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Yorodumi- PDB-1dgq: NMR SOLUTION STRUCTURE OF THE INSERTED DOMAIN OF HUMAN LEUKOCYTE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dgq | ||||||
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Title | NMR SOLUTION STRUCTURE OF THE INSERTED DOMAIN OF HUMAN LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1 | ||||||
Components | LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1 | ||||||
Keywords | IMMUNE SYSTEM / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering ...memory T cell extravasation / integrin alphaL-beta2 complex / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / ICAM-3 receptor activity / RUNX3 Regulates Immune Response and Cell Migration / integrin complex / cell adhesion mediated by integrin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / receptor clustering / Integrin cell surface interactions / specific granule membrane / phagocytosis / cell adhesion molecule binding / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell adhesion / inflammatory response / external side of plasma membrane / Neutrophil degranulation / cell surface / signal transduction / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS SIMULATED ANNEALING | ||||||
Authors | Legge, G.B. / Kriwacki, R.W. / Chung, J. / Hommel, U. / Ramage, P. / Case, D.A. / Dyson, H.J. / Wright, P.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: NMR solution structure of the inserted domain of human leukocyte function associated antigen-1. Authors: Legge, G.B. / Kriwacki, R.W. / Chung, J. / Hommel, U. / Ramage, P. / Case, D.A. / Dyson, H.J. / Wright, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dgq.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1dgq.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1dgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dgq ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dgq | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 21425.561 Da / Num. of mol.: 1 / Fragment: INSERTED DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / References: UniProt: P20701 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: NOESY MIXING TIMES OF 60 AND 100 MS FOR THE 3D 1H-15N AND 3D 1H-13C NOESY-HSQC SPECTRA. NOESY MIXING TIME OF 140 MS FOR THE 15N HSQC-NOESY-HSQC SPECTRA. |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS SIMULATED ANNEALING / Software ordinal: 1 Details: MODEL-BASED APPROACH USED TO ASSIGN NOESY SPECTRA USING EXISTING X-RAY STRUCTURES AS A MODEL. THE STRUCTURES ARE BASED ON A TOTAL OF 5656 RESTRAINTS, 2289 ARE UNIQUE NOE-DERIVED DISTANCE ...Details: MODEL-BASED APPROACH USED TO ASSIGN NOESY SPECTRA USING EXISTING X-RAY STRUCTURES AS A MODEL. THE STRUCTURES ARE BASED ON A TOTAL OF 5656 RESTRAINTS, 2289 ARE UNIQUE NOE-DERIVED DISTANCE CONSTRAINTS, 3082 AMBIGOUS NOE-DERIVED RESTRAINTS, AND 285 DIHEDRAL ANGLE RESTRAINTS. | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON- BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 100 / Conformers submitted total number: 22 |