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- PDB-1vit: THROMBIN:HIRUDIN 51-65 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1vit
TitleTHROMBIN:HIRUDIN 51-65 COMPLEX
Components
  • (EPSILON THROMBIN) x 3
  • ALPHA THROMBIN
  • HIRUDIN
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / COMPLEX (SERINE PROTEASE-INHIBITOR) / HYDROLASE / SERINE PROTEASE / BLOOD COAGULATION / COMPLEX (SERINE PROTEASE-INHIBITOR) complex
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding ...fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, 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 / 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
Prothrombin / Hirudin-3A
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, GRAPHICS / Resolution: 3.2 Å
AuthorsVitali, J. / Edwards, B.F.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of a bovine thrombin-hirudin51-65 complex determined by a combination of molecular replacement and graphics. Incorporation of known structural information in molecular replacement.
Authors: Vitali, J. / Martin, P.D. / Malkowski, M.G. / Olsen, C.M. / Johnson, P.H. / Edwards, B.F.
History
DepositionJan 31, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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.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 2.1Apr 3, 2024Group: 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
L: EPSILON THROMBIN
H: ALPHA THROMBIN
I: HIRUDIN
M: EPSILON THROMBIN
F: EPSILON THROMBIN
G: EPSILON THROMBIN
J: HIRUDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3519
Polymers74,7057
Non-polymers6462
Water0
1
L: EPSILON THROMBIN
H: ALPHA THROMBIN
I: HIRUDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7684
Polymers37,3443
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-13 kcal/mol
Surface area14280 Å2
MethodPISA
2
M: EPSILON THROMBIN
F: EPSILON THROMBIN
G: EPSILON THROMBIN
J: HIRUDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5835
Polymers37,3624
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-65 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.400, 116.400, 200.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsTHERE ARE TWO COMPLEXES PER ASYMMETRIC UNIT. EACH COMPLEX CONSISTS OF ONE MOLECULE OF THROMBIN AND ONE MOLECULE OF HIRUDIN 51 - 65. THROMBIN IN COMPLEX 1 IS ALPHA-THROMBIN AND IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN INDICATOR *L* IS USED FOR RESIDUES 1H - 15, CHAIN INDICATOR *H* IS CHAIN INDICATOR *H* IS USED FOR RESIDUES 16 - 246, AND CHAIN INDICATOR *I* IS USED FOR THE PEPTIDE. THROMBIN IN COMPLEX 2 IS EPSILON THROMBIN AND, IN ADDITION TO THE CUT BETWEEN RESIDUES 15 AND 16, IT IS ALSO CLEAVED BETWEEN RESIDUES 149A AND 149B. CHAIN INDICATORS IN COMPLEX 2 ARE *M* FOR RESIDUES 1H - 15, *F* FOR RESIDUES 15 - 149A, *G* FOR RESIDUES 149B - 247, AND *J* FOR THE PEPTIDE.

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Components

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Protein/peptide , 2 types, 4 molecules LMIJ

#1: Protein/peptide EPSILON THROMBIN


Mass: 5735.240 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin
#3: Protein/peptide HIRUDIN /


Mass: 1835.854 Da / Num. of mol.: 2 / Fragment: RESIDUES 51 - 65
Source method: isolated from a genetically manipulated source
References: UniProt: P28507

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Protein , 3 types, 3 molecules HFG

#2: Protein ALPHA THROMBIN


Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin
#4: Protein EPSILON THROMBIN


Mass: 17525.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin
#5: Protein EPSILON THROMBIN


Mass: 12265.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin

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Sugars , 2 types, 2 molecules

#6: 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.: 1
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
#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 / 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

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Details

Sequence detailsCHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED FOR THROMBIN, BASED ON THE ...CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED FOR THROMBIN, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H. BRANDSTETTER ET AL., 1992, J. MOL. BIOL., V. 226, 1085). THE NUMBERING FOR THE PEPTIDE CORRESPONDS TO THE C-TERMINAL RESIDUES OF HIRUDIN.

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP, RESERVOIRS CONTAINING 39% SATURATED AMMONIUM SULFATE, 0.25 M AMMONIUM PHOSPHATE PH 8.0 AND 1% PEG4000. DROPS CONSISTED OF EQUAL VOLUMES OF RESERVOIR AND PROTEIN SOLUTION ...Details: HANGING DROP, RESERVOIRS CONTAINING 39% SATURATED AMMONIUM SULFATE, 0.25 M AMMONIUM PHOSPHATE PH 8.0 AND 1% PEG4000. DROPS CONSISTED OF EQUAL VOLUMES OF RESERVOIR AND PROTEIN SOLUTION CONTAINING 23.5 MG/ML PROTEIN., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111.75 mg/mlpeptide1drop
319.5 %satammonium sulfate1drop
40.25 Mammonium phosphate1drop
50.5 %PEG40001drop
639 %satammonium sulfate1reservoir
71 %PEG40001reservoir
80.25 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 3.2 Å / Num. obs: 11300 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.126 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.4 Å / Mean I/σ(I) obs: 2 / % possible all: 41
Reflection
*PLUS
Rmerge(I) obs: 0.126

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, GRAPHICS
Starting model: BOVINE THROMBIN IN COMPLEX WITH HIRUDIN

Resolution: 3.2→7 Å / σ(F): 2
Details: RESIDUES 51, 54, 62, 64, AND 65 OF PEPTIDE 1 HAVE POOR DENSITY. MOST OF PEPTIDE 2 IS EFFECTIVELY DISORDERED WITH RESIDUES 53, 54, 58, 59, 60, 61, 64, 65 HAVING POOR DENSITY. EXCEPT FOR A FEW ...Details: RESIDUES 51, 54, 62, 64, AND 65 OF PEPTIDE 1 HAVE POOR DENSITY. MOST OF PEPTIDE 2 IS EFFECTIVELY DISORDERED WITH RESIDUES 53, 54, 58, 59, 60, 61, 64, 65 HAVING POOR DENSITY. EXCEPT FOR A FEW RESIDUES, THE TWO THROMBINS ARE GENERALLY WELL DEFINED IN THE ELECTRON DENSITY MAPS FOR RESIDUES 1C - 14K AND 16 - 243.
RfactorNum. reflection% reflection
Rwork0.192 --
obs0.192 8659 69.8 %
Displacement parametersBiso mean: 24.8 Å2
Refine analyzeLuzzati sigma a obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 42 0 5071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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