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Yorodumi- PDB-2a5r: Complex of tetra-(4-n-methylpyridyl) porphin with monomeric paral... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a5r | ||||||||||||||||||||
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Title | Complex of tetra-(4-n-methylpyridyl) porphin with monomeric parallel-stranded DNA tetraplex, snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, C-MYC promoter, NMR, 6 struct. | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / MONOMERIC PARALLEL-STRANDED QUADRUPLEX / C-MYC PROMOTER 3+1 G-TETRAD / SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP / GAG TRIAD / GAAG LOOP | Function / homology | Chem-POH / DNA / DNA (> 10) | Function and homology information Biological species | Homo sapiens (human) | Method | SOLUTION NMR / DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT | Authors | Phan, A.T. / Kuryavyi, V.V. / Gaw, H.Y. / Patel, D.J. | Citation | Journal: Nat.Chem.Biol. / Year: 2005 | Title: Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter. Authors: Phan, A.T. / Kuryavyi, V. / Gaw, H.Y. / Patel, D.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a5r.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a5r.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a5r_validation.pdf.gz | 407.1 KB | Display | wwPDB validaton report |
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Full document | 2a5r_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 2a5r_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 2a5r_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/2a5r ftp://data.pdbj.org/pub/pdb/validation_reports/a5/2a5r | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 7701.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C-MYC GENE / Source: (natural) Homo sapiens (human) |
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#2: Chemical | ChemComp-POH / ( |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: ONE OF THE EIGHT STRUCTURES OBTAINED FOR FREE DNA TETRAPLEX HAS USED FOR INTERACTIVE MODELING (PDB ID 2A5P). PART OF THE MOLECULE INCLUDING RESIDUES 1,2,3 AND 12 WAS LIFTED AS WHOLE. THE TMPYP4 ...Text: ONE OF THE EIGHT STRUCTURES OBTAINED FOR FREE DNA TETRAPLEX HAS USED FOR INTERACTIVE MODELING (PDB ID 2A5P). PART OF THE MOLECULE INCLUDING RESIDUES 1,2,3 AND 12 WAS LIFTED AS WHOLE. THE TMPYP4 WAS INTERCALATED BETWEEN THE TETRAD G4-G8-G13-G17 AND BASE PAIR A3-A12, GUIDED BY RESTRAINTS BETWEEN THE DRUG AND DNA, AND FAVORABLE POSITIONS OF THE DRUG. BROKEN BONDS BETWEEN THE RESIDUES 11-12-13 AND 3-4 WERE RESTORED, AND MOLECULE WAS SUBJECTED TO MINIMIZATION ROUNDS AND SUBSEQUENT DYNAMICS, WITH THE IMPOSED DNA AND DRUG-DNA RESTRAINTS. INITIALLY, ALL DRUG-DNA RESTRAINTS EXCEPT THESE INVOLVING RESIDUE 1 WERE TREATED AMBIGUOUSLY WITH SUM AVERAGING FROM CONTRIBUTION OF 8 IDENTICAL PROTON ATOMS. THE RESTRAINTS OF THE RESIDUE 1 WERE SPLIT AS ORIGINATING FROM SINGLE (ONE OF 4) PYRIDYL RINGS OF THE TMPYP4 IN FOUR SETS OF COMPUTATIONS. FROM FOUR MOLECULES OBTAINED ONLY ONE WITH LESS VIOLATIONS HAD POSITION OF THE H1' OF THE RESIDUE T1 AS WELL AS H8 OF THE RESIDUE G2 OVER THE AROMATIC RINGS OF THE PORPHYRIN, THUS ACCOUNTING FOR THE UPFIELD SHIFTS OF THESE PROTONS OBSERVED EXPERIMENTALLY. THE POSITION OF THE DRUG IN THE COMPLEX HAS BEEN INCREMENTALLY CHANGED BY ROTATION BY 15 DEG WITHIN THE BOUNDARIES OF VAN DER WAALS SURFACE OF DNA MOLECULE. THE MOLECULE WITH NEW POSITION OF DRUG WAS SUBJECTED TO CONSTRAINED MINIMIZATION AND DYNAMICS RUNS. AFTER THIS ROUND, PYRIDIL RING WAS ALLOWED TO FREE ROTATE AND DYNAMICS AND MINIMIZATION WAS PERFORMED ON SIX COMPLEXES AGAIN. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 90 mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 6 / Conformers submitted total number: 6 |