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- PDB-3vxf: X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5 -

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Basic information

Entry
Database: PDB / ID: 3vxf
TitleX/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5
Components
  • (BIVALIRUDIN) x 2
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLYSIS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / 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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / 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 / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / 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 / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / 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
BIVALIRUDIN N-terminus fragment / BIVALIRUDIN C-terminus fragment / DEUTERATED WATER / Prothrombin / Hirudin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / Resolution: 1.602 Å
AuthorsYamada, T. / Kurihara, K. / Masumi, K. / Tamada, T. / Tomoyori, K. / Ohnishi, Y. / Tanaka, I. / Kuroki, R. / Niimura, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex
Authors: Yamada, T. / Kurihara, K. / Ohnishi, Y. / Tamada, T. / Tomoyori, K. / Masumi, K. / Tanaka, I. / Kuroki, R. / Niimura, N.
History
DepositionSep 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 28, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / pdbx_entity_src_syn
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_value_order / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Thrombin light chain
H: Thrombin heavy chain
J: BIVALIRUDIN
I: BIVALIRUDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2975
Polymers36,0764
Non-polymers2211
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-23 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.998, 107.800, 45.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-1100-

DOD

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Components

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Protein/peptide , 3 types, 3 molecules LJI

#1: Protein/peptide Thrombin light chain / ALPHA-THROMBIN LIGHT CHAIN


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide BIVALIRUDIN


Type: Peptide-like / Class: Thrombin inhibitor / Mass: 1779.813 Da / Num. of mol.: 1 / Fragment: C-TERMINAL / Source method: obtained synthetically
Details: ENZYMATICALLY PRODUCED FROM BIVALIRUDIN DURING THE CRYSTALLIZATION
Source: (synth.) unidentified (others)
References: BIVALIRUDIN N-terminus fragment, UniProt: P28504*PLUS
#4: Protein/peptide BIVALIRUDIN


Type: Peptide-like / Class: Thrombin inhibitor / Mass: 419.498 Da / Num. of mol.: 1 / Fragment: N-TERMINAL / Source method: obtained synthetically
Details: ENZYMATICALLY PRODUCED FROM BIVALIRUDIN DURING THE CRYSTALLIZATION
Source: (synth.) unidentified (others) / References: BIVALIRUDIN C-terminus fragment

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Protein / Sugars / Non-polymers , 3 types, 160 molecules H

#2: Protein Thrombin heavy chain / ALPHA-THROMBIN HEAVY CHAIN


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#6: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: D2O

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Details

Sequence detailsBIVALIRUDIN IS HYDROLYZED AT ARG3-PRO4 BOND DURING CRYSTALLIZATION AND BECOMES TWO CHAINS. THE ...BIVALIRUDIN IS HYDROLYZED AT ARG3-PRO4 BOND DURING CRYSTALLIZATION AND BECOMES TWO CHAINS. THE COMPLETE SEQUENCE OF BIVALIRUDIN IS (DPN)PRPGGGGNGDFEEIPEEYL.

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7855.7
2
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: THE CRYSTAL WAS OBTAINED BY A SITTING DROP VAPOR DIFFUSION AFTER MACROSEEDING. 2% (W/V) TO 10% (W/V) PEG4000, 100MM SODIUM ACETATE PD5.0. THE INITIAL CONCENTRATION OF THROMBIN-BIVALIRUDIN ...Details: THE CRYSTAL WAS OBTAINED BY A SITTING DROP VAPOR DIFFUSION AFTER MACROSEEDING. 2% (W/V) TO 10% (W/V) PEG4000, 100MM SODIUM ACETATE PD5.0. THE INITIAL CONCENTRATION OF THROMBIN-BIVALIRUDIN COMPLEX WAS 5MG/ML, pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22982
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
NUCLEAR REACTORJRR-3M 1G-C22.6
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 4r1CCDJun 13, 2009Bending magnet, monochromator, mirrors
BIX-42IMAGE PLATEMar 23, 2009monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)Mneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.61
Reflection

Entry-ID: 3VXF

Resolution (Å)Num. allNum. obs% possible obs (%)Observed criterion σ(F)Observed criterion σ(I)Rmerge(I) obsDiffraction-IDNet I/σ(I)Biso Wilson estimate (Å2)
1.6-50511825118295.60-30.051134.5
2.8-10085098000.13424.7920.03
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.660.3325.2197.1
1.66-1.720.2436.8197.3
1.72-1.80.17310.9197.6
1.8-1.90.12513.8197.6
1.9-2.020.08817.9198.1
2.02-2.170.06822.7198.5
2.17-2.390.05629.1198.9
2.39-2.740.04739.7198.8
2.74-3.450.0444.9198
3.45-500.03645.6175.3
2.8-2.90.331.81270.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_663)refinement
DENZOdata reduction
SCALEPACKdata scaling
Refinement

Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Baniso 11 (Å2)Baniso 12 (Å2)Baniso 13 (Å2)Baniso 22 (Å2)Baniso 23 (Å2)Baniso 33 (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)FOM work R setSU MLDiffraction-IDσ(F)Phase errorShrinkage radii (Å)VDW probe radii (Å)Bsol (Å2)ksol (e/Å3)
1.602-29.227X-RAY DIFFRACTION17.899-1.0167002.9256-0-1.90890.18420.16090.1619190251136511363.7295.320.85820.1611.3516.971.371.453.5650.425
2.752-44.873NEUTRON DIFFRACTION15.6030.7967-0-0-2.711101.91440.23390.18280.18554048072573.720.28221.091.011.115.6030.558
Refinement stepCycle: LAST / Resolution: 1.602→29.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 14 158 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0165140
NEUTRON DIFFRACTIONf_angle_d2.0449130
NEUTRON DIFFRACTIONf_dihedral_angle_d17.9951339
NEUTRON DIFFRACTIONf_chiral_restr0.117350
NEUTRON DIFFRACTIONf_plane_restr0.01994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.602-1.65930.21361700.19734768X-RAY DIFFRACTION94
1.6593-1.72570.18751810.17694972X-RAY DIFFRACTION97
1.7257-1.80420.21741820.16765002X-RAY DIFFRACTION98
1.8042-1.89930.20171820.1635008X-RAY DIFFRACTION98
1.8993-2.01830.18981830.15245010X-RAY DIFFRACTION98
2.0183-2.17410.17751850.1485077X-RAY DIFFRACTION98
2.1741-2.39280.16651860.14745112X-RAY DIFFRACTION99
2.3928-2.73880.16251860.15385130X-RAY DIFFRACTION99
2.7388-3.44980.19142410.16135083X-RAY DIFFRACTION98
3.4498-29.23210.1852060.1714072X-RAY DIFFRACTION76
2.7523-3.15050.27381060.1942044NEUTRON DIFFRACTION60
3.1505-3.96890.23381410.17852705NEUTRON DIFFRACTION79
3.9689-44.87870.21711570.1812919NEUTRON DIFFRACTION81

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