[English] 日本語
Yorodumi
- PDB-3atk: Crystal structure of trypsin complexed with cycloheptanamine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3atk
TitleCrystal structure of trypsin complexed with cycloheptanamine
ComponentsCationic trypsin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / PROTEIN / INHIBITOR / BOVINE PANCREAS / HYDROLASE-HYDROLASE INHIBITOR complex
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
cycloheptanamine / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsYamane, J. / Yao, M. / Tanaka, I.
CitationJournal: J.Appl.Crystallogr. / Year: 2011
Title: In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities
Authors: Yamane, J. / Yao, M. / Zhou, Y. / Hiramatsu, Y. / Fujiwara, K. / Yamaguchi, T. / Yamaguchi, H. / Togame, H. / Tsujishita, H. / Takemoto, H. / Tanaka, I.
History
DepositionJan 5, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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 / 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6345
Polymers23,3241
Non-polymers3104
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.501, 58.117, 66.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SZ1 / cycloheptanamine


Mass: 113.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M TRIS-HCL, 30% PEG 3350, 0.2M LITHIUM SULFATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 21283 / Num. obs: 21283 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 43.8
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 12.5 / Num. unique all: 2012 / Rsym value: 0.11 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A7T

3a7t


Resolution: 1.74→19.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.74 / SU ML: 0.058 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18413 1072 5 %RANDOM
Rwork0.16245 ---
all0.16355 20173 --
obs0.16355 20173 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.74→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 17 301 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221686
X-RAY DIFFRACTIONr_bond_other_d0.0020.021110
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9552285
X-RAY DIFFRACTIONr_angle_other_deg0.7953.0092724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54425.86258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77215269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.003152
X-RAY DIFFRACTIONr_chiral_restr0.0720.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02305
X-RAY DIFFRACTIONr_nbd_refined0.2330.2323
X-RAY DIFFRACTIONr_nbd_other0.1870.21166
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2839
X-RAY DIFFRACTIONr_nbtor_other0.0820.2867
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.880.258
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.239
X-RAY DIFFRACTIONr_mcbond_it0.4591.51139
X-RAY DIFFRACTIONr_mcbond_other0.0781.5466
X-RAY DIFFRACTIONr_mcangle_it0.72521770
X-RAY DIFFRACTIONr_scbond_it1.1543645
X-RAY DIFFRACTIONr_scangle_it1.754.5515
LS refinement shellResolution: 1.741→1.786 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 79 -
Rwork0.197 1389 -
obs-1389 99.59 %

+
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