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- PDB-2ftm: Crystal structure of trypsin complexed with the BPTI variant (Tyr... -

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Basic information

Entry
Database: PDB / ID: 2ftm
TitleCrystal structure of trypsin complexed with the BPTI variant (Tyr35->Gly)
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
Keywordshydrolase/hydrolase inhibitor / PROTEASE-INHIBITOR COMPLEX / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


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 / trypsin / serpin family protein binding ...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 / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / protease binding / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding
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
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHanson, W.M. / Horvath, M.P. / Goldenberg, D.P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Rigidification of a Flexible Protease Inhibitor Variant upon Binding to Trypsin.
Authors: Hanson, W.M. / Domek, G.J. / Horvath, M.P. / Goldenberg, D.P.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Aug 29, 2018Group: Advisory / Data collection ...Advisory / Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_validate_polymer_linkage
Item: _entity.src_method
Revision 1.5Aug 30, 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 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600Heterogen The residue IAS is connected to residue 116 by a beta-peptide linkage. This is a covalent ...Heterogen The residue IAS is connected to residue 116 by a beta-peptide linkage. This is a covalent bond between CG of IAS and N of the following residue in conformer A of the residues.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,96318
Polymers29,7472
Non-polymers1,21616
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-120 kcal/mol
Surface area11700 Å2
MethodPISA
2
A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules

A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules

A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules

A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,85172
Polymers118,9878
Non-polymers4,86464
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area25450 Å2
ΔGint-614 kcal/mol
Surface area38150 Å2
MethodPISA
3
A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules

A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,92536
Polymers59,4934
Non-polymers2,43232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area10720 Å2
ΔGint-276 kcal/mol
Surface area21000 Å2
MethodPISA
4
A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules

A: Cationic trypsin
B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,92536
Polymers59,4934
Non-polymers2,43232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area9920 Å2
ΔGint-267 kcal/mol
Surface area21880 Å2
MethodPISA
5
A: Cationic trypsin
hetero molecules

A: Cationic trypsin
hetero molecules

B: Pancreatic trypsin inhibitor
hetero molecules

B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,92536
Polymers59,4934
Non-polymers2,43232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
Buried area8100 Å2
ΔGint-280 kcal/mol
Surface area23700 Å2
MethodPISA
6
A: Cationic trypsin
hetero molecules

B: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,96318
Polymers29,7472
Non-polymers1,21616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area3600 Å2
ΔGint-129 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.591, 81.736, 123.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-2003-

CA

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23325.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin
#2: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPI / BPTI / Aprotinin


Mass: 6421.446 Da / Num. of mol.: 1 / Mutation: Y35G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid details: (Biochemistry 1988, 27, 2481-2489) / Plasmid: PTI103 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00974

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Non-polymers , 5 types, 254 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM calcium chloride, 0.1 M HEPES, 2.0 M ammonium sulfate, 0.02% sodium azide; 20% ethylene glycol added upon harvesting and prior to freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: NONIUS KAPPA CCD2000 / Detector: CCD / Date: Aug 4, 2002 / Details: OSMIC CONFOCAL MAX-FLUX (GREEN)
RadiationMonochromator: OSMIC CONFOCAL MAX-FLUX (GREEN) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 45596 / Num. obs: 45459 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4357 / % possible all: 97.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2PTC

2ptc


Resolution: 1.65→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: maximum likelihood for measured reflection intensities (mli) target as implemented in CNS SOLVE 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 3671 8 %RANDOM; SAME SET AS FOR PDB IDS 2FI3, 2FI4 AND 2FI5
Rwork0.2068 ---
all0.2078 45740 --
obs0.2078 45459 99.4 %-
Solvent computationBsol: 22.48 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 64 238 2378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.0011.5
X-RAY DIFFRACTIONc_mcangle_it1.5182
X-RAY DIFFRACTIONc_scbond_it1.5232
X-RAY DIFFRACTIONc_scangle_it2.1762.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.65-1.750.28758280.2536657723996.28
1.75-1.890.2586010.2327552100
1.89-2.080.2295860.2177571100
2.08-2.380.2366320.2197569100
2.38-30.2276150.209765499.98
3-200.196550.1857874100

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