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- PDB-3dy0: Crystal Structure of Cleaved PCI Bound to Heparin -

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Basic information

Entry
Database: PDB / ID: 3dy0
TitleCrystal Structure of Cleaved PCI Bound to Heparin
Components
  • C-terminus Plasma serine protease inhibitor
  • N-terminus Plasma serine protease inhibitor
KeywordsBLOOD CLOTTING / HYDROLASE INHIBITOR / serpin
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 / protein C inhibitor-coagulation factor V complex / protein C inhibitor-coagulation factor Xa complex / protein C inhibitor-coagulation factor XI 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 / 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 / phosphatidylcholine binding / glycosaminoglycan binding / negative regulation of hydrolase activity / retinoic acid binding / lipid transport / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / serine-type endopeptidase inhibitor activity / heparin binding / spermatogenesis / protease binding / external side of plasma membrane / protein-containing complex / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
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 ...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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Plasma serine protease inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLi, W. / Huntington, J.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The heparin binding site of protein C inhibitor is protease-dependent.
Authors: Li, W. / Huntington, J.A.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_xplor_file / refine / refine_ls_restr / reflns / reflns_shell / software / struct_asym / struct_conn / struct_ref_seq_dif / 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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_xplor_file.param_file / _pdbx_xplor_file.topol_file / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_number_reflns_all / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_param_bsol / _reflns.number_all / _reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I / _reflns_shell.number_unique_all / _software.classification / _software.name / _software.version / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _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
A: N-terminus Plasma serine protease inhibitor
B: C-terminus Plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6406
Polymers40,9952
Non-polymers1,6454
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-23 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.051, 49.451, 64.969
Angle α, β, γ (deg.)90.00, 113.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein N-terminus Plasma serine protease inhibitor / protein C inhibitor / Serpin A5 / PCI / Plasminogen activator inhibitor 3 / PAI-3 / PAI3 / ...protein C inhibitor / Serpin A5 / PCI / Plasminogen activator inhibitor 3 / PAI-3 / PAI3 / Acrosomal serine protease inhibitor


Mass: 37484.684 Da / Num. of mol.: 1 / Fragment: PPE cleaved, residues 37-372
Source method: isolated from a genetically manipulated source
Details: complexed with Heparin from Bos taurus lungs / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA5, PCI, PLANH3, PROCI / Production host: Escherichia coli (E. coli) / References: UniProt: P05154
#2: Protein/peptide C-terminus Plasma serine protease inhibitor


Mass: 3510.188 Da / Num. of mol.: 1 / Fragment: PPE cleaved, residues 379-406
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
#3: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 1429.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,5,4/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-1-2-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-L-AltpA]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 318 molecules

#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: obtained synthetically / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.12M Lithium Nitrate, 12% PEG 3350, 25% Glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2007 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.55→34.71 Å / Num. obs: 49709 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.296 / % possible all: 72.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LQ8

1lq8


Resolution: 1.55→26.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 953350.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2500 5 %RANDOM
Rwork0.197 ---
obs0.197 49696 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.06 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å20.74 Å2
2--2.54 Å20 Å2
3---0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.55→26.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 92 315 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.357 313 4.9 %
Rwork0.362 6078 -
obs--74.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEPARIN.PARAMHEPARIN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4NO3.PARNO3.TOP
X-RAY DIFFRACTION5GOL.PARGOL.TOP

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