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- PDB-1shh: Slow form of Thrombin Bound with PPACK -

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Basic information

Entry
Database: PDB / ID: 1shh
TitleSlow form of Thrombin Bound with PPACK
Components(thrombin) x 2
KeywordsHYDROLASE/hydrolase inhibitor / serine protease / HYDROLASE-hydrolase inhibitor complex
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / cytolysis by host of symbiont cells / thrombin / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / cytolysis by host of symbiont cells / thrombin / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of fibrinolysis / negative regulation of cytokine production involved in inflammatory response / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / positive regulation of blood coagulation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Peptide ligand-binding receptors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of release of sequestered calcium ion into cytosol / Intrinsic Pathway of Fibrin Clot Formation / fibrinolysis / Thrombin signalling through proteinase activated receptors (PARs) / lipopolysaccharide binding / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / negative regulation of proteolysis / growth factor activity / response to wounding / positive regulation of protein localization to nucleus / platelet activation / G alpha (q) signalling events / Golgi lumen / multicellular organism development / positive regulation of reactive oxygen species metabolic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / positive regulation of phosphatidylinositol 3-kinase signaling / heparin binding / positive regulation of cell growth / collagen-containing extracellular matrix / regulation of cell shape / blood microparticle / cell surface receptor signaling pathway / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of protein phosphorylation / proteolysis / signaling receptor binding / serine-type endopeptidase activity / endoplasmic reticulum lumen / calcium ion binding / positive regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin light chain domain superfamily / Thrombin light chain / Prothrombin/thrombin / Thrombin light chain / Kringle domain / Kringle domain profile. / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle ...Thrombin light chain domain superfamily / Thrombin light chain / Prothrombin/thrombin / Thrombin light chain / Kringle domain / Kringle domain profile. / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Domain containing Gla (gamma-carboxyglutamate) residues. / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Gla domain profile. / Vitamin K-dependent carboxylation domain. / Gamma-carboxyglutamic acid-rich (GLA) domain / 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 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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / Mathews, F.S. / Di Cera, E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Molecular dissection of na+ binding to thrombin.
Authors: Pineda, A.O. / Carrell, C.J. / Bush, L.A. / Prasad, S. / Caccia, S. / Chen, Z.W. / Mathews, F.S. / Di Cera, E.
History
DepositionFeb 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thrombin
B: thrombin
D: thrombin
E: thrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7107
Polymers67,5814
Non-polymers1,1293
Water8,701483
1
A: thrombin
B: thrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,7912
Non-polymers4541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-14 kcal/mol
Surface area12510 Å2
MethodPISA
2
D: thrombin
E: thrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4664
Polymers33,7912
Non-polymers6752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-10 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)61.340, 68.200, 162.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThere are two biological assemblies in the asymmetric unit. Assembly 1 consists of chains A and B. Assembly 2 consists of chains D and E.

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Components

#1: Protein/peptide thrombin / / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 2 / Fragment: THROMBIN LIGHT CHAIN (A)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734
#2: Protein thrombin / / Coagulation factor II


Mass: 29694.102 Da / Num. of mol.: 2 / Fragment: THROMBIN HEAVY CHAIN (B) / Mutation: R77aA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P00734, thrombin
#3: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / Details: PPAK was chemically synthesized. / References: D-Phe-Pro-Arg-CH2Cl
#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 / N-Acetylglucosamine


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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER ...THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES: 1) VIA A HEMIKETAL GROUP TO OG SER 195 IN CHAINS B AND E, 2) VIA A METHYLENE GROUP TO NE2 HIS 57 IN CHAINS B AND E.

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 16-22% PEG monomethyl ether 2000, 50 mM Bis-tris, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2003
RadiationMonochromator: Bent Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.55→81.47 Å / Num. all: 94467 / Num. obs: 94467 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 18.8 Å2 / Limit h max: 37 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 101 / Limit l min: 0 / Observed criterion F max: 648212.57 / Observed criterion F min: 0.32 / Rsym value: 0.056 / Net I/σ(I): 27.5
Reflection shellResolution: 1.55→1.61 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.351 / % possible all: 62.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPin CCP4phasing
CNS1.1refinement
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→81.47 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4598 5 %random
Rwork0.195 ---
all0.196 99938 --
obs0.196 92091 92.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.4406 Å2 / ksol: 0.393538 e/Å3
Displacement parametersBiso max: 80.58 Å2 / Biso mean: 24.9 Å2 / Biso min: 7.38 Å2
Baniso -1Baniso -2Baniso -3
1-6.73 Å20 Å20 Å2
2---1.37 Å20 Å2
3----5.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.25 Å
Luzzati d res high-1.55
Refinement stepCycle: LAST / Resolution: 1.55→81.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 75 483 5146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_torsion_deg24.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.98
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.55-1.620.3093634.80.3172610.01612360762461.7
1.62-1.710.3215214.90.295100780.014124121059985.4
1.71-1.810.2736245.30.242112530.011123571187796.1
1.81-1.950.2565554.60.221114830.011124191203896.9
1.95-2.150.22461550.196116890.009124561230498.8
2.15-2.460.22162050.195117410.009125021236198.9
2.46-3.10.2126405.10.195118430.008125771248399.3
3.1-81.470.2026605.20.181121450.008129921280598.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4ion.paramwater.top
X-RAY DIFFRACTION5fast1_ppack.paramfast1_ppack.top

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