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- PDB-3b9f: 1.6 A structure of the PCI-thrombin-heparin complex -

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Basic information

Entry
Database: PDB / ID: 3b9f
Title1.6 A structure of the PCI-thrombin-heparin complex
Components
  • (Prothrombin) x 2
  • Plasma serine protease inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Michaelis complex / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Hydrolase / Kringle / Protease / Secreted / Serine protease / Zymogen / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


protein C inhibitor-TMPRSS7 complex / protein C inhibitor-TMPRSS11E complex / protein C inhibitor-PLAT complex / protein C inhibitor-PLAU complex / protein C inhibitor-thrombin complex / protein C inhibitor-KLK3 complex / protein C inhibitor-plasma kallikrein complex / seminal clot liquefaction / protein C inhibitor-coagulation factor V complex / protein C inhibitor-coagulation factor Xa complex ...protein C inhibitor-TMPRSS7 complex / protein C inhibitor-TMPRSS11E complex / protein C inhibitor-PLAT complex / protein C inhibitor-PLAU complex / protein C inhibitor-thrombin complex / protein C inhibitor-KLK3 complex / protein C inhibitor-plasma kallikrein complex / seminal clot liquefaction / protein C inhibitor-coagulation factor V complex / protein C inhibitor-coagulation factor Xa complex / protein C inhibitor-coagulation factor XI complex / acrosin binding / platelet dense tubular network / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / platelet alpha granule / glycosaminoglycan binding / phosphatidylcholine binding / retinoic acid binding / : / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / lipid transport / negative regulation of astrocyte differentiation / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / blood coagulation, fibrin clot formation / positive regulation of blood coagulation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : / Gamma-carboxylation of protein precursors / single fertilization / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / : / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Regulation of Complement cascade / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / lipopolysaccharide binding / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / positive regulation of insulin secretion / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of cell growth / protease binding / blood microparticle / spermatogenesis / G alpha (q) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / endoplasmic reticulum lumen / receptor ligand activity / serine-type endopeptidase activity / signaling receptor binding / external side of plasma membrane / calcium ion binding / positive regulation of cell population proliferation / protein-containing complex / proteolysis / : / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Epsilon-Thrombin; Chain L / Thrombin light chain domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family ...Epsilon-Thrombin; Chain L / Thrombin light chain domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Prothrombin / Plasma serine protease inhibitor / Plasma serine protease inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, W. / Adams, T.E. / Huntington, J.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.
Authors: Li, W. / Adams, T.E. / Nangalia, J. / Esmon, C.T. / Huntington, J.A.
History
DepositionNov 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 11, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _pdbx_entry_details.sequence_details / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 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
L: Prothrombin
H: Prothrombin
I: Plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,64713
Polymers79,9353
Non-polymers1,71110
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-46.2 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.055, 48.825, 97.850
Angle α, β, γ (deg.)78.72, 81.52, 77.69
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 1 types, 1 molecules L

#1: Protein/peptide Prothrombin / Coagulation factor II


Mass: 5641.175 Da / Num. of mol.: 1 / Fragment: Thrombin light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin

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Protein , 2 types, 2 molecules HI

#2: Protein Prothrombin / Coagulation factor II


Mass: 29764.219 Da / Num. of mol.: 1 / Fragment: Thrombin heavy chain / Mutation: S195A (chymotrypsin numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin
#3: Protein Plasma serine protease inhibitor / Protein C inhibitor / Acrosomal serine protease inhibitor / Plasminogen activator inhibitor 3 / ...Protein C inhibitor / Acrosomal serine protease inhibitor / Plasminogen activator inhibitor 3 / PAI3 / PCI / Serpin A5


Mass: 44529.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA5, PCI, PLANH3, PROCI / Production host: Escherichia coli (E. coli) / References: UniProt: P05154, UniProt: Q9N2I2*PLUS

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 595.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 531 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsNatural variant at this position

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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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 11% PEG 3350, 0.12M MgSO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2007
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.6→37.5 Å / Num. all: 102472 / Num. obs: 95914 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.8 / Num. unique all: 13603 / Rsym value: 0.445 / % possible all: 90.3

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Processing

Software
NameVersionClassification
CNS1refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OL2

2ol2


Resolution: 1.6→30.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1049755.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2928 3.1 %RANDOM
Rwork0.208 ---
obs0.208 95905 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1506 Å2 / ksol: 0.358332 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å2-1.98 Å2-2.66 Å2
2---0.68 Å24.78 Å2
3----1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.6→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5113 0 100 523 5736
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.392.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 460 3 %
Rwork0.325 15020 -
obs-15480 90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ligand.paramligand.top

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