HEADER DNA/DNA INHIBITOR 24-JUL-13 2MB3 TITLE SOLUTION STRUCTURE OF AN INTRAMOLECULAR (3+1) HUMAN TELOMERIC G- TITLE 2 QUADRUPLEX BOUND TO A TELOMESTATIN DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA_(5'- COMPND 3 D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP* COMPND 4 GP*A)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS INTRAMOLECULAR G-QUADRUPLEX, HUMAN TELOMERE, ANTICANCER TARGETS, KEYWDS 2 MACROCYCLIC HEXAOXAZOLE, TELOMESTATIN DERIVATIVE, DNA-DNA INHIBITOR KEYWDS 3 COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.J.CHUNG,B.HEDDI,M.TERA,K.IIDA,K.NAGASAWA,A.T.PHAN REVDAT 4 15-MAY-24 2MB3 1 REMARK REVDAT 3 14-JUN-23 2MB3 1 COMPND REMARK HETNAM REVDAT 2 25-SEP-13 2MB3 1 JRNL REVDAT 1 28-AUG-13 2MB3 0 JRNL AUTH W.J.CHUNG,B.HEDDI,M.TERA,K.IIDA,K.NAGASAWA,A.T.PHAN JRNL TITL SOLUTION STRUCTURE OF AN INTRAMOLECULAR (3 + 1) HUMAN JRNL TITL 2 TELOMERIC G-QUADRUPLEX BOUND TO A TELOMESTATIN DERIVATIVE. JRNL REF J.AM.CHEM.SOC. V. 135 13495 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23909929 JRNL DOI 10.1021/JA405843R REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, X-PLOR NIH REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO AND KOLLMAN (AMBER), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000103430. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 298; 298 REMARK 210 PH : 7; 7; 7 REMARK 210 IONIC STRENGTH : 90; 90; 40 REMARK 210 PRESSURE : AMBIENT ATM; NULL; NULL REMARK 210 SAMPLE CONTENTS : 0.2-2 MM DNA (5' REMARK 210 -D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP* REMARK 210 GP*GP*GP*A)-3'), 0.2-2 MM L2H, 90% H2O/10% D2O; 0.2-2 MM DNA (5'- REMARK 210 D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP* REMARK 210 GP*GP*GP*A)-3'), 0.2-2 MM L2H, 100% D2O; 0.2 MM [U-99% 13C; U-99% REMARK 210 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP* REMARK 210 GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 MM L2H, 90% H2O/10% D2O; 0.2 MM REMARK 210 [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP* REMARK 210 GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 MM L2H, 100% REMARK 210 D2O; 0.2-1 MM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP* REMARK 210 GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 MM L2H, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-13C HSQC AROMATIC; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 1D JRHMBC; REMARK 210 2D 1H-31P HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, X-PLOR NIH, TOPSPIN REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO5' DT A 1 OP1 DT A 2 1.54 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 10 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 10 DT A 18 C6 - C5 - C7 ANGL. DEV. = -3.6 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 L2H A 25 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19387 RELATED DB: BMRB DBREF 2MB3 A 1 24 PDB 2MB3 2MB3 1 24 SEQRES 1 A 24 DT DT DG DG DG DT DT DA DG DG DG DT DT SEQRES 2 A 24 DA DG DG DG DT DT DA DG DG DG DA HET L2H A 25 86 HETNAM L2H (12S,27S)-12,27-BIS(4-AMINOBUTYL)-4,30-DIMETHYL-3,7,14, HETNAM 2 L2H 18,22,29-HEXAOXA-11,26,31,32,33,34,35,36- HETNAM 3 L2H OCTAAZAHEPTACYCLO[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17, HETNAM 4 L2H 20~.1~21,24~]HEXATRIACONTA-1(30),2(36),4,6(35),8, HETNAM 5 L2H 13(34),15,17(33),19,21(32),23,28(31)-DODE CAENE-10,25- HETNAM 6 L2H DIONE HETSYN L2H TELOMESTATIN DERIVATIVE FORMUL 2 L2H C32 H34 N10 O8 SITE 1 AC1 9 DT A 2 DG A 3 DA A 8 DG A 9 SITE 2 AC1 9 DG A 17 DT A 18 DT A 19 DA A 20 SITE 3 AC1 9 DG A 21 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