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- PDB-1ets: REFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN ... -

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Entry
Database: PDB / ID: 1ets
TitleREFINED 2.3 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF BOVINE THROMBIN COMPLEXES FORMED WITH THE BENZAMIDINE AND ARGININE-BASED THROMBIN INHIBITORS NAPAP, 4-TAPAP AND MQPA: A STARTING POINT FOR IMPROVING ANTITHROMBOTICS
Components(EPSILON-THROMBIN) x 2
KeywordsHYDROLASE/HYDROLASE inhibitor / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / : / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / 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
N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide / Chem-MID / Prothrombin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBode, W. / Brandstetter, H.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.
Authors: Brandstetter, H. / Turk, D. / Hoeffken, H.W. / Grosse, D. / Sturzebecher, J. / Martin, P.D. / Edwards, B.F. / Bode, W.
#1: Journal: To be Published
Title: Crystallographic Determination of Thrombin Complexes with Small Synthetic Inhibitors as a Starting Point for the Receptor-Based Design of Antithrombotics
Authors: Bode, W. / Brandstetter, H. / Turk, D. / Bauer, M. / Stuerzebecher, J.
#2: Journal: To be Published
Title: X-Ray Crystal Structure of Thrombin in Complex with D-Phe-Pro-Arg and with Small Benzamidine and Arginine-Based "Non-Peptidic" Inhibitors
Authors: Bode, W.
#3: Journal: Protein Sci. / Year: 1992
Title: The Refined 1.9-Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed ...Title: The Refined 1.9-Angstroms X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships
Authors: Bode, W. / Turk, D. / Karshikov, A.
#4: Journal: FEBS Lett. / Year: 1991
Title: Geometry of Binding of the Nalpha-Tosylated Piperidides of M-Amidino-, P-Amidino-and P-Guanidino Phenylalanine to Thrombin and Trypsin: X-Ray Crystal Structures of Their Trypsin Complexes and ...Title: Geometry of Binding of the Nalpha-Tosylated Piperidides of M-Amidino-, P-Amidino-and P-Guanidino Phenylalanine to Thrombin and Trypsin: X-Ray Crystal Structures of Their Trypsin Complexes and Modeling of Their Thrombin Complexes
Authors: Turk, D. / Stuerzebecher, J. / Bode, W.
#5: Journal: Eur.J.Biochem. / Year: 1990
Title: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl- ...Title: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N-Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N-Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin
Authors: Bode, W. / Turk, D. / Stuerzebecher, J.
#6: Journal: Embo J. / Year: 1989
Title: The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment
Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J.
History
DepositionJul 6, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jun 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: EPSILON-THROMBIN
H: EPSILON-THROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0293
Polymers35,5082
Non-polymers5221
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-12 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.730, 88.730, 102.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Atom site foot note1: RESIDUE PRO H 37 IS A CIS PROLINE.

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Components

#1: Protein/peptide EPSILON-THROMBIN


Mass: 5735.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00735, thrombin
#2: Protein EPSILON-THROMBIN


Mass: 29772.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00735, thrombin
#3: Chemical ChemComp-MID / 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine / NAPAP


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 521.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N5O4S
References: N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAMIDINOPHENYLALANINE (OF NAPAP) BINDS TO S1 SPECIFICITY POCKET, PIPERIDINE TO S2 AND NAPHLYL GROUP ...AMIDINOPHENYLALANINE (OF NAPAP) BINDS TO S1 SPECIFICITY POCKET, PIPERIDINE TO S2 AND NAPHLYL GROUP TO "ARYL BINDING SITE".
Sequence detailsTHE NUMBERING OF THROMBIN RESIDUES IS BASED ON TOPOLOGICAL EQUIVALENCES WITH CHYMOTRYPSINOGEN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlbovine thrombin1drop
21 mg/mlinhibitor1drop
31.0 Mammonium sulphate1drop
40.1 Mpotassium phosphate1drop
51.9 Mammonium sulphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 13578 / % possible obs: 78 % / Observed criterion σ(I): 2 / Num. measured all: 84833 / Rmerge(I) obs: 0.142

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / Rfactor Rwork: 0.178 / Rfactor obs: 0.178
Details: THERE IS A CLEAVAGE IN THE CHAIN AT THR 149A - SER 149B IN THE INSERTION LOOP OF THROMBIN. THE AUTHORS DO NOT SEE THIS CLEAVAGE DUE TO DISORDER AT BOTH FLANKING REGIONS. NOTE THAT THE ...Details: THERE IS A CLEAVAGE IN THE CHAIN AT THR 149A - SER 149B IN THE INSERTION LOOP OF THROMBIN. THE AUTHORS DO NOT SEE THIS CLEAVAGE DUE TO DISORDER AT BOTH FLANKING REGIONS. NOTE THAT THE OCCUPANCY OF RESIDUES 148 - 149E IS GIVEN AS 0.0 INDICATING THAT THEY WERE NOT SEEN IN THE ELECTRON DENSITY MAPS.
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 37 228 2649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg3.089
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_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 12503 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.089

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