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- PDB-6q1u: Structure of plasmin and peptide complex -

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Basic information

Entry
Database: PDB / ID: 6q1u
TitleStructure of plasmin and peptide complex
Components
  • GLY-ARG-ALA-TYR-LYS-SER-LYS-PRO-PRO-ILE-ALA-PHE-PRO-ASP
  • Plasminogen
KeywordsBLOOD CLOTTING / serine protease / cyclic peptide / complex / antifibrinolysis
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / negative regulation of endopeptidase activity / tissue remodeling / tissue regeneration / Signaling by PDGF / mononuclear cell migration / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / negative regulation of endopeptidase activity / 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 / endopeptidase inhibitor activity / 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 / serine-type endopeptidase inhibitor activity / 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 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Peptidase S1A, plasmin / 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 / 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
1-methyl-1H-1,2,3-triazole / Plasminogen / Trypsin inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3467 Å
AuthorsWu, G. / Law, R.H.P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Application and Structural Analysis of Triazole-Bridged Disulfide Mimetics in Cyclic Peptides.
Authors: White, A.M. / de Veer, S.J. / Wu, G. / Harvey, P.J. / Yap, K. / King, G.J. / Swedberg, J.E. / Wang, C.K. / Law, R.H.P. / Durek, T. / Craik, D.J.
History
DepositionAug 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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
Revision 1.4Oct 23, 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: Plasminogen
B: Plasminogen
C: GLY-ARG-ALA-TYR-LYS-SER-LYS-PRO-PRO-ILE-ALA-PHE-PRO-ASP
D: GLY-ARG-ALA-TYR-LYS-SER-LYS-PRO-PRO-ILE-ALA-PHE-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7946
Polymers57,6284
Non-polymers1662
Water3,099172
1
A: Plasminogen
C: GLY-ARG-ALA-TYR-LYS-SER-LYS-PRO-PRO-ILE-ALA-PHE-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8973
Polymers28,8142
Non-polymers831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-7 kcal/mol
Surface area10760 Å2
MethodPISA
2
B: Plasminogen
D: GLY-ARG-ALA-TYR-LYS-SER-LYS-PRO-PRO-ILE-ALA-PHE-PRO-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8973
Polymers28,8142
Non-polymers831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-7 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.228, 80.293, 83.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Plasminogen


Mass: 27264.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P00747, plasmin
#2: Protein/peptide GLY-ARG-ALA-TYR-LYS-SER-LYS-PRO-PRO-ILE-ALA-PHE-PRO-ASP


Mass: 1549.791 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: WHM is a triazole motif that replaces the disulphide bond
Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5*PLUS
#3: Chemical ChemComp-WMH / 1-methyl-1H-1,2,3-triazole


Mass: 83.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM Sodium Citrate, 100 mM MgCl2, 18% PEG 4000 / PH range: 4-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732013702 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732013702 Å / Relative weight: 1
ReflectionResolution: 2.3467→46.6908 Å / Num. obs: 22667 / % possible obs: 98.87 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.72 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.097 / Rrim(I) all: 0.214 / Net I/σ(I): 5
Reflection shellResolution: 2.347→2.431 Å / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2197 / CC1/2: 0.819 / Rpim(I) all: 0.379 / Rrim(I) all: 0.814 / % possible all: 98.03

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6d3x

6d3x


Resolution: 2.3467→46.6908 Å / SU ML: 0.3543 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.6329
RfactorNum. reflection% reflection
Rfree0.2874 993 4.4 %
Rwork0.2328 --
obs0.2352 22557 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3467→46.6908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3915 0 6 172 4093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414037
X-RAY DIFFRACTIONf_angle_d0.70235504
X-RAY DIFFRACTIONf_chiral_restr0.0509608
X-RAY DIFFRACTIONf_plane_restr0.0053729
X-RAY DIFFRACTIONf_dihedral_angle_d16.58292428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.47040.39051160.30453033X-RAY DIFFRACTION98.31
2.47-2.630.38981650.29143019X-RAY DIFFRACTION99.53
2.63-2.830.32041350.2643065X-RAY DIFFRACTION99.19
2.83-3.110.32041660.25073046X-RAY DIFFRACTION99.26
3.11-3.560.2897880.2243106X-RAY DIFFRACTION98.85
3.56-4.490.26071800.1913089X-RAY DIFFRACTION99.12
4.49-46.680.20561430.20293206X-RAY DIFFRACTION97.75

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