Header list of 1pik.pdb file
Complete list - 29 20 Bytes
HEADER DNA 11-DEC-96 1PIK
TITLE ESPERAMICIN A1-DNA COMPLEX, NMR, 4 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(C*GP*GP*AP*TP*CP*CP*GP)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: COMPLEXED WITH ESPERAMICIN A1
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS DEOXYRIBONUCLEIC ACID, DRUG COMPLEX, DNA
EXPDTA SOLUTION NMR
NUMMDL 4
AUTHOR R.A.KUMAR,N.IKEMOTO,D.J.PATEL
REVDAT 3 29-JUL-20 1PIK 1 COMPND REMARK HETNAM LINK
REVDAT 3 2 1 SITE ATOM
REVDAT 2 24-FEB-09 1PIK 1 VERSN
REVDAT 1 12-MAR-97 1PIK 0
JRNL AUTH R.A.KUMAR,N.IKEMOTO,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE OF THE ESPERAMICIN A1-DNA COMPLEX
JRNL REF J.MOL.BIOL. V. 265 173 1997
JRNL REFN ISSN 0022-2836
JRNL PMID 9020981
JRNL DOI 10.1006/JMBI.1996.0719
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH N.IKEMOTO,R.A.KUMAR,P.C.DEDON,S.J.DANISHEFSKY,D.J.PATEL
REMARK 1 TITL ESPERAMICIN A1 INTERCALATES INTO DUPLEX DNA FROM THE MINOR
REMARK 1 TITL 2 GROOVE
REMARK 1 REF J.AM.CHEM.SOC. V. 116 9387 1994
REMARK 1 REFN ISSN 0002-7863
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1PIK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000175698.
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 : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR, XEASY, RPEAK, X-PLOR
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 4
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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, C
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 DPA A 25 O3 DLF B 24 2.14
REMARK 500
REMARK 500 REMARK: NULL
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 1 DC A 1 C5' DC A 1 C4' 0.052
REMARK 500 1 DG A 2 C5' DG A 2 C4' 0.046
REMARK 500 1 DA A 4 N9 DA A 4 C4 0.044
REMARK 500 1 DC A 6 C5' DC A 6 C4' 0.045
REMARK 500 1 DC A 7 C5' DC A 7 C4' 0.055
REMARK 500 1 DG A 8 C5' DG A 8 C4' 0.049
REMARK 500 1 DC B 11 C5' DC B 11 C4' 0.045
REMARK 500 1 DG B 13 C5' DG B 13 C4' 0.063
REMARK 500 1 DA B 14 N9 DA B 14 C4 0.039
REMARK 500 1 DC B 16 C5' DC B 16 C4' 0.053
REMARK 500 1 DC B 16 C2' DC B 16 C1' 0.061
REMARK 500 1 DC B 17 C5' DC B 17 C4' 0.043
REMARK 500 2 DG A 2 C5' DG A 2 C4' 0.045
REMARK 500 2 DG A 3 C5' DG A 3 C4' 0.046
REMARK 500 2 DA A 4 N9 DA A 4 C4 0.051
REMARK 500 2 DT A 5 N1 DT A 5 C2 0.051
REMARK 500 2 DC A 7 C5' DC A 7 C4' 0.062
REMARK 500 2 DC A 7 C3' DC A 7 C2' 0.074
REMARK 500 2 DG B 13 C5' DG B 13 C4' 0.068
REMARK 500 2 DT B 15 C3' DT B 15 C2' 0.085
REMARK 500 2 DC B 16 C5' DC B 16 C4' 0.047
REMARK 500 2 DC B 17 C5' DC B 17 C4' 0.052
REMARK 500 2 DG B 18 C5' DG B 18 C4' 0.050
REMARK 500 3 DG A 2 C5' DG A 2 C4' 0.043
REMARK 500 3 DG A 3 C3' DG A 3 C2' 0.082
REMARK 500 3 DG A 3 N9 DG A 3 C4 0.050
