HEADER DNA 03-APR-14 2MNE TITLE RECOGNITION COMPLEX OF DNA D(CGACTAGTCG)2 WITH THIAZOTROPSIN ANALOGUE TITLE 2 AIK-18/51 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS THIAZOTROPSINS, DNA RECOGNITION, ISOTHERMAL TITRATION CALORIMETRY KEYWDS 2 NMR, SELF-ASSEMBLY, MINOR GROOVE BINDER, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR H.Y.ALNISS,M.-V.SALVIA,M.SADIKOV,I.GOLOVCHENKO,N.G.ANTHONY, AUTHOR 2 A.I.KHALAF,S.P.MACKAY,C.J.SUCKLING,J.A.PARKINSON REVDAT 3 01-MAY-24 2MNE 1 REMARK HETSYN REVDAT 2 17-SEP-14 2MNE 1 JRNL REVDAT 1 30-JUL-14 2MNE 0 JRNL AUTH H.Y.ALNISS,M.V.SALVIA,M.SADIKOV,I.GOLOVCHENKO,N.G.ANTHONY, JRNL AUTH 2 A.I.KHALAF,S.P.MACKAY,C.J.SUCKLING,J.A.PARKINSON JRNL TITL RECOGNITION OF THE DNA MINOR GROOVE BY THIAZOTROPSIN JRNL TITL 2 ANALOGUES. JRNL REF CHEMBIOCHEM V. 15 1978 2014 JRNL REFN ISSN 1439-4227 JRNL PMID 25045155 JRNL DOI 10.1002/CBIC.201402202 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, AMBER REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MNE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000103823. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM AIK-18/51, 2 MM 5' REMARK 210 -D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3', 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, SYBYL, REMARK 210 MARDIGRAS, AMBER REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC A 1 C2 DC A 1 N3 0.089 REMARK 500 DC A 1 N3 DC A 1 C4 -0.064 REMARK 500 DC A 1 C4 DC A 1 C5 0.057 REMARK 500 DG A 2 N3 DG A 2 C4 0.090 REMARK 500 DG A 2 C4 DG A 2 C5 -0.048 REMARK 500 DG A 2 C5 DG A 2 N7 0.047 REMARK 500 DG A 2 N7 DG A 2 C8 -0.044 REMARK 500 DG A 2 C8 DG A 2 N9 -0.071 REMARK 500 DG A 2 N9 DG A 2 C4 -0.065 REMARK 500 DA A 3 C5 DA A 3 N7 -0.050 REMARK 500 DA A 3 N7 DA A 3 C8 -0.044 REMARK 500 DA A 3 C8 DA A 3 N9 -0.064 REMARK 500 DC A 4 C2 DC A 4 N3 0.091 REMARK 500 DC A 4 N3 DC A 4 C4 -0.063 REMARK 500 DC A 4 C4 DC A 4 C5 0.052 REMARK 500 DA A 6 C5 DA A 6 N7 -0.050 REMARK 500 DA A 6 N7 DA A 6 C8 -0.044 REMARK 500 DA A 6 C8 DA A 6 N9 -0.064 REMARK 500 DG A 7 N3 DG A 7 C4 0.092 REMARK 500 DG A 7 C4 DG A 7 C5 -0.048 REMARK 500 DG A 7 C5 DG A 7 N7 0.047 REMARK 500 DG A 7 N7 DG A 7 C8 -0.045 REMARK 500 DG A 7 C8 DG A 7 N9 -0.070 REMARK 500 DG A 7 N9 DG A 7 C4 -0.061 REMARK 500 DC A 9 C2 DC A 9 N3 0.091 REMARK 500 DC A 9 N3 DC A 9 C4 -0.064 REMARK 500 DC A 9 C4 DC A 9 C5 0.054 REMARK 500 DG A 10 N3 DG A 10 C4 0.089 REMARK 500 DG A 10 C4 DG A 10 C5 -0.050 REMARK 500 DG A 10 C5 DG A 10 N7 0.048 REMARK 500 DG A 10 N7 DG A 10 C8 -0.043 REMARK 500 DG A 10 C8 DG A 10 N9 -0.071 REMARK 500 DG A 10 N9 DG A 10 C4 -0.065 REMARK 500 DC B 11 C2 DC B 11 N3 0.089 REMARK 500 DC B 11 N3 DC B 11 C4 -0.064 REMARK 500 DC B 11 C4 DC B 11 C5 0.056 REMARK 500 DG B 12 N3 DG B 12 C4 0.091 REMARK 500 DG B 12 C4 DG B 12 C5 -0.049 REMARK 500 DG B 12 C5 DG B 12 N7 0.048 REMARK 500 DG B 12 N7 DG B 12 C8 -0.045 REMARK 500 DG B 12 C8 DG B 12 N9 -0.071 REMARK 500 DG B 12 N9 DG B 12 C4 -0.066 REMARK 500 DA B 13 C5 DA B 13 N7 -0.050 REMARK 500 DA B 13 N7 DA B 13 C8 -0.043 REMARK 500 DA B 13 C8 DA B 13 N9 -0.064 REMARK 500 DC B 14 C2 DC B 14 N3 0.089 REMARK 500 DC B 14 N3 DC B 14 C4 -0.064 REMARK 500 DC B 14 C4 DC B 14 C5 0.056 REMARK 500 DA B 16 C5 DA B 16 N7 -0.049 REMARK 500 DA B 16 N7 DA B 16 C8 -0.044 REMARK 500 REMARK 500 THIS ENTRY HAS 66 BOND DEVIATIONS. 