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- PDB-2ody: Thrombin-bound boophilin displays a functional and accessible rea... -

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Basic information

Entry
Database: PDB / ID: 2ody
TitleThrombin-bound boophilin displays a functional and accessible reactive-site loop
Components
  • (Prothrombin (EC 3.4.21. ...) x 2
  • Boophilin
KeywordsBLOOD CLOTTING/BLOOD CLOTTING INHIBITOR / kunitz-type thrombin inhibitor / BLOOD CLOTTING-BLOOD CLOTTING INHIBITOR COMPLEX
Function / homology
Function and homology information


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 ...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 / extracellular region
Similarity search - Function
Epsilon-Thrombin; Chain L / Thrombin light chain domain / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. ...Epsilon-Thrombin; Chain L / Thrombin light chain domain / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / 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 / Few Secondary Structures / Irregular / 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
PHOSPHATE ION / Prothrombin / Boophilin-H2
Similarity search - Component
Biological speciesRhipicephalus microplus (southern cattle tick)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMacedo-Ribeiro, S. / Fuentes-Prior, P. / Pereira, P.J.B.
CitationJournal: Plos One / Year: 2008
Title: Isolation, cloning and structural characterisation of boophilin, a multifunctional kunitz-type proteinase inhibitor from the cattle tick.
Authors: Macedo-Ribeiro, S. / Almeida, C. / Calisto, B.M. / Friedrich, T. / Mentele, R. / Sturzebecher, J. / Fuentes-Prior, P. / Pereira, P.J.
History
DepositionDec 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999 SEQUENCE AUTHORS STATE THAT THE CHAINS A,C AND B,D ARE PRODUCTS OF CLEAVAGE OF THE PRECURSOR ... SEQUENCE AUTHORS STATE THAT THE CHAINS A,C AND B,D ARE PRODUCTS OF CLEAVAGE OF THE PRECURSOR SEQUENCE BEFORE CRYSTALLIZATION OF THIS COMPLEX.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prothrombin (EC 3.4.21.5)
B: Prothrombin (EC 3.4.21.5)
C: Prothrombin (EC 3.4.21.5)
D: Prothrombin (EC 3.4.21.5)
E: Boophilin
F: Boophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,66713
Polymers99,0206
Non-polymers6477
Water8,161453
1
A: Prothrombin (EC 3.4.21.5)
B: Prothrombin (EC 3.4.21.5)
E: Boophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8187
Polymers49,5103
Non-polymers3084
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-52 kcal/mol
Surface area18630 Å2
MethodPISA, PQS
2
C: Prothrombin (EC 3.4.21.5)
D: Prothrombin (EC 3.4.21.5)
F: Boophilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8496
Polymers49,5103
Non-polymers3393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-40 kcal/mol
Surface area19020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.500, 104.200, 129.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Prothrombin (EC 3.4.21. ... , 2 types, 4 molecules ACBD

#1: Protein/peptide Prothrombin (EC 3.4.21.5) / Coagulation factor II


Mass: 5735.240 Da / Num. of mol.: 2 / Fragment: Thrombin light chain, residues 318-366 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#2: Protein Prothrombin (EC 3.4.21.5) / Coagulation factor II


Mass: 29772.422 Da / Num. of mol.: 2 / Fragment: Thrombin heavy chain, residues 367-625 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin

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Protein / Sugars , 2 types, 3 molecules EF

#3: Protein Boophilin


Mass: 14002.282 Da / Num. of mol.: 2 / Fragment: Boophilin (isoform H2), Residues 16-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus microplus (southern cattle tick)
Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q8WPI2
#6: 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 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 , 3 types, 459 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 8000, 0.05M Potassium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.35→54.9 Å / Num. all: 51554 / Num. obs: 51554 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 9.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7400 / Rsym value: 0.29 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MKX

1mkx


Resolution: 2.35→47.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.203 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.276 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22995 2627 5.1 %RANDOM
Rwork0.1903 ---
all0.19235 48886 --
obs0.19235 48886 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.989 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20 Å2
2--1.22 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 0 37 453 7258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9549397
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86923.983344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.964151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7581550
X-RAY DIFFRACTIONr_chiral_restr0.0810.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025379
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.22958
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24616
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2522
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.61924201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11936737
X-RAY DIFFRACTIONr_scbond_it0.64222877
X-RAY DIFFRACTIONr_scangle_it1.01932660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 192 -
Rwork0.23 3540 -
obs--96.94 %
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)
12.52840.06330.03552.33890.56580.47010.02570.07290.1728-0.2987-0.02780.3781-0.2725-0.26980.0021-0.04320.0308-0.022-0.02260.0796-0.074141.857174.230160.6801
21.69650.0063-0.3321.244-0.35621.05260.0684-0.0722-0.1881-0.04940.0274-0.0586-0.0368-0.0182-0.0958-0.088-0.0032-0.0144-0.08030.0386-0.037153.864564.143765.7657
32.18990.22090.2432.70930.60871.4150.2383-0.4053-0.41320.3115-0.1834-0.33840.30570.0339-0.05490.0345-0.0805-0.12190.03650.042-0.167945.388475.1241101.4026
41.82790.7060.70431.40170.29530.86060.124-0.29490.17670.1796-0.18260.13050.0068-0.06910.0586-0.0532-0.04670.00620.0078-0.0839-0.104835.176686.834395.7916
54.32661.986-1.30871.2377-0.61610.4364-0.0258-0.0701-0.1424-0.08370.0125-0.04680.0327-0.01170.0134-0.0733-0.0191-0.0699-0.06610.0885-0.017155.268550.704475.0604
60.98951.89010.7326.68021.01960.623-0.0703-0.09850.0245-0.04930.16240.117-0.0631-0.0461-0.0922-0.10370.00730.004-0.0674-0.048-0.038623.347186.966884.8377
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1522 - 49
2X-RAY DIFFRACTION2BB16 - 2431 - 255
3X-RAY DIFFRACTION3CC1 - 1422 - 35
4X-RAY DIFFRACTION4DD16 - 2431 - 255
5X-RAY DIFFRACTION5EE16 - 1421 - 127
6X-RAY DIFFRACTION6FF16 - 1421 - 127

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