REMARK 500 3 DC A 7 C5' DC A 7 C4' 0.062
REMARK 500 3 DG B 12 C5' DG B 12 C4' 0.045
REMARK 500 3 DG B 13 C5' DG B 13 C4' 0.049
REMARK 500 3 DA B 14 N9 DA B 14 C4 0.039
REMARK 500 3 DC B 16 C5' DC B 16 C4' 0.050
REMARK 500 3 DG B 18 C5' DG B 18 C4' 0.042
REMARK 500 4 DG A 2 N9 DG A 2 C4 0.052
REMARK 500 4 DT A 5 N1 DT A 5 C2 0.056
REMARK 500 4 DC A 7 N1 DC A 7 C6 0.037
REMARK 500 4 DA B 14 N9 DA B 14 C4 0.042
REMARK 500 4 DC B 16 N1 DC B 16 C6 0.037
REMARK 500 4 DG B 18 C5' DG B 18 C4' 0.047
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. = 4.8 DEGREES
REMARK 500 1 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DC A 1 C3' - O3' - P ANGL. DEV. = 11.3 DEGREES
REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 DG A 2 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG A 2 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES
REMARK 500 1 DG A 3 P - O5' - C5' ANGL. DEV. = 12.1 DEGREES
REMARK 500 1 DG A 3 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG A 3 C3' - O3' - P ANGL. DEV. = 14.7 DEGREES
REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DA A 4 C3' - O3' - P ANGL. DEV. = 22.0 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DT A 5 C3' - O3' - P ANGL. DEV. = 10.5 DEGREES
REMARK 500 1 DC A 6 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 1 DC A 6 C3' - O3' - P ANGL. DEV. = 16.1 DEGREES
REMARK 500 1 DC A 7 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES
REMARK 500 1 DC A 7 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DC A 7 C3' - O3' - P ANGL. DEV. = 20.4 DEGREES
REMARK 500 1 DG A 8 P - O5' - C5' ANGL. DEV. = 10.0 DEGREES
REMARK 500 1 DG A 8 N3 - C2 - N2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 DC B 11 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES
REMARK 500 1 DG B 12 P - O5' - C5' ANGL. DEV. = 9.7 DEGREES
REMARK 500 1 DG B 12 C3' - O3' - P ANGL. DEV. = 20.7 DEGREES
REMARK 500 1 DG B 13 P - O5' - C5' ANGL. DEV. = 15.4 DEGREES
REMARK 500 1 DG B 13 C3' - O3' - P ANGL. DEV. = 12.8 DEGREES
REMARK 500 1 DA B 14 P - O5' - C5' ANGL. DEV. = 18.5 DEGREES
REMARK 500 1 DA B 14 C3' - O3' - P ANGL. DEV. = 12.7 DEGREES
REMARK 500 1 DT B 15 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 DT B 15 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES
REMARK 500 1 DC B 16 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DC B 16 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES
REMARK 500 1 DC B 17 P - O5' - C5' ANGL. DEV. = 16.3 DEGREES
REMARK 500 1 DC B 17 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 DC B 17 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DC B 17 C3' - O3' - P ANGL. DEV. = 14.9 DEGREES
REMARK 500 1 DG B 18 P - O5' - C5' ANGL. DEV. = 15.9 DEGREES
