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- PDB-1toc: STRUCTURE OF SERINE PROTEINASE -

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Basic information

Entry
Database: PDB / ID: 1toc
TitleSTRUCTURE OF SERINE PROTEINASE
Components
  • (THROMBIN) x 2
  • ORNITHODORIN
KeywordsCOMPLEX (HYDROLASE/INHIBITOR) / VITAMIN K / ZYMOGEN / GAMMA-CARBOXYGLUTAMIC ACID / ACUTE PHASE / LIVER / HYDROLASE / SERINE PROTEASE KUNITZ-LIKE INHIBITOR / KRINGLE / COMPLEX (HYDROLASE-INHIBITOR) COMPLEX
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / transport vesicle / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / : / toxin activity ...fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / transport vesicle / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / : / toxin activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Pancreatic trypsin inhibitor Kunitz domain superfamily / Kringle domain / Kringle ...Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Pancreatic trypsin inhibitor Kunitz domain superfamily / 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 / Few Secondary Structures / Irregular / 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
Prothrombin / Ornithodorin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Ornithodoros moubata (arthropod)
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsVan De Locht, A. / Huber, R. / Bode, W.
Citation
Journal: EMBO J. / Year: 1996
Title: The ornithodorin-thrombin crystal structure, a key to the TAP enigma?
Authors: van de Locht, A. / Stubbs, M.T. / Bode, W. / Friedrich, T. / Bollschweiler, C. / Hoffken, W. / Huber, R.
#1: Journal: Embo J. / Year: 1995
Title: Two Heads are Better Than One: Crystal Structure of the Insect Derived Double Domain Kazal Inhibitor Rhodniin in Complex with Thrombin
Authors: Van De Locht, A. / Lamba, D. / Bauer, M. / Huber, R. / Friedrich, T. / Kroger, B. / Hoffken, W. / Bode, W.
#2: Journal: Embo J. / Year: 1989
Title: The Refined 1.9 A Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment
Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J.
History
DepositionJul 20, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
A: THROMBIN
B: THROMBIN
R: ORNITHODORIN
C: THROMBIN
D: THROMBIN
S: ORNITHODORIN
E: THROMBIN
F: THROMBIN
T: ORNITHODORIN
G: THROMBIN
H: THROMBIN
U: ORNITHODORIN


Theoretical massNumber of molelcules
Total (without water)192,93812
Polymers192,93812
Non-polymers00
Water55831
1
A: THROMBIN
B: THROMBIN
R: ORNITHODORIN


Theoretical massNumber of molelcules
Total (without water)48,2343
Polymers48,2343
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-16 kcal/mol
Surface area17960 Å2
MethodPISA
2
C: THROMBIN
D: THROMBIN
S: ORNITHODORIN


Theoretical massNumber of molelcules
Total (without water)48,2343
Polymers48,2343
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-15 kcal/mol
Surface area18130 Å2
MethodPISA
3
G: THROMBIN
H: THROMBIN
U: ORNITHODORIN


Theoretical massNumber of molelcules
Total (without water)48,2343
Polymers48,2343
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-18 kcal/mol
Surface area17830 Å2
MethodPISA
4
E: THROMBIN
F: THROMBIN
T: ORNITHODORIN


Theoretical massNumber of molelcules
Total (without water)48,2343
Polymers48,2343
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-14 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.300, 89.900, 101.400
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
THROMBIN


Mass: 5735.240 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PLASMA / Plasmid: PMD8A / Production host: Escherichia coli (E. coli) / References: UniProt: P00735, thrombin
#2: Protein
THROMBIN


Mass: 29772.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PLASMA / Plasmid: PMD8A / Production host: Escherichia coli (E. coli) / References: UniProt: P00735, thrombin
#3: Protein
ORNITHODORIN


Mass: 12726.731 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ornithodoros moubata (arthropod) / Plasmid: PMD8A / Production host: Escherichia coli (E. coli) / References: UniProt: P56409
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %PEG40001reservoir
2160 mMammonium acetate1reservoir
380 mMsodium acetate1reservoir
4200 mMammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 94484 / % possible obs: 89 % / Observed criterion σ(I): 3 / Redundancy: 2.39 % / Rmerge(I) obs: 0.14
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 9999 Å
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.13 Å / % possible obs: 75.2 %

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.1→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.23 -
obs0.23 30140
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12820 0 0 31 12851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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