10 20 30 40 50 60 70 80 1EKI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 08-MAR-00 1EKI
TITLE AVERAGE SOLUTION STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND TITLE 2 COBALT
CAVEAT 1EKI CHIRALITY INCORRECT C3' OF A 8 AND OF B 18
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TWO MOLECULES OF THE DRUG CHROMOMYCIN A3 (1GL-2GL-DXB- COMPND 6 DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS DRUG BOUND IN THE MINOR GROOVE OF DNA, DNA
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR M.GOCHIN
REVDAT 4 28-DEC-11 1EKI 1 CAVEAT VERSN REVDAT 3 24-FEB-09 1EKI 1 VERSN REVDAT 2 23-MAY-00 1EKI 1 JRNL REVDAT 1 20-MAR-00 1EKI 0
JRNL AUTH M.GOCHIN JRNL TITL A HIGH-RESOLUTION STRUCTURE OF A DNA-CHROMOMYCIN-CO(II) JRNL TITL 2 COMPLEX DETERMINED FROM PSEUDOCONTACT SHIFTS IN NUCLEAR JRNL TITL 3 MAGNETIC RESONANCE. JRNL REF STRUCTURE FOLD.DES. V. 8 441 2000 JRNL REFN ISSN 0969-2126 JRNL PMID 10801486 JRNL DOI 10.1016/S0969-2126(00)00124-6
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.TU,M.GOCHIN REMARK 1 TITL STRUCTURE DETERMINATION BY RESTRAINED MOLECULAR DYNAMICS REMARK 1 TITL 2 USING NMR PSEUDOCONTACT SHIFTS AS EXPERIMENTALLY DETERMINED REMARK 1 TITL 3 CONSTRAINTS REMARK 1 REF J.AM.CHEM.SOC. V. 121 9276 1999 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA9904540
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.0, 3.851 REMARK 3 AUTHORS : BRUNGER (MODIFIED GOCHIN AND TU) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS, ISOLATED SPIN-PAIR REMARK 3 APPROXIMATION FOR NOE'S; PSEUDOCONTACT SHIFT REFINEMENT
REMARK 4 REMARK 4 1EKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAR-00. REMARK 100 THE RCSB ID CODE IS RCSB010675.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 110MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2MM DNA-DRUG COMPLEX, 25 DEGREES REMARK 210 C, IN BUFFER (100MM NACL, 10MM NA REMARK 210 BORATE), FINAL PH 6. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 13C-1H HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : OMEGA REMARK 210 SPECTROMETER MANUFACTURER : GE REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.7, SPARKY 3.0, FELIX REMARK 210 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGE STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES AS WELL AS 2D 13C-1H HETERONUCLEAR REMARK 210 CORRELATION
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: 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 O1 2GL B 22 C6 CPH B 23 1.41 REMARK 500 O1 2GL A 32 C6 CPH A 33 1.42 REMARK 500 O1 DDA B 26 C2 CPH B 23 1.42 REMARK 500 O1 DDA B 36 C2 CPH A 33 1.45 REMARK 500 O2 DC A 6 H21 DG B 13 1.59 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG A 3 C4' - C3' - C2' ANGL. DEV. = -9.9 DEGREES REMARK 500 DG A 4 P - O5' - C5' ANGL. DEV. = 18.1 DEGREES REMARK 500 DG A 4 N3 - C2 - N2 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG A 3 C3' - O3' - P ANGL. DEV. = 17.6 DEGREES REMARK 500 DC A 5 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 4 C3' - O3' - P ANGL. DEV. = 9.6 DEGREES REMARK 500 DA A 7 P - O5' - C5' ANGL. DEV. = 11.0 DEGREES REMARK 500 DA A 7 C3' - O3' - P ANGL. DEV. = 16.1 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 13 P - O5' - C5' ANGL. DEV. = 9.9 DEGREES REMARK 500 DG B 13 C4' - C3' - C2' ANGL. DEV. = -9.8 DEGREES REMARK 500 DG B 14 P - O5' - C5' ANGL. DEV. = 17.6 DEGREES REMARK 500 DG B 14 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 DG B 13 C3' - O3' - P ANGL. DEV. = 17.3 DEGREES REMARK 500 DC B 15 C4' - C3' - C2' ANGL. DEV. = -5.3 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 14 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA B 17 C3' - O3' - P ANGL. DEV. = 16.1 DEGREES 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 DT A 2 0.10 SIDE CHAIN REMARK 500 DA A 7 0.08 SIDE CHAIN REMARK 500 DT B 12 0.10 SIDE CHAIN REMARK 500 DG B 14 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2GL B 22 REMARK 610 DDA B 25 REMARK 610 DDA B 26 REMARK 610 2GL A 32 REMARK 610 DDA B 35 REMARK 610 DDA B 36
