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- PDB-1lq8: Crystal structure of cleaved protein C inhibitor -

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Basic information

Entry
Database: PDB / ID: 1lq8
TitleCrystal structure of cleaved protein C inhibitor
Components(plasma serine protease ...) x 2
KeywordsBLOOD CLOTTING / serpin / protease / inhibitor / heparin / retinoic acid / protein C
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 / negative regulation of hydrolase activity / platelet alpha granule / phosphatidylcholine binding / glycosaminoglycan binding / retinoic acid binding / lipid transport / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of peptidase activity / serine-type endopeptidase inhibitor activity / heparin binding / protease binding / spermatogenesis / 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
ISOPROPYL ALCOHOL / Plasma serine protease inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuntington, J.A. / Kjellberg, M. / Stenflo, J.
CitationJournal: Structure / Year: 2003
Title: Crystal Structure of Protein C Inhibitor Provides Insights into Hormone Binding and Heparin Activation
Authors: Huntington, J.A. / Kjellberg, M. / Stenflo, J.
History
DepositionMay 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
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 / 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_validate_close_contact / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: plasma serine protease inhibitor
B: plasma serine protease inhibitor
C: plasma serine protease inhibitor
D: plasma serine protease inhibitor
E: plasma serine protease inhibitor
F: plasma serine protease inhibitor
G: plasma serine protease inhibitor
H: plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,60019
Polymers169,5548
Non-polymers3,04611
Water1,78399
1
A: plasma serine protease inhibitor
B: plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2975
Polymers42,3882
Non-polymers9093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-14 kcal/mol
Surface area16460 Å2
MethodPISA, PQS
2
C: plasma serine protease inhibitor
D: plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3156
Polymers42,3882
Non-polymers9274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-13 kcal/mol
Surface area16350 Å2
MethodPISA, PQS
3
E: plasma serine protease inhibitor
F: plasma serine protease inhibitor


Theoretical massNumber of molelcules
Total (without water)42,3882
Polymers42,3882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-31 kcal/mol
Surface area15930 Å2
MethodPISA, PQS
4
G: plasma serine protease inhibitor
H: plasma serine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5996
Polymers42,3882
Non-polymers1,2104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-10 kcal/mol
Surface area16490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.200, 244.030, 66.400
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Plasma serine protease ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
plasma serine protease inhibitor / PCI / Protein C inhibitor / Plasminogen activator inhibitor-3 / PAI3 / Acrosomal serine protease ...PCI / Protein C inhibitor / Plasminogen activator inhibitor-3 / PAI3 / Acrosomal serine protease inhibitor / serine/cysteine proteinase inhibitor clade A member 5


Mass: 38651.000 Da / Num. of mol.: 4
Fragment: N-terminal fragment from elastase cleavage, residues 30-375
Source method: isolated from a natural source / Details: Human PCI purified from discarded blood plasma. / Source: (natural) Homo sapiens (human) / Organ: liver / Tissue: blood / Tissue fraction: plasma / References: UniProt: P05154
#2: Protein/peptide
plasma serine protease inhibitor / PCI / Protein C inhibitor / Plasminogen activator inhibitor-3 / PAI3 / Acrosomal serine protease ...PCI / Protein C inhibitor / Plasminogen activator inhibitor-3 / PAI3 / Acrosomal serine protease inhibitor / serine/cysteine proteinase inhibitor clade A member 5


Mass: 3737.448 Da / Num. of mol.: 4
Fragment: C-terminal fragment from elastase cleavage, residues 376-405
Source method: isolated from a natural source / Details: Human PCI purified from discarded blood plasma. / Source: (natural) Homo sapiens (human) / Organ: liver / Tissue: blood / Tissue fraction: plasma / References: UniProt: P05154

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Sugars , 4 types, 8 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 2
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
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#7: 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.: 3
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 , 2 types, 102 molecules

#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, sodium fluoride, isopropanol, pH 7, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
217 %PEG33501drop
33 %isopropanol1drop
4170 mM1dropNaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jan 1, 2002
RadiationMonochromator: Double crystal: Si-111, Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→45.64 Å / Num. all: 68208 / Num. obs: 55034 / % possible obs: 80.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 53.85 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.112 / Net I/σ(I): 19.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.45 / % possible all: 27.8
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 45.6 Å / % possible obs: 81.7 % / Num. measured all: 68208

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EZX

1ezx


Resolution: 2.4→45.66 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1619 2.9 %randomly in thin shells
Rwork0.222 ---
all-68280 --
obs-55034 80.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-27.2 Å20 Å2-3.92 Å2
2---18.95 Å20 Å2
3----8.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.4→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11359 0 200 99 11658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 45.6 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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