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- PDB-2uuk: Thrombin-hirugen-gw420128 ternary complex at 1.39A resolution -

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Basic information

Entry
Database: PDB / ID: 2uuk
TitleThrombin-hirugen-gw420128 ternary complex at 1.39A resolution
Components
  • HIRUDIN I
  • HUMAN ALPHA THROMBIN
  • THROMBIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / BLOOD CLOTTING / GLYCOPROTEIN / SERINE PROTEASE / CLEAVAGE ON PAIR OF BASIC RESIDUES / THROMBIN / SERINE PROTEASE INHIBITOR / HIRUGEN / ZYMOGEN / PROTEASE / SULFATION / HIGH RESOLUTION / SERINE PROTEINASE / BLOOD COAGULATION / PROTEASE INHIBITOR / NON-COVALENT ACTIVE SITE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of serine-type peptidase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin ...negative regulation of serine-type peptidase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / 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 / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / toxin activity / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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-897 / Prothrombin / Hirudin variant-1 / Hirudin variant-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HIRUDO MEDICINALIS (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsAhmed, H.U. / Blakeley, M.P. / Cianci, M. / Cruickshank, D.W.J. / Hubbard, J.A. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The Determination of Protonation States in Proteins.
Authors: Ahmed, H.U. / Blakeley, M.P. / Cianci, M. / Cruickshank, D.W.J. / Hubbard, J.A. / Helliwell, J.R.
History
DepositionMar 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other
Revision 1.4Aug 7, 2013Group: Atomic model / Other
Revision 1.5May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN ALPHA THROMBIN
B: THROMBIN
H: HIRUDIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7586
Polymers35,2403
Non-polymers5183
Water6,215345
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-21.1 kcal/mol
Surface area15820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.346, 71.436, 72.116
Angle α, β, γ (deg.)90.00, 100.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1104-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules AH

#1: Protein/peptide HUMAN ALPHA THROMBIN


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: RESIDUES 328-363 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin
#3: Protein/peptide HIRUDIN I / HIRUGEN


Mass: 1363.399 Da / Num. of mol.: 1 / Fragment: RESIDUES 55-64 / Source method: obtained synthetically
Details: THIS POLYPEPTIDE CHAIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE FOR THIS CHAIN OCCURS NATURALLY IN THE C-TERMINAL OF MEDICINAL LEECH(HIRUDO MEDICINALIS).
Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P28501, UniProt: P01050*PLUS

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Protein , 1 types, 1 molecules B

#2: Protein THROMBIN / HUMAN ALPHA THROMBIN / COAGULATION FACTOR II


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 364-622 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin

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Non-polymers , 4 types, 348 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-897 / N-[3-(TERT-BUTYLAMINO)-3-OXOPROPYL]-N-ISOPROPYL-3-METHYL-5-{[(2S)-2-(PYRIDIN-4-YLAMINO)PROPYL]OXY}BENZAMIDE


Mass: 454.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H38N4O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-GLU1C AND GLY14M-ARG15. RESIDUES THAT ARE MISSING ...RESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-GLU1C AND GLY14M-ARG15. RESIDUES THAT ARE MISSING FROM CHAIN B ARE TRP148-LYS149E TYR H 63 IS SULFONATED

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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: 2.27 Å3/Da / Density % sol: 45.9 % / Description: NONE
Crystal growpH: 7
Details: CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 28% PEG4K,500MM NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→18.55 Å / Num. obs: 67018 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.9
Reflection shellResolution: 1.39→1.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.32 / % possible all: 92.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5phasing
SHELXL-97phasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUF

2uuf


Resolution: 1.39→18.55 Å / Num. parameters: 25160 / Num. restraintsaints: 30942 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE COORDINATES LIST BELOW HAS AMINO ACID NUMBERING FOLLOWING THE CHYMOTRYPSINOGEN NUMBERING SCHEME I.E. A MIXTURE OF SEQUENTIAL NUMBERS AND ALPHABETICAL LETTERS. ASN60G IN CHAIN B IS ...Details: THE COORDINATES LIST BELOW HAS AMINO ACID NUMBERING FOLLOWING THE CHYMOTRYPSINOGEN NUMBERING SCHEME I.E. A MIXTURE OF SEQUENTIAL NUMBERS AND ALPHABETICAL LETTERS. ASN60G IN CHAIN B IS GLYCOSYLATED. THE MODEL WAS INITIALLY REFINED AGAINST F IN REFMAC-5, THEN FINALLY REFINED AGAINST F(SQUARED) USING SHELXL-97. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.173 3345 5 %RANDOM
obs0.118 -95.9 %-
all-67018 --
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 2233.97 / Occupancy sum non hydrogen: 2739.94
Refinement stepCycle: LAST / Resolution: 1.39→18.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 35 345 2740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.064
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0.104

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