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- PDB-7a0e: The Crystal Structure of Bovine Thrombin in complex with Hirudin ... -

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Basic information

Entry
Database: PDB / ID: 7a0e
TitleThe Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9 Angstroms Resolution
Components
  • (Prothrombin) 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
Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / 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: 1.9 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)42,8195
Polymers42,5753
Non-polymers2442
Water3,873215
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 (C6U/C14U) (I)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-35 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.099, 101.995, 144.044
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-543-

HOH

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Components

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Protein , 2 types, 2 molecules HHHIII

#1: Protein Prothrombin / 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: C6U/C14U / 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 / 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: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural 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 , 2 types, 216 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


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→72.02 Å / Num. obs: 33481 / % possible obs: 98.05 % / Redundancy: 10.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.062 / Rrim(I) all: 0.216 / Rsym value: 0.206 / Net I/σ(I): 5
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.848 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 1323 / CC1/2: 0.873 / Rpim(I) all: 1.061 / Rrim(I) all: 2.148 / Rsym value: 1.848

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Processing

Software
NameVersionClassification
xia2data processing
xia2data reduction
xia2data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A0D

7a0d


Resolution: 1.9→72.02 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.583 / SU ML: 0.192 / Cross valid method: FREE R-VALUE / ESU R: 0.166 / ESU R Free: 0.159
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2629 1572 4.703 %
Rwork0.2139 31852 -
all0.216 --
obs-33424 97.894 %
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: 40.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.548 Å20 Å2-0 Å2
2---0.38 Å20 Å2
3----0.168 Å2
Refinement stepCycle: LAST / Resolution: 1.9→72.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 15 215 3082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122957
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.6463994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3625360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67222.785158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3315505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2361518
X-RAY DIFFRACTIONr_chiral_restr0.1080.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022263
X-RAY DIFFRACTIONr_nbd_refined0.2160.21384
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2198
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.28
X-RAY DIFFRACTIONr_mcbond_it2.783.8561440
X-RAY DIFFRACTIONr_mcangle_it4.2085.7621794
X-RAY DIFFRACTIONr_scbond_it3.9064.2771517
X-RAY DIFFRACTIONr_scangle_it5.7346.2562198
X-RAY DIFFRACTIONr_lrange_it8.38452.9554562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3811010.4071923X-RAY DIFFRACTION81.0573
1.949-2.0030.381040.3882113X-RAY DIFFRACTION91.6494
2.003-2.0610.4031090.3572197X-RAY DIFFRACTION98.1694
2.061-2.1240.381920.3462208X-RAY DIFFRACTION99.9565
2.124-2.1940.41880.3272152X-RAY DIFFRACTION100
2.194-2.2710.3491170.2922046X-RAY DIFFRACTION100
2.271-2.3570.296830.2642017X-RAY DIFFRACTION100
2.357-2.4530.312940.2431901X-RAY DIFFRACTION100
2.453-2.5620.2841120.2421820X-RAY DIFFRACTION100
2.562-2.6870.306730.2321775X-RAY DIFFRACTION100
2.687-2.8320.297900.2181661X-RAY DIFFRACTION100
2.832-3.0040.256980.2071574X-RAY DIFFRACTION100
3.004-3.2110.285790.2061504X-RAY DIFFRACTION100
3.211-3.4680.239540.1921417X-RAY DIFFRACTION100
3.468-3.7990.232670.1681286X-RAY DIFFRACTION100
3.799-4.2470.229680.1541173X-RAY DIFFRACTION100
4.247-4.9030.143710.1161040X-RAY DIFFRACTION100
4.903-6.0040.312290.148903X-RAY DIFFRACTION100
6.004-8.4830.179250.177723X-RAY DIFFRACTION100
8.483-72.020.279180.219419X-RAY DIFFRACTION100

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