HEADER DNA 30-JUN-05 2A5R TITLE COMPLEX OF TETRA-(4-N-METHYLPYRIDYL) PORPHIN WITH MONOMERIC PARALLEL- TITLE 2 STRANDED DNA TETRAPLEX, SNAP-BACK 3+1 3' G-TETRAD, SINGLE-RESIDUE TITLE 3 CHAIN REVERSAL LOOPS, GAG TRIAD IN THE CONTEXT OF GAAG DIAGONAL LOOP, TITLE 4 C-MYC PROMOTER, NMR, 6 STRUCT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP COMPND 3 *GP*GP*AP*AP*GP*G)-3'; COMPND 4 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: C-MYC GENE KEYWDS MONOMERIC PARALLEL-STRANDED QUADRUPLEX; C-MYC PROMOTER 3+1 G-TETRAD; KEYWDS 2 SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP; GAG TRIAD; GAAG LOOP, DNA EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR A.T.PHAN,V.V.KURYAVYI,H.Y.GAW,D.J.PATEL REVDAT 4 13-JUL-11 2A5R 1 VERSN REVDAT 3 23-FEB-11 2A5R 1 FORMUL REVDAT 2 24-FEB-09 2A5R 1 VERSN REVDAT 1 26-JUL-05 2A5R 0 JRNL AUTH A.T.PHAN,V.KURYAVYI,H.Y.GAW,D.J.PATEL JRNL TITL SMALL-MOLECULE INTERACTION WITH A FIVE-GUANINE-TRACT JRNL TITL 2 G-QUADRUPLEX STRUCTURE FROM THE HUMAN MYC PROMOTER. JRNL REF NAT.CHEM.BIOL. V. 1 167 2005 JRNL REFN ISSN 1552-4450 JRNL PMID 16408022 JRNL DOI 10.1038/NCHEMBIO723 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, INSIGHTII 2000 REMARK 3 AUTHORS : AT BRUNGER (X-PLOR), ACCELRYS (INSIGHTII) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2A5R COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-05. REMARK 100 THE RCSB ID CODE IS RCSB033521. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 90 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 70 MM KCL 20 MM POTASSIUM REMARK 210 PHOSPHATE, 90% H2O, 10% D2O; 70 REMARK 210 MM KCL 20 MM POTASSIUM PHOSPHATE, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY; 1H-1H TOCSY; 1H-31P REMARK 210 COSY; 1H-1H COSY; 1H-15N JRHMQC; REMARK 210 1H-15N HMBC; 1H-13C JRHM 1H-13C REMARK 210 HMBC; 1H-13C HSQC; 1H-13C SHMBC; REMARK 210 1H-31P TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN UNITY INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.0, FELIX 2000 REMARK 210 METHOD USED : DISTANCE RESTRAINED MOLECULAR REMARK 210 DYNAMICS REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 6 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: ONE OF THE EIGHT STRUCTURES OBTAINED FOR FREE DNA REMARK 210 TETRAPLEX HAS USED FOR INTERACTIVE MODELING (PDB ID 2A5P). PART REMARK 210 OF THE MOLECULE INCLUDING RESIDUES 1,2,3 AND 12 WAS LIFTED AS REMARK 210 WHOLE. THE TMPYP4 WAS INTERCALATED BETWEEN THE TETRAD G4-G8-G13- REMARK 210 G17 AND BASE PAIR A3-A12, GUIDED BY RESTRAINTS BETWEEN THE DRUG REMARK 210 AND DNA, AND FAVORABLE POSITIONS OF THE DRUG. BROKEN BONDS REMARK 210 BETWEEN THE RESIDUES 11-12-13 AND 3-4 WERE RESTORED, AND MOLECULE REMARK 210 WAS SUBJECTED TO MINIMIZATION ROUNDS AND SUBSEQUENT DYNAMICS, REMARK 210 WITH THE IMPOSED DNA AND DRUG-DNA RESTRAINTS. INITIALLY, ALL DRUG REMARK 210 -DNA RESTRAINTS EXCEPT THESE INVOLVING RESIDUE 1 WERE TREATED REMARK 210 AMBIGUOUSLY WITH SUM AVERAGING FROM CONTRIBUTION OF 8 IDENTICAL REMARK 210 PROTON ATOMS. THE RESTRAINTS OF THE RESIDUE 1 WERE SPLIT AS REMARK 210 ORIGINATING FROM SINGLE (ONE OF 4) PYRIDYL RINGS OF THE TMPYP4 IN REMARK 210 FOUR SETS OF COMPUTATIONS. FROM FOUR MOLECULES OBTAINED ONLY ONE REMARK 210 WITH LESS VIOLATIONS HAD POSITION OF THE H1' OF THE RESIDUE T1 AS REMARK 210 WELL AS H8 OF THE RESIDUE G2 OVER THE AROMATIC RINGS OF THE REMARK 210 PORPHYRIN, THUS ACCOUNTING FOR THE UPFIELD SHIFTS OF THESE REMARK 210 PROTONS OBSERVED EXPERIMENTALLY. THE POSITION OF THE DRUG IN THE REMARK 210 COMPLEX HAS BEEN INCREMENTALLY CHANGED BY ROTATION BY 15 DEG REMARK 210 WITHIN THE BOUNDARIES OF VAN DER WAALS SURFACE OF DNA MOLECULE. REMARK 210 THE MOLECULE WITH NEW POSITION OF DRUG WAS SUBJECTED TO REMARK 210 CONSTRAINED MINIMIZATION AND DYNAMICS RUNS. AFTER THIS ROUND, REMARK 210 PYRIDIL RING WAS ALLOWED TO FREE ROTATE AND DYNAMICS AND REMARK 210 MINIMIZATION WAS PERFORMED ON SIX COMPLEXES AGAIN. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DT A 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 9 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 4 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 5 DT A 1 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 5 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DT A 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 6 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 6 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POH A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EEG RELATED DB: PDB REMARK 900 A(GGG)A HEXAD REMARK 900 RELATED ID: 1JJP RELATED DB: PDB REMARK 900 A(GGGG) PENTAD, 3' 3+1 TETRAD REMARK 900 RELATED ID: 1Y8D RELATED DB: PDB REMARK 900 A(GGGG) PENTAD, 3' 3+1 TETRAD REMARK 900 RELATED ID: 1D6D RELATED DB: PDB REMARK 900 AAT TRIAD IN DIAGONAL LOOP REMARK 900 RELATED ID: 2A5P RELATED DB: PDB DBREF 2A5R A 1 24 PDB 2A5R 2A5R 1 24 SEQRES 1 A 24 DT DG DA DG DG DG DT DG DG DI DG DA DG SEQRES 2 A 24 DG DG DT DG DG DG DG DA DA DG DG HET POH A 25 90 HETNAM POH (1Z,4Z,9Z,15Z)-5,10,15,20-TETRAKIS(1-METHYLPYRIDIN-1- HETNAM 2 POH IUM-4-YL)-21,23-DIHYDROPORPHYRIN HETSYN POH TMPYP4 FORMUL 2 POH C44 H38 N8 4+ SITE 1 AC1 8 DT A 1 DG A 2 DA A 3 DG A 4 SITE 2 AC1 8 DG A 8 DA A 12 DG A 13 DG A 17 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1