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- PDB-1o2g: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Bindin... -

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Basic information

Entry
Database: PDB / ID: 1o2g
TitleElaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Components
  • (THROMBIN) x 2
  • ACETYL HIRUDIN
KeywordsBLOOD CLOTTING / HYDROLASE/INHIBITOR / serine protease / short hydrogen bond / inhibition mechanism / shift of pKa / trypsin / thrombin / urokinase / factor Xa / hydrolase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / 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 / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / 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 / lipopolysaccharide binding / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / 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 / 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 / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / 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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-696 / Prothrombin / Hirudin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.58 Å
AuthorsKatz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. ...Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, W.F. / Hui, H. / Breitenbucher, G. / Allen, D. / Janc, J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors
Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, ...Authors: Katz, B.A. / Elrod, K. / Verner, E. / Mackman, R.L. / Luong, C. / Shrader, W.D. / Sendzik, M. / Spencer, J.R. / Sprengeler, P.A. / Kolesnikov, A. / Tai, V.W.-F. / Hui, H.C. / Breitenbucher, J.G. / Allen, D. / Janc, J.W.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 13, 2013Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: THROMBIN
H: THROMBIN
I: ACETYL HIRUDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7195
Polymers35,3683
Non-polymers3502
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.36, 72.06, 72.96
Angle α, β, γ (deg.)90.0, 101.77, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-411-

HOH

21H-412-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules LI

#1: Protein/peptide THROMBIN / E.C.3.4.21.5 / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 328-363 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide ACETYL HIRUDIN


Mass: 1491.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P28504

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Protein , 1 types, 1 molecules H

#2: Protein THROMBIN / E.C.3.4.21.5 / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 364-620 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin

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Non-polymers , 3 types, 310 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-696 / 3-{5-[AMINO(IMINIO)METHYL]-1H-INDOL-2-YL}-1,1'-BIPHENYL-2-OLATE / CRA_8696


Mass: 327.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17N3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 2-propanol, PEG 4000, pH 6.5, vapor diffusion at 298 K, pH 6.50
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.0 mg/mlprotein1drop
250 mMHEPES1drop
350 %glycerol1droppH7.0
40.10 MHEPES1reservoir
50.30 M1reservoirNaCl
622 %PEG5000 MME1reservoirpH7.5 or 8.2

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Data collection

DiffractionMean temperature: 285 K / Ambient temp details: Crystal Cooler
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→32.19 Å / Num. all: 49555 / Num. obs: 45048 / % possible obs: 90.91 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.6
Reflection shellResolution: 1.58→1.65 Å / % possible obs: 48.34 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.2 / Num. unique all: 7062
Reflection
*PLUS
Highest resolution: 1.38 Å / Num. obs: 46254 / Num. measured all: 93493
Reflection shell
*PLUS
Rmerge(I) obs: 0.34

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Processing

Software
NameVersionClassification
CrystalClear1.3data collection
CrystalClear1.3data reduction
X-PLOR3.851refinement
CrystalClear(MSC/RIGAKU)data scaling
Quantamodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→7 Å / Cross valid method: THROUGHOUT / σ(F): 0.7
Details: Met_H84, Leu_H130, Val_H157, Pro_H166, and Ile_H174 were simultaneously refined in two conformations. No density was observed for Thr147, Trp148, Thr149, Ala149A, Asn149B, Val149C, Gly149D, ...Details: Met_H84, Leu_H130, Val_H157, Pro_H166, and Ile_H174 were simultaneously refined in two conformations. No density was observed for Thr147, Trp148, Thr149, Ala149A, Asn149B, Val149C, Gly149D, and Lys149E in the autolysis loop, and these residues are not included in the model. In the non-active site peptide inhibitor (acetylhirudin) the tyrosine hydroxyl is sulfonated. HOH477, OgSer195 and O6' of the inhibitor make a 3-centered short hydrogen bond array. Disordered waters include: HOH395 is close to a symmetry related equivalent of itself. HOH396 is close to a symmetry related equivalent of itself. HOH397 is close to a symmetry related equivalent of itself. HIS_H57 IS doubly protonated. HIS_H91 and His_H119 are monoprotonated on the epsilon nitrogen
RfactorNum. reflection% reflection
Rfree0.25 4349 10 %
Rwork0.219 --
obs0.222 42749 87.3 %
all-48956 -
Refinement stepCycle: LAST / Resolution: 1.58→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 26 308 2757
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg3.7
Refinement
*PLUS
Highest resolution: 1.58 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
LS refinement shell
*PLUS
Highest resolution: 1.58 Å / Lowest resolution: 1.65 Å / Rfactor Rfree: 0.25

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