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- PDB-1ql9: FACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT -

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Basic information

Entry
Database: PDB / ID: 1ql9
TitleFACTOR XA SPECIFIC INHIBITOR IN COMPLEX WITH RAT TRYPSIN MUTANT X99RT
ComponentsTRYPSIN
KeywordsHYDROLASE / SERINE PROTEASE / SERINE PROTEINASE
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
Chem-ZEN / Anionic trypsin-2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsStubbs, M.T.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-Induced Structural Plasticity
Authors: Reyda, S. / Sohn, C. / Klebe, G. / Rall, K. / Ullmann, D. / Jakubke, H.D. / Stubbs, M.T.
#1: Journal: J.Med.Chem. / Year: 1998
Title: Structural and Functional Analyses of Benzamidine-Based Inhibitors in Complex with Trypsin: Implications for the Inhibition of Factor Xa, Tpa, and Urokinase
Authors: Renatus, M. / Bode, W. / Huber, R. / Stuerzebecher, J. / Stubbs, M.T.
#2: Journal: Curr.Pharm.Des. / Year: 1996
Title: Structural Aspects of Factor Xa Inhibition
Authors: Stubbs, M.T.
#3: Journal: FEBS Lett. / Year: 1995
Title: Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin
Authors: Stubbs, M.T. / Huber, R. / Bode, W.
History
DepositionAug 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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.status_code_sf / _pdbx_entry_details.has_protein_modification / _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

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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)24,5004
Polymers23,8651
Non-polymers6353
Water1,26170
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.140, 124.140, 124.140
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 / TRYPSINOGEN / BETA-TRYPSIN


Mass: 23864.787 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: VARIANT X99RT\: RAT TRYPSIN CONTAINING THE "99"-LOOP OF FACTOR XA
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: PANCREAS / Plasmid: PYT / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZEN / [4-(6-CHLORO-NAPHTHALENE-2-SULFONYL)-PIPERAZIN-1-YL]- (3,4,5,6-TETRAHYDRO-2H-[1,4']BIPYRIDINYL-4-YL)- METHANONE


Mass: 499.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27ClN4O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE 223 AMINO ACIDS OF RAT TRYPSIN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS ...THE 223 AMINO ACIDS OF RAT TRYPSIN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS CHYMOTRYPSINOGEN. THE BINDING MODE OF THE INHIBITOR IS NOT AS EXPECTED: THE CHLORINATED NAPHTHALENE MOIETY REACHES DEEP INTO THE PRIMARY SPECIFICITY POCKET, WHERE THE BURIED WATER MOLECULE W416 IS DISPLACED BY THE CHLORINE ATOM (COMPARE WITH DAIICHI STRUCTURE 1MTW.PDB). CONCOMMITANT WITH THIS, (I) THE HYDROXYL FUNCTION OF SER190 (ALA IN FXA) ROTATES AWAY FROM THE INHIBITOR (II) A NEW WATER MOLECULE (PROVOCATIVELY LABELLED W416) APPEARS, COORDINATED BY ASP189OD2, GLY219O, ASN224O, AND W329 (W415) (III) THE PEPTIDE BOND SER217-GLY219 FLIPS (MAYBE TO ALLOW CLOSER APPROACH OF GLY219O TO W216) (IV) THE SIDE CHAIN OF TYR217 FLIPS UP TO FORM ONE SIDE OF A NOVEL "HYDROPHOBIC BOX", MIMICKING THE FACTOR XA STRUCTURE (ALTHOUGH WITH A DIFFERENT APPROACH TO PHE174) THE PIPERIDINYLPYRIDINE MOITIES OCCUPY LOCATIONS STRONGLY REMINISCENT OF THE DX9065A:TRYPSIN COMPLEXES (CF 1MTS.PDB, 1MTU.PDB, 1MTV.PDB); THE WEAKLY BASIC PYRIDINE WOULD OCCUPY THE "CATION HOLE" OF FACTOR XA THE SAME INHIBITOR HAS ALSO BEEN CRYSTALLIZED (A) WITH BOVINE TRYPSIN AT PH 8 (SEE PDB FILE EBI-2917), WHICH SHOWS SIMILAR STRUCTURAL REARRANGEMENTS, AND (B) WITH BOVINE TRYPSIN AT PH7, WHERE IT BINDS IN THE REVERSE DIRECTION (SEE PDB FILE EBI-2919)
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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growpH: 7 / Details: 25MM TRIS PH7, 10MM CACL2, 40% MGSO4, pH 7.00
Crystal grow
*PLUS
Method: unknown / Details: a single crystal was soaked
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113.5 mg/mlprotein11
2100 mMbenzamidine11
325 mMTris-HCl11
410 mM11CaCl2
540 %11MgSO4

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. obs: 16310 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.456 / Rsym value: 0.456 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 57863 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.189 --
obs0.189 14100 99.9 %
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 40 70 1780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
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
LS refinement shellResolution: 2.3→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.263 714 -
obs--99.9 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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