[English] 日本語
Yorodumi
- PDB-2cmy: Crystal complex between bovine trypsin and Veronica hederifolia t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cmy
TitleCrystal complex between bovine trypsin and Veronica hederifolia trypsin inhibitor
Components
  • CATIONIC TRYPSIN
  • VERONICA HEDERIFOLIA TRYPSIN INHIBITOR
KeywordsHYDROLASE / ACYL-ENZYME INTERMEDIATE / SERINE PROTEASE INHIBITOR / ZYMOGEN / PROTEASE / DIGESTION / METAL-BINDING / SERINE PROTEASE
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / 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
Serine protease 1 / Trypsin inhibitor
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
VERONICA HEDERIFOLIA (ivyleaf speedwell)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsConners, R. / Yardley, J.L. / Konarev, A. / Shewry, P. / Brady, R.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: An Unusual Helix-Turn-Helix Protease Inhibitory Motif in a Novel Trypsin Inhibitor from Seeds of Veronica (Veronica Hederifolia L.).
Authors: Conners, R. / Konarev, A. / Forsyth, J. / Lovegrove, A. / Marsh, J. / Joseph-Horne, T. / Shewry, P. / Brady, R.L.
History
DepositionMay 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATIONIC TRYPSIN
B: VERONICA HEDERIFOLIA TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7056
Polymers27,3812
Non-polymers3244
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6.4 kcal/mol
Surface area12240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)60.657, 63.928, 71.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein CATIONIC TRYPSIN / BETA TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURIFIED PROTEIN OBTAINED FROM SIGMA / Source: (natural) BOS TAURUS (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Protein/peptide VERONICA HEDERIFOLIA TRYPSIN INHIBITOR


Mass: 4056.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM SEEDS / Source: (natural) VERONICA HEDERIFOLIA (ivyleaf speedwell) / Tissue: SEED / References: UniProt: P85981*PLUS

-
Non-polymers , 4 types, 114 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsVERONICA HEDERIFOLIA TRYPSIN INHIBITOR SEQUENCE IS NOT PRESENT IN ANY SEQUENCE DATABASE. WE WILL ...VERONICA HEDERIFOLIA TRYPSIN INHIBITOR SEQUENCE IS NOT PRESENT IN ANY SEQUENCE DATABASE. WE WILL SUBMIT THE SEQUENCE ON PUBLICATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 51.96 % / Description: NONE
Crystal growpH: 8
Details: CRYSTALS OF TRYPSIN WERE GROWN IN 2.5M AMMONIUM SULPHATE, 6MM CALCIUM CHLORIDE, 0.1M TRIS PH 8.15, 60MM BENZAMIDINE. THEY WERE BACKSOAKED IN 0.1M NA PHOSPHATE PH 5.8, 2.5M AMMONIUM SULPHATE ...Details: CRYSTALS OF TRYPSIN WERE GROWN IN 2.5M AMMONIUM SULPHATE, 6MM CALCIUM CHLORIDE, 0.1M TRIS PH 8.15, 60MM BENZAMIDINE. THEY WERE BACKSOAKED IN 0.1M NA PHOSPHATE PH 5.8, 2.5M AMMONIUM SULPHATE TO REMOVE BENZAMIDINE. CRYSTALS WERE MOVED TO 2.5M AMMONIUM SULPHATE, 1MM CALCIUM CHLORDIE, 0.1M TRIS PH 8 AND PEPTIDE INHIBITOR ADDED AT 10MM AND INCUBATED FOR 16 HOURS.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2003 / Details: MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.25→47.73 Å / Num. obs: 13342 / % possible obs: 97.5 % / Observed criterion σ(I): 1.4 / Redundancy: 4.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.4 / % possible all: 84.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFI

1sfi


Resolution: 2.25→47.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 12.837 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-6, 16-17 AND 30-34 OF THE VERONICA HEDERIFOLIA INHIBITOR (CHAIN B) ARE DISORDERED AND NOT INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 661 5 %RANDOM
Rwork0.194 ---
obs0.196 12681 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 73.66 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å20 Å20 Å2
2---2.78 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 17 110 1925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221849
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.9592490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8535235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.1425.30366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56815304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.147155
X-RAY DIFFRACTIONr_chiral_restr0.130.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021332
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.2793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21237
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.931.51235
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55521907
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4813721
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3164.5583
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 32
Rwork0.281 716
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.89690.03150.81712.1983-0.43521.48020.077-0.01-0.0754-0.01630.0011-0.04750.0122-0.0207-0.0781-0.172-0.0151-0.0253-0.19430.0023-0.234925.022-4.95315.045
24.5123-4.00433.20627.9233-1.02453.4520.0361-0.2457-0.04280.00450.07880.0919-0.24480.1152-0.1149-0.2182-0.0420.0777-0.23670.0125-0.281729.0990.69112.602
31.10310.6191.15321.9486-0.20682.32880.1405-0.14390.0548-0.1904-0.00970.25310.0106-0.1822-0.1308-0.21510.0006-0.0466-0.19260.0033-0.221417.023-3.1273.256
40.91510.7151.70831.72360.56653.6955-0.2703-0.19320.1514-0.43560.09720.2088-0.4313-0.28480.173-0.12070.0767-0.0637-0.14980.0071-0.195215.7645.6672.277
511.833-4.09610.25135.5308-2.78619.6865-0.12590.2246-0.1711-0.12240.5665-1.0606-0.31990.3467-0.4406-0.1905-0.08240.1606-0.1992-0.0579-0.122738.3877.1388.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 94
2X-RAY DIFFRACTION2A95 - 118
3X-RAY DIFFRACTION3A119 - 166
4X-RAY DIFFRACTION4A167 - 234
5X-RAY DIFFRACTION5A235 - 245

+
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