REMARK 500 1 DG B 18 N3 - C2 - N2 ANGL. DEV. = 6.3 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DC A 1 C3' - O3' - P ANGL. DEV. = 12.9 DEGREES
REMARK 500 2 DG A 2 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 2 DG A 3 P - O5' - C5' ANGL. DEV. = 10.3 DEGREES
REMARK 500 2 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 2 DG A 3 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 DG A 3 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES
REMARK 500 2 DG A 3 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 162 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 0.12 SIDE CHAIN
REMARK 500 1 DG A 3 0.08 SIDE CHAIN
REMARK 500 1 DT A 5 0.07 SIDE CHAIN
REMARK 500 1 DG A 8 0.08 SIDE CHAIN
REMARK 500 1 DC B 11 0.09 SIDE CHAIN
REMARK 500 1 DA B 14 0.06 SIDE CHAIN
REMARK 500 2 DC A 1 0.07 SIDE CHAIN
REMARK 500 2 DG A 3 0.08 SIDE CHAIN
REMARK 500 2 DC A 6 0.09 SIDE CHAIN
REMARK 500 2 DC A 7 0.12 SIDE CHAIN
REMARK 500 2 DC B 11 0.12 SIDE CHAIN
REMARK 500 2 DA B 14 0.12 SIDE CHAIN
REMARK 500 3 DC A 1 0.14 SIDE CHAIN
REMARK 500 3 DA A 4 0.07 SIDE CHAIN
REMARK 500 3 DT A 5 0.13 SIDE CHAIN
REMARK 500 3 DC A 6 0.08 SIDE CHAIN
REMARK 500 3 DC A 7 0.13 SIDE CHAIN
REMARK 500 3 DC B 11 0.08 SIDE CHAIN
REMARK 500 3 DG B 12 0.06 SIDE CHAIN
REMARK 500 3 DA B 14 0.10 SIDE CHAIN
REMARK 500 4 DA A 4 0.06 SIDE CHAIN
REMARK 500 4 DC A 6 0.08 SIDE CHAIN
REMARK 500 4 DG A 8 0.06 SIDE CHAIN
REMARK 500 4 DC B 11 0.09 SIDE CHAIN
REMARK 500 4 DA B 14 0.09 SIDE CHAIN
REMARK 500 4 DC B 16 0.08 SIDE CHAIN
REMARK 500 4 DC B 17 0.12 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1PIK A 1 8 PDB 1PIK 1PIK 1 8
DBREF 1PIK B 11 18 PDB 1PIK 1PIK 11 18
SEQRES 1 A 8 DC DG DG DA DT DC DC DG
SEQRES 1 B 8 DC DG DG DA DT DC DC DG
HET DAG C 1 21
HET MAT C 2 31
HET DPA A 25 33
HET TMR B 22 24
HET DLF B 24 20
HET MTC B 26 41
HETNAM DAG 4-AMINO-4,6-DIDEOXY-BETA-D-GLUCOPYRANOSE
HETNAM MAT 2,4-DIDEOXY-3-O-METHYL-4-(PROPAN-2-YLAMINO)-ALPHA-L-
HETNAM 2 MAT THREO-PENTOPYRANOSE
HETNAM DPA 4,5-DIMETHOXY-N-(2'-METHOXYPROPENOYL ANTHRANILATE)
HETNAM TMR 2,6-DIDEOXY-4-S-METHYL-4-THIO-BETA-D-RIBO-HEXOPYRANOSE
HETNAM DLF 2-DEOXY-ALPHA-L-FUCOPYRANOSE
HETNAM MTC [1,8-DIHYDROXY-11-OXO-13-(2-METHYLTRITHIO-ETHYLIDENE)-
HETNAM 2 MTC BICYCLO[7.3.1]TRIDECA-4,9-DIENE-2,6-DIYN-10-YL]-
HETNAM 3 MTC CARBAMIC ACID METHYL ESTER
FORMUL 3 DAG C6 H13 N O4
FORMUL 3 MAT C9 H19 N O3
FORMUL 4 DPA C13 H15 N O5
FORMUL 5 TMR C7 H14 O3 S
FORMUL 6 DLF C6 H12 O4
FORMUL 7 MTC C18 H17 N O4 S3
LINK C1 DPA A 25 O3 DLF B 24 1555 1555 1.31
LINK O1 TMR B 22 N4 DAG C 1 1555 1555 1.46
LINK O1 DLF B 24 C9 MTC B 26 1555 1555 1.44
LINK C1 MTC B 26 O1 DAG C 1 1555 1555 1.43
LINK O2 DAG C 1 C1 MAT C 2 1555 1555 1.40
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
Complete list - 29 20 Bytes