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- PDB-4ufe: Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- c... -

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Basic information

Entry
Database: PDB / ID: 4ufe
TitleThrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-butyl)-3-phenyl-propanamide
Components
  • HIRUDIN VARIANT-2
  • THROMBIN HEAVY CHAIN
  • THROMBIN LIGHT CHAIN
KeywordsHYDROLASE / HYDROLASE INHIBITOR COMPLEX / SERINE PROTEASE / BLOOD COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / THROMBIN INHIBITOR / PREORGANIZATION / GLYCOSYLATION / BLOOD
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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-3ZD / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HIRUDO MEDICINALIS (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.593 Å
AuthorsRuehmann, E. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2016
Title: Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.
Authors: Ruhmann, E.H. / Rupp, M. / Betz, M. / Heine, A. / Klebe, G.
History
DepositionMar 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET 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
H: THROMBIN HEAVY CHAIN
I: HIRUDIN VARIANT-2
L: THROMBIN LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5168
Polymers34,6333
Non-polymers8845
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-40.1 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.006, 71.360, 72.524
Angle α, β, γ (deg.)90.00, 100.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-2088-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules IL

#2: Protein/peptide HIRUDIN VARIANT-2


Mass: 1548.580 Da / Num. of mol.: 1 / Fragment: RESIDUES 61-72 / Source method: obtained synthetically / Details: HIRUDIN (54-65) (SULFATED) / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P09945
#3: Protein/peptide THROMBIN LIGHT CHAIN /


Mass: 3432.829 Da / Num. of mol.: 1 / Fragment: RESIDUES 333-361 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN BLOOD PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin

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Protein / Sugars , 2 types, 2 molecules H

#1: Protein THROMBIN HEAVY CHAIN /


Mass: 29651.105 Da / Num. of mol.: 1 / Fragment: RESIDUES 364-621 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN BLOOD PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 293 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-3ZD / (2R)-N-[(2S)-1-[(4-carbamimidoylphenyl)methylamino]-1-oxidanylidene-propan-2-yl]-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanamide


Mass: 521.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N5O4S
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsASP 14L WAS NOT BUILD DUE TO LACK OF ELECTRON DENSITY RESIDUES 148-149E WERE NOT BUILD DUE TO LACK ...ASP 14L WAS NOT BUILD DUE TO LACK OF ELECTRON DENSITY RESIDUES 148-149E WERE NOT BUILD DUE TO LACK OF ELECTRON DENSITY RESIDUE G554 WAS NOT BUILD DUE TO LACK OF ELECTRON DESITY

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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: 2.47 Å3/Da / Density % sol: 50.3 % / Description: NONE
Crystal growpH: 7.5
Details: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, PH 7.5

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.59→29 Å / Num. obs: 42965 / % possible obs: 91.5 % / Observed criterion σ(I): 2.6 / Redundancy: 3.2 % / Biso Wilson estimate: 14.51 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.9
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 80.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8D

