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- PDB-1xuf: TRYPSIN-BABIM-ZN+2, PH 8.2 -

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Basic information

Entry
Database: PDB / ID: 1xuf
TitleTRYPSIN-BABIM-ZN+2, PH 8.2
ComponentsTRYPSIN
KeywordsSERINE PROTEASE / COMPLEX / TRYPSIN-ZN+2-SMALL MOLECULE LIGAND / DESIGNED SMALL MOLECULE LIGAND WITH NANOMOLAR 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-BENZIMIDAZOLYL)METHANE ZINC / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 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 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)23,7623
Polymers23,3241
Non-polymers4382
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.800, 58.700, 67.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRYPSIN


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRYPSIN/ZN+2/SMALL MOLECULE LIGAND COMPLEX / Source: (natural) Bos taurus (domestic cattle) / 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-BAZ / BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE ZINC


Mass: 397.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N8Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 20 %
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 BABIM, 5.0 MM ZN+2. COMPLEX PRODUCED BY SOAKING TRYPSIN-BENZAMIDINE CO-CRYSTAL.
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionAmbient temp details: ROOM
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 14155 / % possible obs: 57 % / Observed criterion σ(I): 0.5 / Redundancy: 1.6 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.04→2.13 Å / % possible all: 51
Reflection shell
*PLUS
% possible obs: 51 %

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Processing

Software
NameVersionClassification
MSCSOFTWAREdata collection
X-PLORmodel building
X-PLORrefinement
MSCdata reduction
X-PLORphasing
RefinementHighest resolution: 1.9 Å / σ(F): 1
RfactorNum. reflection
Rfree0.229 -
Rwork0.153 -
obs0.153 8337
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 27 213 1869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.7
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_d26.5
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 noParam file
X-RAY DIFFRACTION1PARAM19XB2_MEOH.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
LS refinement shell
*PLUS
Highest resolution: 2.04 Å / Lowest resolution: 2.13 Å / Num. reflection Rfree: 2.04 / Num. reflection Rwork: 2.13

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