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- PDB-1ceb: THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE ... -

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Basic information

Entry
Database: PDB / ID: 1ceb
TitleTHE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH AMCHA (TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID)
ComponentsPLASMINOGEN
KeywordsSERINE PROTEASE
Function / homology
Function and homology information


plasmin / tissue remodeling / protein antigen binding / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases / apolipoprotein binding ...plasmin / tissue remodeling / protein antigen binding / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of cell-substrate adhesion / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / : / endopeptidase activity / blood microparticle / protein domain specific binding / external side of plasma membrane / signaling receptor binding / negative regulation of cell population proliferation / serine-type endopeptidase activity / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle ...Peptidase S1A, plasmin / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.07 Å
AuthorsTulinsky, A. / Mathews, I.I.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structures of the recombinant kringle 1 domain of human plasminogen in complexes with the ligands epsilon-aminocaproic acid and trans-4-(aminomethyl)cyclohexane-1-carboxylic Acid.
Authors: Mathews, I.I. / Vanderhoff-Hanaver, P. / Castellino, F.J. / Tulinsky, A.
#1: Journal: Eur.J.Biochem. / Year: 1994
Title: 1H-NMR Assignments and Secondary Structure of Human Plasminogen Kringle 1
Authors: Rejante, M.R. / Llinas, M.
#2: Journal: Blood Coagulation Fibrinolysis / Year: 1994
Title: The Structure of Recombinant Plasminogen Kringle 1 and the Fibrin Binding Site
Authors: Wu, T.-P. / Padmanabhan, K.P. / Tulinsky, A.
#3: Journal: Proteins / Year: 1988
Title: Lysine(Slash)Fibrin Binding Sites of Kringles Modeled After the Structure of Kringle 1 of Prothrombin
Authors: Tulinsky, A. / Park, C.H. / Mao, B. / Llinas, M.
History
DepositionDec 3, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMINOGEN
B: PLASMINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6474
Polymers20,3322
Non-polymers3142
Water2,702150
1
A: PLASMINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3232
Polymers10,1661
Non-polymers1571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PLASMINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3232
Polymers10,1661
Non-polymers1571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.300, 51.700, 46.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 30 / 2: CIS PROLINE - PRO B 30
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99956, -0.02947, 0.003414), (-0.029442, -0.999535, -0.007949), (0.003647, 0.007845, -0.999963)
Vector: -0.4161, -25.19968, 80.78391)

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Components

#1: Protein PLASMINOGEN / K1PG


Mass: 10166.165 Da / Num. of mol.: 2 / Fragment: KRINGLE 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: BLOOD / Production host: Escherichia coli (E. coli) / References: UniProt: P00747, plasmin
#2: Chemical ChemComp-AMH / TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 157.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO2 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.91 Å3/Da / Density % sol: 35.65 %
Crystal
*PLUS
Density % sol: 37 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mcitric acid1drop
21.4-1.5 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.06 Å / Num. obs: 7028 / % possible obs: 70 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.0795 / Net I/σ(I): 1
Reflection shellResolution: 2.07→2.25 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 1 / % possible all: 56
Reflection
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 10 Å / Num. measured all: 17924
Reflection shell
*PLUS
Highest resolution: 2.07 Å / Lowest resolution: 2.5 Å / % possible obs: 60 % / Rmerge(I) obs: 0.133

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Processing

Software
NameClassification
RAXISdata collection
PROLSQrefinement
R-AXISdata reduction
RefinementResolution: 2.07→7 Å / σ(F): 3
Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE INTERKRINGLE RESIDUES 3A - 2A AND 80 - 86 IN BOTH MOLECULES.
RfactorNum. reflection% reflection
obs0.178 5900 57 %
Refinement stepCycle: LAST / Resolution: 2.07→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 22 150 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.050.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it11.5
X-RAY DIFFRACTIONp_mcangle_it1.42
X-RAY DIFFRACTIONp_scbond_it22.5
X-RAY DIFFRACTIONp_scangle_it2.63
X-RAY DIFFRACTIONp_plane_restr0.030.04
X-RAY DIFFRACTIONp_chiral_restr0.180.15
X-RAY DIFFRACTIONp_singtor_nbd0.230.6
X-RAY DIFFRACTIONp_multtor_nbd0.320.6
X-RAY DIFFRACTIONp_xhyhbond_nbd0.280.6
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.73
X-RAY DIFFRACTIONp_staggered_tor21.715
X-RAY DIFFRACTIONp_orthonormal_tor2520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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