Header list of 1w86.pdb file
Complete list - r 25 2 Bytes
HEADER DNA 16-SEP-04 1W86
TITLE SOLUTION STRUCTURE OF AN DSDNA:LNA TRIPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INTRAMOLECULAR DSDNA-LNA TRIPLEX;
COMPND 3 CHAIN: A;
COMPND 4 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN
COMPND 5 A8 AND T9;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: INTRAMOLECULAR DSDNA-LNA TRIPLEX;
COMPND 8 CHAIN: B;
COMPND 9 OTHER_DETAILS: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN
COMPND 10 T16 AND T17;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: INTRAMOLECULAR DSDNA-LNA TRIPLEX;
COMPND 13 CHAIN: C;
COMPND 14 OTHER_DETAILS: C18, C20 AND C22 (LNA NUCLEOTIDES) ARE
COMPND 15 PROTONATED AT N3
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 SYNTHETIC: YES
KEYWDS DNA COMPLEX, LNA, DNA, TRIPLEX, NMR SPECTROSCOPY, STRUCTURE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.J.SORENSEN,J.T.NIELSEN,M.PETERSEN
REVDAT 4 24-NOV-09 1W86 1 VERSN
REVDAT 3 24-FEB-09 1W86 1 VERSN
REVDAT 2 01-DEC-05 1W86 1 REMARK ATOM HETATM CONECT
REVDAT 1 25-NOV-04 1W86 0
JRNL AUTH J.J.SORENSEN,J.T.NIELSEN,M.PETERSEN
JRNL TITL SOLUTION STRUCTURE OF A DSDNA:LNA TRIPLEX
JRNL REF NUCLEIC ACIDS RES. V. 32 6078 2004
JRNL REFN ISSN 0305-1048
JRNL PMID 15550567
JRNL DOI 10.1093/NAR/GKH942
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,
REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN
REMARK 3 THE JRNL CITATION ABOVE
REMARK 4
REMARK 4 1W86 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-SEP-04.
REMARK 100 THE PDBE ID CODE IS EBI-21072.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308.0
REMARK 210 PH : 5.1
REMARK 210 IONIC STRENGTH : 100 MM NACL
REMARK 210 PRESSURE : 1.0
REMARK 210 SAMPLE CONTENTS : D2O OR 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY,COSY,TOCSY,NOESY-
REMARK 210 TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800
REMARK 210 SPECTROMETER MODEL : UNITYINOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : AMBER
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NONE
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 GENERATING THE BIOMOLECULE
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2030 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 3840 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16 KCAL/MOL
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: 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 DG A 2 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DA A 3 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES
REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DC B 11 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 1 DT C 17 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 DT C 19 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DT C 21 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 DT C 21 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 1 DT C 23 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 DT C 23 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 1 DT C 24 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 DT C 24 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES
REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DA A 3 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES
REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 2 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 DT B 9 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DT B 10 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES
REMARK 500 2 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 2 DC B 11 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 2 DC B 13 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 2 DT B 14 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES
REMARK 500 2 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 2 DT C 17 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 2 DT C 19 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DT C 21 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DT C 21 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 2 DT C 23 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES
REMARK 500 2 DT C 23 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 3 DA A 3 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES
REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES
REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 474 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 DA A 8 0.07 SIDE CHAIN
REMARK 500 1 DC B 15 0.06 SIDE CHAIN
REMARK 500 3 DC B 15 0.12 SIDE CHAIN
REMARK 500 3 DT C 21 0.07 SIDE CHAIN
REMARK 500 4 DA A 8 0.05 SIDE CHAIN
REMARK 500 5 DA A 1 0.05 SIDE CHAIN
REMARK 500 5 DA A 8 0.06 SIDE CHAIN
REMARK 500 5 DT C 17 0.07 SIDE CHAIN
REMARK 500 6 DC B 15 0.07 SIDE CHAIN
REMARK 500 6 DT C 17 0.06 SIDE CHAIN
REMARK 500 7 DA A 8 0.06 SIDE CHAIN
REMARK 500 7 DC B 15 0.12 SIDE CHAIN
REMARK 500 7 DT B 16 0.06 SIDE CHAIN
REMARK 500 7 DT C 21 0.06 SIDE CHAIN
REMARK 500 8 DA A 5 0.05 SIDE CHAIN
REMARK 500 8 DA A 8 0.05 SIDE CHAIN
REMARK 500 9 DA A 5 0.07 SIDE CHAIN
REMARK 500 9 DT C 17 0.08 SIDE CHAIN
REMARK 500 10 DC B 15 0.07 SIDE CHAIN
REMARK 500 10 DT C 17 0.06 SIDE CHAIN
REMARK 500 11 DA A 8 0.05 SIDE CHAIN
REMARK 500 11 DT C 21 0.06 SIDE CHAIN
REMARK 500 12 DT C 17 0.08 SIDE CHAIN
REMARK 500 12 DT C 21 0.07 SIDE CHAIN
REMARK 500 13 DA A 1 0.06 SIDE CHAIN
REMARK 500 13 DA A 8 0.06 SIDE CHAIN
REMARK 500 13 DT B 9 0.06 SIDE CHAIN
REMARK 500 14 DA A 1 0.06 SIDE CHAIN
REMARK 500 14 DC B 11 0.08 SIDE CHAIN
REMARK 500 14 DC B 15 0.06 SIDE CHAIN
REMARK 500 17 DA A 8 0.06 SIDE CHAIN
REMARK 500 17 DT B 9 0.06 SIDE CHAIN
REMARK 500 18 DA A 8 0.06 SIDE CHAIN
REMARK 500 19 DA A 5 0.06 SIDE CHAIN
REMARK 500 19 DT C 17 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1W86 A 1 8 PDB 1W86 1W86 1 8
DBREF 1W86 B 9 16 PDB 1W86 1W86 9 16
DBREF 1W86 C 17 24 PDB 1W86 1W86 17 24
SEQRES 1 A 8 DA DG DA DG DA DG DA DA
SEQRES 1 B 8 DT DT DC DT DC DT DC DT
SEQRES 1 C 8 DT LCC DT LCC DT LCC DT DT
MODRES 1W86 LCC C 18 C MODIFIED CYTOSINE NUCLEOTIDE
MODRES 1W86 LCC C 20 C MODIFIED CYTOSINE NUCLEOTIDE
MODRES 1W86 LCC C 22 C MODIFIED CYTOSINE NUCLEOTIDE
HET LCC C 18 35
HET LCC C 20 35
HET LCC C 22 35
HETNAM LCC [(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-
HETNAM 2 LCC 1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL
HETNAM 3 LCC DIHYDROGEN PHOSPHATE
FORMUL 3 LCC 3(C11 H16 N3 O8 P)
LINK O3' DT C 17 P LCC C 18 1555 1555 1.62
LINK O3' LCC C 18 P DT C 19 1555 1555 1.61
LINK O3' DT C 19 P LCC C 20 1555 1555 1.62
LINK O3' LCC C 20 P DT C 21 1555 1555 1.62
LINK O3' DT C 21 P LCC C 22 1555 1555 1.62
LINK O3' LCC C 22 P DT C 23 1555 1555 1.62
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 - r 25 2 Bytes