[English] 日本語
Yorodumi
- PDB-1mtn: BOVINE ALPHA-CHYMOTRYPSIN:BPTI CRYSTALLIZATION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mtn
TitleBOVINE ALPHA-CHYMOTRYPSIN:BPTI CRYSTALLIZATION
Components
  • (ALPHA-CHYMOTRYPSIN) x 3
  • BASIC PANCREATIC TRYPSIN INHIBITOR
KeywordsCOMPLEX (HYDROLASE/INHIBITOR) / COMPLEX / PROTEASE INHIBITOR / TRYPSIN / HYDROLASE / SERINE / COMPLEX (HYDROLASE-INHIBITOR) COMPLEX
Function / homology
Function and homology information


chymotrypsin / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serpin family protein binding ...chymotrypsin / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular / 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
Chymotrypsinogen A / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCapasso, C. / Rizzi, M. / Menegatti, E. / Ascenzi, P. / Bolognesi, M.
CitationJournal: J.Mol.Recog. / Year: 1997
Title: Crystal structure of the bovine alpha-chymotrypsin:Kunitz inhibitor complex. An example of multiple protein:protein recognition sites.
Authors: Capasso, C. / Rizzi, M. / Menegatti, E. / Ascenzi, P. / Bolognesi, M.
History
DepositionMar 28, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Advisory / Data collection
Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_detector.pdbx_collection_date
Revision 1.4Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA-CHYMOTRYPSIN
B: ALPHA-CHYMOTRYPSIN
C: ALPHA-CHYMOTRYPSIN
D: BASIC PANCREATIC TRYPSIN INHIBITOR
E: ALPHA-CHYMOTRYPSIN
F: ALPHA-CHYMOTRYPSIN
G: ALPHA-CHYMOTRYPSIN
H: BASIC PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,96512
Polymers63,5808
Non-polymers3844
Water1,44180
1
A: ALPHA-CHYMOTRYPSIN
B: ALPHA-CHYMOTRYPSIN
C: ALPHA-CHYMOTRYPSIN
D: BASIC PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9826
Polymers31,7904
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-93 kcal/mol
Surface area13030 Å2
MethodPISA
2
E: ALPHA-CHYMOTRYPSIN
F: ALPHA-CHYMOTRYPSIN
G: ALPHA-CHYMOTRYPSIN
H: BASIC PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9826
Polymers31,7904
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-92 kcal/mol
Surface area12880 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20340 Å2
ΔGint-208 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.450, 102.450, 207.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.62, 0.784, -0.014), (0.784, -0.621, -0.011), (-0.017, -0.005, -1)
Vector: -49.63, 103.27, 35.9)
DetailsTHE TWO INDEPENDENT CHYMOTRYPSIN MOLECULES IN THE ASYMMETRIC UNIT HAVE BEEN ASSIGNED CHAIN IDENTIFIERS A, B, C, AND E, F, G. THE TRANSFORMATION SUPPLIED IN THE *MTRIX* RECORDS BELOW WILL GENERATE APPROXIMATE COORDINATES FOR CHAINS E, F, F WHEN APPLIED TO CHAINS A, B, C.

-
Components

-
Protein/peptide , 1 types, 2 molecules AE

#1: Protein/peptide ALPHA-CHYMOTRYPSIN / A-CHT


Mass: 1253.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin

-
Protein , 3 types, 6 molecules BFCGDH

#2: Protein ALPHA-CHYMOTRYPSIN / A-CHT


Mass: 13934.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin
#3: Protein ALPHA-CHYMOTRYPSIN / A-CHT


Mass: 10074.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin
#4: Protein BASIC PANCREATIC TRYPSIN INHIBITOR / BPTI / KUNITZ TYPE


Mass: 6527.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00974

-
Non-polymers , 2 types, 84 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTHE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ...THE ALPHA CHYMOTRYPSIN MOLECULE IS COMPRISED OF THREE POLYPEPTIDE CHAINS WHICH ARE DERIVED FROM THE ZYMOGEN OF THIS ENZYME BY EXCISION OF RESIDUES 14 - 15 AND 147 - 148.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.94 Å3/Da / Density % sol: 74 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.0 mg/mlalpha-CHT1drop
24.0 mg/mlBPTI1drop
31.0 Mmagnesium sulfate1drop
40.025 Msodium acetate1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: PINHOLE COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 27327 / % possible obs: 90.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.096
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. measured all: 106612

-
Processing

Software
NameClassification
MOSFLMdata reduction
AMoREphasing
TNTrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CHA

2cha


Resolution: 2.8→20 Å
Details: B FACTORS FOR SULFATE IONS ARE HIGHER THAN AVERAGE.
RfactorNum. reflection% reflection
Rfree0.24 -3.8 %
obs-27254 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 20 80 4520
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0130.02
X-RAY DIFFRACTIONt_angle_deg2.48
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0180.02
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_planar_d0.018
X-RAY DIFFRACTIONt_plane_restr0.017

+
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