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- PDB-1bra: RELOCATING A NEGATIVE CHARGE IN THE BINDING POCKET OF TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1bra
TitleRELOCATING A NEGATIVE CHARGE IN THE BINDING POCKET OF TRYPSIN
ComponentsTRYPSIN
KeywordsPROTEINASE/INHIBITOR / PROTEINASE-INHIBITOR complex
Function / homology
Function and homology information


Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
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
BENZAMIDINE / Anionic trypsin-2
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPerona, J.J. / Mcgrath, M.E. / Fletterick, R.J.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Relocating a negative charge in the binding pocket of trypsin.
Authors: Perona, J.J. / Tsu, C.A. / McGrath, M.E. / Craik, C.S. / Fletterick, R.J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structures of Rat Anionic Trypsin Complexed with the Protein Inhibitors Appi and Bpti
Authors: Perona, J.J. / Tsu, C.A. / Craik, C.S. / Fletterick, R.J.
History
DepositionDec 17, 1992Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _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)23,9753
Polymers23,8151
Non-polymers1602
Water2,468137
1
A: TRYPSIN
hetero molecules

A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9506
Polymers47,6302
Non-polymers3204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Unit cell
Length a, b, c (Å)124.400, 124.400, 124.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein TRYPSIN


Mass: 23814.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P00763, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsBENZAMIDINE IS AN ANALOG OF ARGININE WHICH POSSESSES A POSITIVELY CHARGED AMIDINIUM GROUP RATHER ...BENZAMIDINE IS AN ANALOG OF ARGININE WHICH POSSESSES A POSITIVELY CHARGED AMIDINIUM GROUP RATHER THAN A GUANIDINIUM. TWO BENZAMIDINES ARE MODELLED PER TRYPSIN. BEN 246 BINDS IN THE PRIMARY SPECIFICITY POCKET; BEN 247 BINDS NONSPECIFICALLY ON THE SURFACE OF THE MOLECULE AT A LATTICE CONTACT. RAT TRYPSIN CRYSTALS IN THIS CUBIC SPACE GROUP DO NOT GROW IN THE ABSENCE OF ADDED BENZAMIDINE IN THE CRYSTALLIZATION DROP.
Sequence detailsSEQUENCE ADVISORY NOTICE: SEQUENCE FOR THIS STRUCTURE WAS TAKEN FROM GENEMBL WHICH DIFFERS FROM ...SEQUENCE ADVISORY NOTICE: SEQUENCE FOR THIS STRUCTURE WAS TAKEN FROM GENEMBL WHICH DIFFERS FROM SWISSPROT SEQUENCE AT POSITIONS 61 AND 65.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mltrypsin1reservoir
225 %1reservoirMgSO4
340 mMTris-HCl1reservoir
475 mMbenzamidine1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 18200 / % possible obs: 73 % / Num. measured all: 50400 / Rmerge(I) obs: 0.089

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→6 Å / Rfactor obs: 0.156
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 10 137 1813
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d3.2
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

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