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 CO A 41 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CPH A 33 O9 REMARK 620 2 CPH B 23 O9 120.4 REMARK 620 3 CPH B 23 O1 127.9 98.9 REMARK 620 4 CPH A 33 O1 102.5 115.3 88.0 REMARK 620 5 CPH A 33 C9 35.6 155.1 97.9 83.5 REMARK 620 6 CPH B 23 C9 151.5 32.3 77.0 90.9 172.6 REMARK 620 7 CPH A 33 C1 85.3 138.1 86.6 22.9 61.2 112.8 REMARK 620 8 CPH B 23 C1 146.1 78.7 20.9 91.8 118.8 56.3 98.1 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 1GL B 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2GL B 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERI B 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1GL A 31 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2GL A 32 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERI B 34 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 35 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DDA B 36 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 41 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPH B 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPH A 33
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EKH RELATED DB: PDB REMARK 900 FAMILY OF 6 STRUCTURES REMARK 900 RELATED ID: 1D83 RELATED DB: PDB
DBREF 1EKI A 1 8 PDB 1EKI 1EKI 1 8 DBREF 1EKI B 11 18 PDB 1EKI 1EKI 11 18
SEQRES 1 A 8 DT DT DG DG DC DC DA DA SEQRES 1 B 8 DT DT DG DG DC DC DA DA
HET 1GL B 21 24 HET 2GL B 22 24 HET ERI B 24 29 HET DDA B 25 19 HET DDA B 26 19 HET 1GL A 31 24 HET 2GL A 32 24 HET ERI B 34 29 HET DDA B 35 19 HET DDA B 36 19 HET CO A 41 1 HET CPH B 23 49 HET CPH A 33 49
HETNAM 1GL 4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE HETNAM 2GL 4-O-ACETYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE HETNAM ERI 4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO- HETNAM 2 ERI HEXOPYRANOSE HETNAM DDA 2,6-DIDEOXY-BETA-D-GLUCOSE HETNAM CO COBALT (II) ION HETNAM CPH 1,8-DIHYDROXY-7-METHYL-3-(1,3,4-TRIHYDROXY-2-OXO- HETNAM 2 CPH PENTYL)-3,10-DIHYDRO-2H-ANTHRACEN-9-ONE
HETSYN DDA 2,6-DIDEOXY-BETA-D-MANNOSE
FORMUL 3 1GL 2(C7 H14 O4) FORMUL 3 2GL 2(C8 H14 O5) FORMUL 4 ERI 2(C9 H16 O5) FORMUL 4 DDA 4(C6 H12 O4) FORMUL 7 CO CO 2+ FORMUL 8 CPH 2(C21 H24 O7)
LINK O5 1GL B 21 C3 2GL B 22 1555 1555 3.02 LINK O1 ERI B 24 C3 DDA B 25 1555 1555 2.97 LINK O5 DDA B 25 C3 DDA B 26 1555 1555 2.94 LINK O5 1GL A 31 C3 2GL A 32 1555 1555 3.04 LINK O1 ERI B 34 C3 DDA B 35 1555 1555 2.96 LINK O5 DDA B 35 C3 DDA B 36 1555 1555 3.03 LINK OGL ERI B 24 C3 DDA B 25 1555 1555 1.44 LINK OGL ERI B 34 C3 DDA B 35 1555 1555 1.45 LINK O1 1GL B 21 C3 2GL B 22 1555 1555 1.45 LINK O1 DDA B 25 C3 DDA B 26 1555 1555 1.45 LINK O1 1GL A 31 C3 2GL A 32 1555 1555 1.45 LINK O1 DDA B 35 C3 DDA B 36 1555 1555 1.45 LINK CO CO A 41 O9 CPH A 33 1555 1555 1.90 LINK CO CO A 41 O9 CPH B 23 1555 1555 1.91 LINK CO CO A 41 O1 CPH B 23 1555 1555 1.86 LINK CO CO A 41 O1 CPH A 33 1555 1555 1.93 LINK CO CO A 41 C9 CPH A 33 1555 1555 2.41 LINK CO CO A 41 C9 CPH B 23 1555 1555 2.57 LINK CO CO A 41 C1 CPH A 33 1555 1555 2.75 LINK CO CO A 41 C1 CPH B 23 1555 1555 2.77
SITE 1 AC1 2 DG B 14 2GL B 22 SITE 1 AC2 6 DG B 14 DC B 15 1GL B 21 CPH B 23 SITE 2 AC2 6 ERI B 34 DDA B 35 SITE 1 AC3 7 DG A 3 DG A 4 1GL A 31 2GL A 32 SITE 2 AC3 7 CPH A 33 DA B 17 DDA B 25 SITE 1 AC4 5 2GL A 32 CPH A 33 DA B 17 ERI B 24 SITE 2 AC4 5 DDA B 26 SITE 1 AC5 3 DC B 16 CPH B 23 DDA B 25 SITE 1 AC6 3 DG A 4 2GL A 32 ERI B 24 SITE 1 AC7 6 DG A 4 DC A 5 1GL A 31 CPH A 33 SITE 2 AC7 6 ERI B 24 DDA B 25 SITE 1 AC8 7 DA A 7 DA A 8 DG B 13 DG B 14 SITE 2 AC8 7 2GL B 22 CPH B 23 DDA B 35 SITE 1 AC9 4 2GL B 22 CPH B 23 ERI B 34 DDA B 36 SITE 1 BC1 3 CPH A 33 CPH B 23 DDA B 35 SITE 1 BC2 2 CPH A 33 CPH B 23 SITE 1 BC3 13 DC A 6 CPH A 33 CO A 41 DG B 13 SITE 2 BC3 13 DG B 14 DC B 15 DC B 16 DA B 17 SITE 3 BC3 13 2GL B 22 DDA B 26 ERI B 34 DDA B 35 SITE 4 BC3 13 DDA B 36 SITE 1 BC4 12 DG A 3 DG A 4 DC A 5 DC A 6 SITE 2 BC4 12 DA A 7 2GL A 32 CO A 41 DC B 16 SITE 3 BC4 12 CPH B 23 ERI B 24 DDA B 25 DDA B 36
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