HEADER DNA 05-NOV-09 2KQH TITLE A G-RICH SEQUENCE WITHIN THE C-KIT ONCOGENE PROMOTER FORMS A PARALLEL TITLE 2 G-QUADRUPLEX HAVING ASYMMETRIC G-TETRAD DYNAMICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*GP*AP*GP*GP*GP*AP*GP COMPND 3 *GP*GP*T)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS C-KIT2, ONCOGENE, PROMOTER, G-QUADRUPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.-T.D.HSU,P.VARNAI,A.BUGAUT,A.P.RESZKA,S.NEIDLE,S.BALASUBRAMANIAN REVDAT 2 01-MAY-24 2KQH 1 REMARK LINK REVDAT 1 24-NOV-09 2KQH 0 SPRSDE 24-NOV-09 2KQH 2KJ2 JRNL AUTH S.-T.D.HSU,P.VARNAI,A.BUGAUT,A.P.RESZKA,S.NEIDLE, JRNL AUTH 2 S.BALASUBRAMANIAN JRNL TITL A G-RICH SEQUENCE WITHIN THE C-KIT ONCOGENE PROMOTER FORMS A JRNL TITL 2 PARALLEL G-QUADRUPLEX HAVING ASYMMETRIC G-TETRAD DYNAMICS JRNL REF J.AM.CHEM.SOC. V. 131 13399 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19705869 JRNL DOI 10.1021/JA904007P REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.FERNANDO,A.P.RESZKA,J.HUPPERT,S.LADAME,S.RANKIN, REMARK 1 AUTH 2 A.R.VENKITARAMAN,S.NEIDLE,S.BALASUBRAMANIAN REMARK 1 TITL A CONSERVED QUADRUPLEX MOTIF LOCATED IN A TRANSCRIPTION REMARK 1 TITL 2 ACTIVATION SITE OF THE HUMAN C-KIT ONCOGENE REMARK 1 REF BIOCHEMISTRY V. 45 7854 2006 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 16784237 REMARK 1 DOI 10.1021/BI0601510 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SPARKY, AMBER REMARK 3 AUTHORS : GODDARD (SPARKY), CASE, DARDEN, CHEATHAM, III, REMARK 3 SIMMERLING, WANG, DUKE, LUO, ... AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EXPLICIT WATER REFINEMENT INCLUDING REMARK 3 POTASSIUM IONS WITHIN THE G-TETRADS. REMARK 4 REMARK 4 2KQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000101446. 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 : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 200 MICRO-M DNA; 10MM POTASSIUM REMARK 210 PHOSPHATE; 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, AMBER REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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' DC A 1 OP1 DG 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 1 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 9 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 13 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 13 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 13 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 17 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 17 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 17 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT A 21 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 21 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 5 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DC A 9 N3 - C4 - C5 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC A 9 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC A 11 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 13 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DA A 13 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DA A 13 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DG A 15 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 15 N3 - C2 - N2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DA A 17 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 DA A 17 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DA A 17 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 263 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DC A 1 0.09 SIDE CHAIN REMARK 500 1 DG A 2 0.06 SIDE CHAIN REMARK 500 1 DG A 15 0.07 SIDE CHAIN REMARK 500 1 DG A 16 0.06 SIDE CHAIN REMARK 500 1 DG A 20 0.08 SIDE CHAIN REMARK 500 2 DG A 8 0.07 SIDE CHAIN REMARK 500 2 DG A 16 0.06 SIDE CHAIN REMARK 500 2 DG A 19 0.07 SIDE CHAIN REMARK 500 3 DG A 3 0.06 SIDE CHAIN REMARK 500 3 DG A 4 0.06 SIDE CHAIN REMARK 500 3 DG A 8 0.06 SIDE CHAIN REMARK 500 3 DG A 18 0.07 SIDE CHAIN REMARK 500 3 DG A 19 0.07 SIDE CHAIN REMARK 500 4 DG A 2 0.06 SIDE CHAIN REMARK 500 4 DG A 4 0.06 SIDE CHAIN REMARK 500 4 DC A 5 0.08 SIDE CHAIN REMARK 500 4 DG A 8 0.09 SIDE CHAIN REMARK 500 4 DG A 15 0.05 SIDE CHAIN REMARK 500 4 DA A 17 0.10 SIDE CHAIN REMARK 500 4 DG A 18 0.07 SIDE CHAIN REMARK 500 4 DG A 20 0.09 SIDE CHAIN REMARK 500 4 DT A 21 0.09 SIDE CHAIN REMARK 500 5 DG A 4 0.11 SIDE CHAIN REMARK 500 5 DC A 5 0.08 SIDE CHAIN REMARK 500 5 DG A 12 0.06 SIDE CHAIN REMARK 500 6 DG A 10 0.06 SIDE CHAIN REMARK 500 6 DG A 20 0.08 SIDE CHAIN REMARK 500 7 DC A 1 0.08 SIDE CHAIN REMARK 500 7 DG A 2 0.07 SIDE CHAIN REMARK 500 7 DG A 3 0.07 SIDE CHAIN REMARK 500 7 DG A 6 0.07 SIDE CHAIN REMARK 500 7 DG A 10 0.06 SIDE CHAIN REMARK 500 7 DG A 14 0.08 SIDE CHAIN REMARK 500 7 DG A 15 0.07 SIDE CHAIN REMARK 500 7 DG A 18 0.07 SIDE CHAIN REMARK 500 8 DC A 1 0.08 SIDE CHAIN REMARK 500 8 DG A 2 0.09 SIDE CHAIN REMARK 500 8 DG A 3 0.06 SIDE CHAIN REMARK 500 8 DA A 13 0.11 SIDE CHAIN REMARK 500 8 DG A 19 0.07 SIDE CHAIN REMARK 500 9 DC A 1 0.13 SIDE CHAIN REMARK 500 9 DG A 2 0.07 SIDE CHAIN REMARK 500 9 DG A 4 0.05 SIDE CHAIN REMARK 500 9 DG A 8 0.07 SIDE CHAIN REMARK 500 9 DC A 11 0.11 SIDE CHAIN REMARK 500 9 DG A 15 0.07 SIDE CHAIN REMARK 500 9 DA A 17 0.06 SIDE CHAIN REMARK 500 9 DG A 19 0.07 SIDE CHAIN REMARK 500 10 DC A 1 0.08 SIDE CHAIN REMARK 500 10 DG A 3 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 55 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 22 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 2 O6 REMARK 620 2 DG A 3 O6 70.3 REMARK 620 3 DG A 6 O6 77.7 87.1 REMARK 620 4 DG A 7 O6 128.1 66.0 73.5 REMARK 620 5 DG A 14 O6 126.3 154.7 79.4 89.5 REMARK 620 6 DG A 15 O6 147.4 99.2 133.8 67.9 75.9 REMARK 620 7 DG A 18 O6 76.9 131.3 120.1 154.9 74.0 89.5 REMARK 620 8 DG A 19 O6 80.4 64.8 149.0 104.1 131.5 67.4 75.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 23 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 68.9 REMARK 620 3 DG A 7 O6 63.4 94.7 REMARK 620 4 DG A 8 O6 119.2 81.4 67.9 REMARK 620 5 DG A 15 O6 99.7 157.7 63.1 88.3 REMARK 620 6 DG A 16 O6 157.9 127.7 122.2 80.5 69.1 REMARK 620 7 DG A 19 O6 64.3 121.8 93.6 152.4 64.6 93.7 REMARK 620 8 DG A 20 O6 92.5 79.3 155.5 133.2 121.4 78.6 70.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 23 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KQG RELATED DB: PDB DBREF 2KQH A 1 21 PDB 2KQH 2KQH 1 21 SEQRES 1 A 21 DC DG DG DG DC DG DG DG DC DG DC DG DA SEQRES 2 A 21 DG DG DG DA DG DG DG DT HET K A 22 1 HET K A 23 1 HETNAM K POTASSIUM ION FORMUL 2 K 2(K 1+) LINK O6 DG A 2 K K A 22 1555 1555 2.66 LINK O6 DG A 3 K K A 22 1555 1555 2.97 LINK O6 DG A 3 K K A 23 1555 1555 2.88 LINK O6 DG A 4 K K A 23 1555 1555 2.69 LINK O6 DG A 6 K K A 22 1555 1555 2.73 LINK O6 DG A 7 K K A 22 1555 1555 2.74 LINK O6 DG A 7 K K A 23 1555 1555 3.05 LINK O6 DG A 8 K K A 23 1555 1555 2.64 LINK O6 DG A 14 K K A 22 1555 1555 2.65 LINK O6 DG A 15 K K A 22 1555 1555 2.82 LINK O6 DG A 15 K K A 23 1555 1555 2.89 LINK O6 DG A 16 K K A 23 1555 1555 2.65 LINK O6 DG A 18 K K A 22 1555 1555 2.65 LINK O6 DG A 19 K K A 22 1555 1555 2.77 LINK O6 DG A 19 K K A 23 1555 1555 2.92 LINK O6 DG A 20 K K A 23 1555 1555 2.71 SITE 1 AC1 8 DG A 2 DG A 3 DG A 6 DG A 7 SITE 2 AC1 8 DG A 14 DG A 15 DG A 18 DG A 19 SITE 1 AC2 8 DG A 3 DG A 4 DG A 7 DG A 8 SITE 2 AC2 8 DG A 15 DG A 16 DG A 19 DG A 20 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