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 1 N3 - C4 - N4 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 2 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = 9.0 DEGREES REMARK 500 DG A 2 N3 - C4 - C5 ANGL. DEV. = -9.6 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = -9.4 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 2 N9 - C4 - C5 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG A 2 C6 - C5 - N7 ANGL. DEV. = 7.7 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = 4.9 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -8.9 DEGREES REMARK 500 DA A 3 OP1 - P - OP2 ANGL. DEV. = -9.9 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA A 3 C2 - N3 - C4 ANGL. DEV. = 7.4 DEGREES REMARK 500 DA A 3 N3 - C4 - C5 ANGL. DEV. = -7.4 DEGREES REMARK 500 DA A 3 C4 - C5 - C6 ANGL. DEV. = 5.8 DEGREES REMARK 500 DA A 3 C4 - C5 - N7 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA A 3 C5 - N7 - C8 ANGL. DEV. = 6.0 DEGREES REMARK 500 DA A 3 N3 - C4 - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 DC A 4 OP1 - P - OP2 ANGL. DEV. = -9.4 DEGREES REMARK 500 DC A 4 N3 - C4 - C5 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC A 4 C4 - C5 - C6 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC A 4 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 4 N3 - C4 - N4 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT A 5 OP1 - P - OP2 ANGL. DEV. = -10.6 DEGREES REMARK 500 DT A 5 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 DT A 5 N1 - C2 - N3 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A 5 C5 - C4 - O4 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA A 6 OP1 - P - OP2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DA A 6 N1 - C2 - N3 ANGL. DEV. = -6.6 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = 7.6 DEGREES REMARK 500 DA A 6 N3 - C4 - C5 ANGL. DEV. = -7.6 DEGREES REMARK 500 DA A 6 C4 - C5 - C6 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA A 6 C4 - C5 - N7 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 6 C5 - N7 - C8 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA A 6 N3 - C4 - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA A 6 N1 - C6 - N6 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 173 ANGLE DEVIATIONS. 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 3B5 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3B5 B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19889 RELATED DB: BMRB REMARK 900 RELATED ID: 2MND RELATED DB: PDB REMARK 900 RELATED ID: 2MNF RELATED DB: PDB DBREF 2MNE A 1 10 PDB 2MNE 2MNE 1 10 DBREF 2MNE B 11 20 PDB 2MNE 2MNE 11 20 SEQRES 1 A 10 DC DG DA DC DT DA DG DT DC DG SEQRES 1 B 10 DC DG DA DC DT DA DG DT DC DG HET 3B5 A 101 82 HET 3B5 B 101 82 HETNAM 3B5 AIK-18/51 HETSYN 3B5 N,N-DIMETHYL-3-[({2-[({1-METHYL-4-[({1-METHYL-4- HETSYN 2 3B5 [(PYRIDIN-3-YLCARBONYL)AMINO]-1H-PYRROL-2- HETSYN 3 3B5 YL}CARBONYL)AMINO]-1H-PYRROL- 2-YL}CARBONYL)AMINO]-5- HETSYN 4 3B5 (PROPAN-2-YL)-1,3-THIAZOL-4-YL}CARBONYL)AMINO]PROPAN- HETSYN 5 3B5 1-AMINIUM FORMUL 3 3B5 2(C30 H38 N9 O4 S 1+) SITE 1 AC1 8 DC A 4 DT A 5 DA A 6 DG A 7 SITE 2 AC1 8 DT A 8 DC A 9 DC B 14 3B5 B 101 SITE 1 AC2 11 DG A 2 DA A 3 DC A 4 DG A 7 SITE 2 AC2 11 3B5 A 101 DC B 14 DT B 15 DA B 16 SITE 3 AC2 11 DG B 17 DT B 18 DC B 19 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