10 20 30 40 50 60 70 80 2KQH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 05-NOV-09 2KQH
TITLE A G-RICH SEQUENCE WITHIN THE C-KIT ONCOGENE PROMOTER FORMS A TITLE 2 PARALLEL G-QUADRUPLEX HAVING ASYMMETRIC G-TETRAD DYNAMICS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(*CP*GP*GP*GP*CP*GP*GP*GP*CP*GP*CP*GP*AP*GP*GP*GP*AP*GP*GP COMPND 4 *GP*T)-3'; COMPND 5 CHAIN: A; COMPND 6 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, AUTHOR 2 S.BALASUBRAMANIAN
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 JRNL TITL 2 PROMOTER FORMS A PARALLEL G-QUADRUPLEX HAVING JRNL TITL 3 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 REMARK 1 TITL 2 TRANSCRIPTION ACTIVATION SITE OF THE HUMAN C-KIT REMARK 1 TITL 3 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 : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM 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. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-NOV-09. REMARK 100 THE RCSB ID CODE IS RCSB101446.
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 REMARK 210 POTASSIUM PHOSPHATE; 93% H2O/ REMARK 210 7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 TOCSY; 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 : SPARKY, NMRPIPE, AMBER REMARK 210 METHOD USED : 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 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 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 HO5' DC A 1 OP1 DG A 2 1.60 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 1 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 1 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 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 23 1555 1555 2.88 LINK O6 DG A 3 K K A 22 1555 1555 2.97 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 23 1555 1555 2.89 LINK O6 DG A 15 K K A 22 1555 1555 2.82 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 23 1555 1555 2.92 LINK O6 DG A 19 K K A 22 1555 1555 2.77 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