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Yorodumi- PDB-2kj4: Solution structure of the complex of VEK-30 and plasminogen kringle 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kj4 | ||||||
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Title | Solution structure of the complex of VEK-30 and plasminogen kringle 2 | ||||||
Components |
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Keywords | BLOOD CLOTTING / Protein/peptide | ||||||
Function / homology | Plasminogen ligand, VEK-30 / Plasminogen (Pg) ligand in fibrinolytic pathway / Plasminogen Kringle 4 / Plasminogen Kringle 4 / YSIRK Gram-positive signal peptide / Beta Barrel / Mainly Beta / M protein Function and homology information | ||||||
Biological species | Homo sapiens (human) Streptococcus pyogenes (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Wang, M. / Zajicek, J. / Prorok, M. / Castellin, F.J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Solution structure of the complex of VEK-30 and plasminogen kringle 2. Authors: Wang, M. / Zajicek, J. / Geiger, J.H. / Prorok, M. / Castellino, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kj4.cif.gz | 729.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kj4.ent.gz | 635 KB | Display | PDB format |
PDBx/mmJSON format | 2kj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/2kj4 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/2kj4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10166.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) |
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#2: Protein/peptide | Mass: 3779.151 Da / Num. of mol.: 1 / Fragment: Fragment of M protein, residues 85-113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V4L8 |
Sequence details | THE ATOM NUMBERING IN THE PDB FILE DIFFERS FROM THAT IN THE CITATION. THE NUMBERING IN THE CITATION ...THE ATOM NUMBERING IN THE PDB FILE DIFFERS FROM THAT IN THE CITATION. THE NUMBERING IN THE CITATION IS AS FOLLOWS. CHAIN A: TYR(-7) - ALA(80); CHAIN B: GLY(-2) - TYR(30) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.2 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 / Details: CNS, RECOORD | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |