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- PDB-7a0d: The Crystal Structure of Bovine Thrombin in complex with Hirudin ... -

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Basic information

Entry
Database: PDB / ID: 7a0d
TitleThe Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6 Angstroms Resolution
Components
  • (ProthrombinThrombin) x 2
  • Hirudin variant-1
KeywordsHYDROLASE / Inhibitor / Hirudin / Thrombin / Selenocysteine / Derivative
Function / homology
Function and homology information


negative regulation of serine-type peptidase activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity ...negative regulation of serine-type peptidase activity / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Prothrombin / Hirudin variant-1
Similarity search - Component
Biological speciesBos taurus (cattle)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHidmi, T. / Mousa, R. / Pomyalov, S. / Lansky, S. / Khouri, L. / Metanis, N. / Shoham, G.
CitationJournal: Commun Chem / Year: 2021
Title: Diselenide crosslinks for enhanced and simplified oxidative protein folding
Authors: Mousa, R. / Hidmi, T. / Pomyalov, S. / Lansky, S. / Khouri, L. / Shalev, D.E. / Shoham, G. / Metanis, N.
History
DepositionAug 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HHH: Prothrombin
III: Hirudin variant-1
LLL: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0225
Polymers42,5753
Non-polymers4472
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Bovine thrombin composed of heavy chain (H) and light chain (L) complexed with selenocysteine Hirudin (C16U/C28U) (I)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-29 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.672, 102.374, 142.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11HHH-637-

HOH

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Components

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Protein , 2 types, 2 molecules HHHIII

#1: Protein Prothrombin / Thrombin / Coagulation factor II


Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#2: Protein Hirudin variant-1 / Hirudin-1 / Hirudin-I


Mass: 7067.295 Da / Num. of mol.: 1 / Mutation: C16U/C28U / Source method: obtained synthetically / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01050

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Protein/peptide / Sugars , 2 types, 2 molecules LLL

#3: Protein/peptide Prothrombin / Thrombin / Coagulation factor II


Mass: 5735.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 358 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.6→48.18 Å / Num. obs: 56998 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Rsym value: 0.096 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 12.5 % / Rmerge(I) obs: 2.37 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2752 / CC1/2: 0.421 / Rpim(I) all: 0.693 / Rrim(I) all: 2.47 / Rsym value: 2.37 / % possible all: 98.3

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Processing

Software
NameVersionClassification
DIALSdata processing
Aimlessdata scaling
Aimlessdata reduction
PHENIXphasing
Cootmodel building
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HRT
Resolution: 1.6→48.18 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.002 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2154 2797 4.911 %
Rwork0.1828 54156 -
all0.184 --
obs-56953 99.865 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.401 Å2-0 Å2-0 Å2
2---0.722 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 29 357 3187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122924
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.6543960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0145360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56822.273154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73315502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7211520
X-RAY DIFFRACTIONr_chiral_restr0.1360.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022234
X-RAY DIFFRACTIONr_nbd_refined0.2070.21273
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2230
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2830.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2080.220
X-RAY DIFFRACTIONr_mcbond_it2.9042.841428
X-RAY DIFFRACTIONr_mcangle_it4.1224.2271780
X-RAY DIFFRACTIONr_scbond_it4.5863.4621496
X-RAY DIFFRACTIONr_scangle_it6.8034.9772176
X-RAY DIFFRACTIONr_lrange_it8.48140.9954448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.281580.3173974X-RAY DIFFRACTION98.7808
1.642-1.6870.3182320.2933828X-RAY DIFFRACTION100
1.687-1.7350.2822120.2633766X-RAY DIFFRACTION100
1.735-1.7890.2741680.243666X-RAY DIFFRACTION99.9739
1.789-1.8470.2641880.2283522X-RAY DIFFRACTION100
1.847-1.9120.2491680.2043422X-RAY DIFFRACTION100
1.912-1.9840.231690.1933312X-RAY DIFFRACTION100
1.984-2.0650.1971660.1773184X-RAY DIFFRACTION99.9702
2.065-2.1570.2171900.1783051X-RAY DIFFRACTION100
2.157-2.2630.2641320.1842985X-RAY DIFFRACTION100
2.263-2.3850.2191340.1682783X-RAY DIFFRACTION100
2.385-2.530.2131300.1772667X-RAY DIFFRACTION100
2.53-2.7040.2011280.1782504X-RAY DIFFRACTION100
2.704-2.9210.2311320.1872319X-RAY DIFFRACTION100
2.921-3.1990.288920.2062170X-RAY DIFFRACTION100
3.199-3.5770.1921160.1761931X-RAY DIFFRACTION100
3.577-4.130.186950.1371741X-RAY DIFFRACTION100
4.13-5.0570.154750.1261490X-RAY DIFFRACTION100
5.057-7.1470.201690.2041163X-RAY DIFFRACTION99.9189
7.147-48.180.194430.211678X-RAY DIFFRACTION99.4483

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