1h8d


Resolution: 1.593→28.996 Å / SU ML: 0.14 / σ(F): 1.92 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1817 2188 5.1 %
Rwork0.1578 --
obs0.159 42961 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.593→28.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 58 289 2684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072507
X-RAY DIFFRACTIONf_angle_d1.0783392
X-RAY DIFFRACTIONf_dihedral_angle_d15.227990
X-RAY DIFFRACTIONf_chiral_restr0.044354
X-RAY DIFFRACTIONf_plane_restr0.005432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5928-1.62750.26371200.22472131X-RAY DIFFRACTION77
1.6275-1.66530.24141230.19872420X-RAY DIFFRACTION87
1.6653-1.7070.22821430.19062320X-RAY DIFFRACTION86
1.707-1.75310.21191040.17842432X-RAY DIFFRACTION86
1.7531-1.80470.1871570.17072341X-RAY DIFFRACTION86
1.8047-1.86290.19771290.16482395X-RAY DIFFRACTION86
1.8629-1.92950.1731080.15652404X-RAY DIFFRACTION86
1.9295-2.00670.1911350.14912468X-RAY DIFFRACTION89
2.0067-2.0980.16621220.15212536X-RAY DIFFRACTION91
2.098-2.20860.16471390.14642639X-RAY DIFFRACTION95
2.2086-2.34690.18791560.15592707X-RAY DIFFRACTION97
2.3469-2.5280.17981390.15722766X-RAY DIFFRACTION99
2.528-2.78230.20481630.17072772X-RAY DIFFRACTION100
2.7823-3.18440.18211540.16832788X-RAY DIFFRACTION100
3.1844-4.01040.16981680.14282773X-RAY DIFFRACTION100
4.0104-29.00110.15391280.14582881X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0752-0.16780.80065.0690.19221.53970.1653-0.0126-0.1990.0191-0.16710.4167-0.0002-0.24960.0040.08840.01370.00040.1251-0.02480.13571.1423-0.562717.2746
22.3557-0.6895-0.65252.75631.22423.09730.22220.7206-0.1578-0.4735-0.2355-0.0830.20260.2082-0.010.19150.10350.00310.2575-0.030.134215.2163-1.90038.8029
30.34-0.41870.47481.6019-0.59510.95460.31350.4003-0.0255-0.3627-0.2964-0.1070.25120.1678-0.01880.18740.09420.00120.2355-0.02770.120216.2394-4.01428.4823
42.0768-0.96750.40681.11420.0911.22080.15380.28890.1657-0.101-0.1436-0.1849-0.03970.2501-0.01150.09930.01870.0260.15040.01730.120120.97631.927815.7705
52.691-0.60930.18471.7472-0.22282.3128-0.0959-0.34670.15190.24870.108-0.07350.00370.20130.00040.13650.02810.00110.1419-0.02540.12869.51723.784932.1625
61.2321-0.6237-0.09271.7268-0.76211.21330.1540.0874-0.4041-0.17670.05230.24430.335-0.0684-0.11590.1438-0.0002-0.04340.1022-0.02040.20164.1141-8.77219.9951
70.25850.6794-0.56624.7095-1.11570.9432-0.0744-0.1281-0.11570.32850.0837-0.13510.02980.06430.00080.18090.039-0.0170.13990.01780.146218.4978-11.244835.9023
84.07431.24710.09422.9248-0.62153.52790.1297-0.1322-0.26620.16730.03250.30650.3453-0.2676-0.090.14910.01850.01410.06840.02750.19576.735-9.741227.8745
91.5421-0.49380.16981.22980.10071.29360.0334-0.0884-0.11470.00480.00680.06220.0916-0.0192-0.03490.09420.01730.01310.08070.00410.097810.4068-1.927727.3396
107.52921.6302-4.64415.1879-2.66694.09480.2301-0.05960.6998-0.0444-0.1277-0.3886-0.50010.558-0.15960.159-0.02420.01650.1637-0.00320.297126.71367.910422.5464
111.113-0.0277-0.38171.70410.00231.4420.20070.684-0.1846-0.8142-0.0274-0.1763-0.03570.0416-0.03490.41440.17230.06080.6322-0.0820.152512.0099-1.8202-3.271
125.98010.21845.09647.66361.57257.2176-0.04990.25460.2599-0.154-0.0642-0.2924-0.52050.1310.1140.16620.05390.04780.07530.0210.09755.041213.821718.2187
132.883-0.1145-0.0353.533-4.7836.59140.0687-0.02340.1584-0.1741-0.0520.1905-0.0975-0.2497-0.04840.10630.06250.00740.1384-0.03020.1274-3.635111.026620.7145
143.73290.80861.46144.60070.27052.05010.0137-0.39310.07440.30160.09230.26080.0097-0.354-0.0140.13510.04320.06650.13880.00430.1464-1.21874.94632.4242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'H' AND (RESID 16 THROUGH 29 )
2X-RAY DIFFRACTION2CHAIN 'H' AND (RESID 30 THROUGH 50 )
3X-RAY DIFFRACTION3CHAIN 'H' AND (RESID 51 THROUGH 80 )
4X-RAY DIFFRACTION4CHAIN 'H' AND (RESID 81 THROUGH 125 )
5X-RAY DIFFRACTION5CHAIN 'H' AND (RESID 126 THROUGH 140 )
6X-RAY DIFFRACTION6CHAIN 'H' AND (RESID 141 THROUGH 164 )
7X-RAY DIFFRACTION7CHAIN 'H' AND (RESID 165 THROUGH 179 )
8X-RAY DIFFRACTION8CHAIN 'H' AND (RESID 180 THROUGH 197 )
9X-RAY DIFFRACTION9CHAIN 'H' AND (RESID 198 THROUGH 231 )
10X-RAY DIFFRACTION10CHAIN 'H' AND (RESID 232 THROUGH 246 )
11X-RAY DIFFRACTION11CHAIN 'I' AND (RESID 555 THROUGH 565 )
12X-RAY DIFFRACTION12CHAIN 'L' AND (RESID 1C THROUGH 7 )
13X-RAY DIFFRACTION13CHAIN 'L' AND (RESID 8 THROUGH 14B )
14X-RAY DIFFRACTION14CHAIN 'L' AND (RESID 14C THROUGH 14K )

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