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- PDB-1pml: KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1pml
TitleKRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES
ComponentsTISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
KeywordsHYDROLASE(SERINE PROTEASE)
Function / homology
Function and homology information


t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis ...t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis / serine protease inhibitor complex / fibrinolysis / negative regulation of proteolysis / secretory granule / phosphoprotein binding / protein modification process / Schaffer collateral - CA1 synapse / apical part of cell / blood coagulation / response to hypoxia / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Tissue plasminogen activator / Fibronectin type I domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / Kringle domain ...Tissue plasminogen activator / Fibronectin type I domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / 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
Tissue-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.38 Å
AuthorsPadmanabhan, K. / Tulinsky, A.
Citation
Journal: Protein Sci. / Year: 1994
Title: Kringle-kringle interactions in multimer kringle structures.
Authors: Padmanabhan, K. / Wu, T.P. / Ravichandran, K.G. / Tulinsky, A.
#1: Journal: Biochemistry / Year: 1992
Title: Crystal Structure of the Kringle 2 Domain of Tissue Plasminogen Activator at 2.4 A Resolution
Authors: De Vos, A.M. / Ultsch, M.H. / Kelly, R.F. / Padmanabhan, K. / Tulinsky, A. / Westbrook, M.L. / Kossiakoff, A.A.
#2: Journal: Biochemistry / Year: 1991
Title: Crystal and Molecular Structure of Human Plasminogen Kringle 4 Refined to 1.9A Resolution
Authors: Mulichak, A.M. / Tulinsky, A. / Ravichandran, K.G.
#3: Journal: Biochemistry / Year: 1991
Title: The Refined Structure of the Epsilon-Aminocaproic Acid Complex of Human Plasminogen Kringle 4
Authors: Wu, T.-P. / Padmanabhan, K. / Tulinsky, A. / Mulichak, A.M.
History
DepositionApr 25, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: 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

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Assembly

Deposited unit
A: TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
B: TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
C: TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5546
Polymers28,4483
Non-polymers1063
Water3,423190
1
A: TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5182
Polymers9,4831
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5182
Polymers9,4831
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5182
Polymers9,4831
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.800, 63.580, 46.580
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99997, -0.0059, 0.024), (0.01606, -0.5848, -0.811), (0.01882, 0.81117, -0.585)
Vector: 36.65871, -63.1518, 6.12101)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B.

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Components

#1: Protein TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2


Mass: 9482.614 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00750, t-plasminogen activator
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
27 %satammonium chloride1reservoir
350 mMammonium bicarbonate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.38 Å / Num. obs: 11621 / % possible obs: 91 % / Num. measured all: 30076 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.38 Å / Lowest resolution: 2.5 Å / % possible obs: 52 % / Num. possible: 2105 / Num. unique obs: 1101 / Mean I/σ(I) obs: 3.7

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.38→8 Å / σ(F): 4
Details: NO ELECTRON DENSITY WAS OBSERVED FOR THE INTERKRINGLE RESIDUES -3 - -2 IN MOLECULE A AND MOLECULE B AND -3 - -2 AND 82 IN MOLECULE C.
RfactorNum. reflection
obs0.145 8827
Refinement stepCycle: LAST / Resolution: 2.38→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 3 190 2105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.030.054
X-RAY DIFFRACTIONp_planar_d0.040.058
X-RAY DIFFRACTIONp_chiral_restr0.150.26
X-RAY DIFFRACTIONp_mcbond_it1.51.4
X-RAY DIFFRACTIONp_scbond_it2.52.7
X-RAY DIFFRACTIONp_mcangle_it21.9
X-RAY DIFFRACTIONp_scangle_it33.5

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