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- PDB-1xuh: TRYPSIN-KETO-BABIM-CO+2, PH 8.2 -

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Basic information

Entry
Database: PDB / ID: 1xuh
TitleTRYPSIN-KETO-BABIM-CO+2, PH 8.2
ComponentsTRYPSIN
KeywordsSERINE PROTEASE / COMPLEX / TRYPSIN-COBALT-SMALL MOLECULE LIGAND / DESIGNED SMALL MOLECULE LIGAND WITH MICROMOLAR AFFINITY
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
BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANONE / : / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKatz, B.A. / Clark, J.M. / Finer-Moore, J.S. / Jenkins, T.E. / Johnson, C.R. / Rose, M.J. / Luong, C. / Moore, W.R. / Stroud, R.M.
CitationJournal: Nature / Year: 1998
Title: Design of potent selective zinc-mediated serine protease inhibitors.
Authors: Katz, B.A. / Clark, J.M. / Finer-Moore, J.S. / Jenkins, T.E. / Johnson, C.R. / Ross, M.J. / Luong, C. / Moore, W.R. / Stroud, R.M.
History
DepositionOct 10, 1997Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_ins_code / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8665
Polymers23,3241
Non-polymers5414
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.990, 54.990, 109.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 129 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#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-BAO / BIS(5-AMIDINO-2-BENZIMIDAZOLYL)METHANONE


Mass: 346.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.05 Å3/Da / Density % sol: 14.7 %
Description: DATA WITH RSYM > 50 % WERE REJECTED ALONG WITH DATA WHOSE VALUES WERE > 3.5 SIGMA FROM THE MEAN FOR EACH SET OF SYMMETRY EQUIVALENTS
Crystal growpH: 8.2
Details: SYNTHETIC MOTHER LIQUOR = 75% SATURATED MAGNESIUM SULFATE, 25 % 1.0 M TRIS ADJUSTED TO PH 8.2; SATURATED IN KETO-BABIM, 5.0 MM CO+2. COMPLEX PRODUCED BY SOAKING TRYPSIN-BENZAMIDINE CO-CRYSTAL.
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionAmbient temp details: ROOM
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.45 Å / Num. obs: 7146 / % possible obs: 76.4 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.128
Reflection shellResolution: 2.37→2.47 Å / % possible all: 47.1
Reflection
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 7.5 Å / Num. measured all: 15007

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Processing

Software
NameVersionClassification
SADIEdata collection
SAINT(SIEMENS)data scaling
X-PLORmodel building
X-PLORrefinement
SADIEdata reduction
SAINT(SIEMENS)data reduction
X-PLORphasing
RefinementHighest resolution: 2.2 Å / σ(F): 1
Details: RESIDUES SIMULTANEOUSLY REFINED IN TWO OR MORE CONFORMATIONS ARE: SER88, SER110, LEU1123, GLN135, SER170, SER190, GLN192, SER236, ILE242. BULK SOLVENT WAS REFINED. HIS40 AND HIS91 ARE ...Details: RESIDUES SIMULTANEOUSLY REFINED IN TWO OR MORE CONFORMATIONS ARE: SER88, SER110, LEU1123, GLN135, SER170, SER190, GLN192, SER236, ILE242. BULK SOLVENT WAS REFINED. HIS40 AND HIS91 ARE MONOPROTONATED ON THE EPSILON NITROGEN, HIS57 IS MONOPROTONATED ON THE DELTA NITROGEN.
RfactorNum. reflection
Rfree0.188 -
Rwork0.135 -
obs0.135 6599
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 33 125 1787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noTopol file
X-RAY DIFFRACTION1TOPH19XB2_KBCO.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 7.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg27
LS refinement shell
*PLUS
Highest resolution: 2.37 Å / Lowest resolution: 2.47 Å

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