Header list of 1k1r.pdb file
Complete list - 23 202 Bytes
HEADER DNA 25-SEP-01 1K1R
TITLE HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*TP*GP*TP*TP*TP*GP*GP*C)-3';
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*CP*(CMR)P*(RMP)P*(RMP)P*(RMP)P*(CMR)P*(RMP))-3';
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS METHYL PHOSPHONATE, MODIFIED DNA, ANTI SENSE, APTAMERS, DNA
EXPDTA SOLUTION NMR
AUTHOR V.THIVIYANATHAN,K.V.VYAZOVKINA,E.K.GOZANSKY,E.BICHENKOVA,
AUTHOR 2 T.V.ABRAMOVA,B.A.LUXON,A.V.LEBEDEV,D.G.GORENSTEIN
REVDAT 4 23-FEB-22 1K1R 1 REMARK LINK
REVDAT 3 24-FEB-09 1K1R 1 VERSN
REVDAT 2 01-APR-03 1K1R 1 JRNL
REVDAT 1 19-JUN-02 1K1R 0
JRNL AUTH V.THIVIYANATHAN,K.V.VYAZOVKINA,E.K.GOZANSKY,E.BICHENCHOVA,
JRNL AUTH 2 T.V.ABRAMOVA,B.A.LUXON,A.V.LEBEDEV,D.G.GORENSTEIN
JRNL TITL STRUCTURE OF HYBRID BACKBONE METHYLPHOSPHONATE DNA
JRNL TITL 2 HETERODUPLEXES: EFFECT OF R AND S STEREOCHEMISTRY.
JRNL REF BIOCHEMISTRY V. 41 827 2002
JRNL REFN ISSN 0006-2960
JRNL PMID 11790104
JRNL DOI 10.1021/BI011551K
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 5.1, AMBER 5.0
REMARK 3 AUTHORS : VARIAN (VNMR), UCSF (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1K1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-01.
REMARK 100 THE DEPOSITION ID IS D_1000014451.
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 : 100 MM
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 100 MM NACL, 10 MM PHOSPHATE,
REMARK 210 0.1 MM EDTA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 400 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MORASS 2.0
REMARK 210 METHOD USED : MOLECULAR DYNAMICS MATRIX
REMARK 210 RELAXATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
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
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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DC A 8 N3 - C2 - O2 ANGL. DEV. = -4.4 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 DG A 7 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1K1H RELATED DB: PDB
REMARK 900 HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE / DNA DUPLEX
REMARK 900 CHIRAL CENTER AT THE FIFTH POSITION OF CHAIN B IS CHANGED TO S.
DBREF 1K1R A 1 8 PDB 1K1R 1K1R 1 8
DBREF 1K1R B 9 15 PDB 1K1R 1K1R 9 15
SEQRES 1 A 8 DT DG DT DT DT DG DG DC
SEQRES 1 B 7 DC CMR RMP RMP RMP CMR RMP
MODRES 1K1R CMR B 10 DC
MODRES 1K1R RMP B 11 DA
MODRES 1K1R RMP B 12 DA
MODRES 1K1R RMP B 13 DA
MODRES 1K1R CMR B 14 DC
MODRES 1K1R RMP B 15 DA
HET CMR B 10 33
HET RMP B 11 35
HET RMP B 12 35
HET RMP B 13 35
HET CMR B 14 33
HET RMP B 15 33
HETNAM CMR 2'-DEOXY-CYTIDINE-5'-RP-MONOMETHYLPHOSPHONATE
HETNAM RMP 2'-DEOXY-ADENOSINE-5'-RP-MONOMETHYLPHOSPHONATE
FORMUL 2 CMR 2(C10 H16 N3 O6 P)
FORMUL 2 RMP 4(C11 H16 N5 O5 P)
LINK O3' DC B 9 P CMR B 10 1555 1555 1.62
LINK O3' CMR B 10 P RMP B 11 1555 1555 1.62
LINK O3' RMP B 11 P RMP B 12 1555 1555 1.61
LINK O3' RMP B 12 P RMP B 13 1555 1555 1.62
LINK O3' RMP B 13 P CMR B 14 1555 1555 1.62
LINK O3' CMR B 14 P RMP B 15 1555 1555 1.63
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
Complete list - 23 202 Bytes