X-RAY DIFFRACTIONf_dihedral_angle_d9.24531060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.22721300.19452476X-RAY DIFFRACTION95.21
1.55-1.60.19691350.16942586X-RAY DIFFRACTION99.96
1.6-1.660.18861370.15132597X-RAY DIFFRACTION99.74
1.66-1.730.17861370.1422605X-RAY DIFFRACTION100
1.73-1.80.16711370.13692594X-RAY DIFFRACTION99.85
1.8-1.90.17241360.13322599X-RAY DIFFRACTION99.74
1.9-2.020.15641390.132623X-RAY DIFFRACTION99.78
2.02-2.170.14911370.12732612X-RAY DIFFRACTION100
2.17-2.390.151390.13092634X-RAY DIFFRACTION99.68
2.39-2.740.18771390.14482651X-RAY DIFFRACTION99.93
2.74-3.450.1671410.15182682X-RAY DIFFRACTION99.68
3.45-43.220.17391480.1642797X-RAY DIFFRACTION99.7
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2043029708650.006207357453340.02737490697850.2054332983540.07131275389220.2550230564430.00582637874208-0.0717621593684-0.05262400275230.120847617276-0.0170569520782-0.07605460494060.00371307519282-0.0193081323291-2.6673077433E-50.181229045656-0.013657444277-0.01132157051660.1565130353630.007247962774610.142937215702-2.47747374934-22.23078787620.3708987504
20.257681041037-0.243369757684-0.04154557920160.268750162705-0.03035962575560.120823370358-0.0240096530587-0.0763460438830.008386590523110.0505213512963-0.003588583667030.0236909734588-0.061330697874-0.0706634897673-3.094091674E-50.180990159293-0.0276294838536-0.0009739345805690.1571536595160.008139475059550.152394798399-9.7389832819-21.211391324413.4789199307
30.3209352080230.0342307588128-0.3021989034360.3571121326910.0764795460440.3676553544450.03666585456370.0781518018245-0.0261665362166-0.0483868832282-0.0194467181002-0.03068280787410.019042670768-0.01639736951913.47734625458E-50.124871023204-0.000300475338996-0.006232838854170.1414234981610.003418711495570.1438130919620.711448099332-21.80686782240.641628111824
40.3967745045450.09085084129430.1771919773610.317167056589-0.1816622824640.2498430253490.01076088025770.0839450351126-0.0850716830282-0.00857106013922-0.08011165894090.03411769921190.0571556552771-0.0584094526274-0.0001352546991230.140453299778-0.00638137442475-0.01241981311860.158128884865-0.009638160260820.142884152576-8.56663644806-22.01169473624.03289255713
50.115352468407-0.07535749882460.0984277940390.2354182901240.118055282440.2634562003350.0621515689784-0.07975853318930.05363681442590.128877647715-0.0173984474084-0.0257460624611-0.02337710455490.0387667539257-1.94395521335E-50.173552267684-0.023652594046-0.001048412689310.1744130293790.009443222068260.1579437455313.60873657754-23.932811727614.111678438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 156 through 215 )
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 245 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 155 )

+
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://pdbjlvh1.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