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- PDB-135d: SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 135d | ||||||
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Title | SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES | ||||||
![]() | DNA TRIPLEX | ||||||
![]() | DNA / TRIPLEX | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY | ||||||
![]() | Radhakrishnan, I. / Patel, D.J. | ||||||
![]() | ![]() Title: Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples. Authors: Radhakrishnan, I. / Patel, D.J. #1: ![]() Title: Solution Structure of an Intramolecular Purine(Dot)Purine(Dot)Pyrimidine DNA Triplex Authors: Radhakrishnan, I. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.7 KB | Display | ![]() |
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PDB format | ![]() | 17.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 238.4 KB | Display | ![]() |
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Full document | ![]() | 238.1 KB | Display | |
Data in XML | ![]() | 2.8 KB | Display | |
Data in CIF | ![]() | 3.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 9552.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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Processing
Software |
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NMR software | Name: ![]() | ||||||||||||
Refinement | Method: RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY / Software ordinal: 1 Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE ...Details: RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ONIDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045. | ||||||||||||
NMR ensemble | Conformers submitted total number: 1 | ||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||
Refine LS restraints | *PLUS
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