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- PDB-2pk4: THE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID COMPLEX OF... -

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Entry
Database: PDB / ID: 2pk4
TitleTHE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID COMPLEX OF HUMAN PLASMINOGEN KRINGLE
ComponentsHUMAN PLASMINOGEN KRINGLE 4
KeywordsHYDROLASE(SERINE PROTEASE)
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / myoblast differentiation / labyrinthine layer blood vessel development / biological process involved in interaction with symbiont / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of fibrinolysis / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / protein processing / kinase binding / Schaffer collateral - CA1 synapse / 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 / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / glutamatergic synapse / 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
6-AMINOHEXANOIC ACID / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsTulinsky, A. / Wu, T.-P.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution
Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H.
#2: Journal: Blood Coagulation Fibrinolysis / Year: 1990
Title: Structure of the Lysine-Fibrin Binding Subsite of Human Plasminogen Kringle 4
Authors: Mulichak, A.M. / 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.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Structure of Prothrombin Fragment 1 Refined at 2.8 Angstroms Resolution
Authors: Tulinsky, A. / Park, C.H. / Skrzypczak-Jankun, E.
History
DepositionJul 18, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / Item: _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN PLASMINOGEN KRINGLE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3002
Polymers9,1691
Non-polymers1311
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.210, 35.460, 25.430
Angle α, β, γ (deg.)90.00, 102.94, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 30

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Components

#1: Protein HUMAN PLASMINOGEN KRINGLE 4


Mass: 9169.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00747
#2: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE NUMBERING OF KRINGLE 4 IS BASED ON PLASMINOGEN KRINGLE 5. THE FINAL STRUCTURE HAS RESIDUE ...SEQUENCE NUMBERING OF KRINGLE 4 IS BASED ON PLASMINOGEN KRINGLE 5. THE FINAL STRUCTURE HAS RESIDUE GLN -1 TO CYS 80 ALONG WITH LIGAND, RESIDUE ACA 100. 106 WATER MOLECULES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mMACA1drop
230 %PEG80001reservoir
30.12 Mammonium sulfate1reservoir
41.4 %DMF1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.25 Å / Num. all: 3400 / Num. obs: 3381 / % possible obs: 95 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.148 / Highest resolution: 2.25 Å
Details: RESIDUES THR 18 AND ARG 32 HAD NO ELECTRON DENSITY AND WERE THEREFORE REFINED AS ALA.
Refinement stepCycle: LAST / Highest resolution: 2.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms630 0 9 106 745
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
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
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 7 Å / Num. reflection obs: 2993 / Rfactor obs: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d0.0420.025
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_planar_d0.050.035
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.230.13
X-RAY DIFFRACTIONp_mcbond_it1.81.5
X-RAY DIFFRACTIONp_scbond_it2.32.5
X-RAY DIFFRACTIONp_mcangle_it2.62
X-RAY DIFFRACTIONp_scangle_it3.62.5

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