spacer
spacer

PDBsum entry 1xv6

Go to PDB code: 
Top Page ligands links
RNA PDB id
1xv6
Jmol
Contents
Ligands
C2L-G2L-C2L-G2L-
A2L-A2L-U2L-U2L-
C2L-G2L-C2L-G2L
HEADER    RNA                                     27-OCT-04   1XV6
TITLE     THE SOLUTION STRUCTURE OF 2',5'-LINKED 3'-O-(2-
TITLE    2 METHOXYETHYL)-RNA HAIRPIN
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: 5'-R(*(C2L)P*(G2L)P*(C2L)P*(G2L)P*(A2L)P*(A2L)
COMPND   3 P*(U2L)P*(U2L)P*(C2L)P*(G2L)P*(C2L)P*(G2L))-2';
COMPND   4 CHAIN: A;
COMPND   5 SYNONYM: 2'-MOE RNA;
COMPND   6 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 SYNTHETIC: YES;
SOURCE   3 OTHER_DETAILS: SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE
SOURCE   4 CHEMISTRY
KEYWDS    HAIRPIN, (2',5')-RNA, 3'-O-(2-METHOXYETHYL) RIBOSE
EXPDTA    SOLUTION NMR
NUMMDL    30
AUTHOR    M.PLEVNIK,Z.GDANIEC,J.PLAVEC
REVDAT   2   24-FEB-09 1XV6    1       VERSN
REVDAT   1   05-APR-05 1XV6    0
JRNL        AUTH   M.PLEVNIK,Z.GDANIEC,J.PLAVEC
JRNL        TITL   SOLUTION STRUCTURE OF A MODIFIED 2',5'-LINKED RNA
JRNL        TITL 2 HAIRPIN INVOLVED IN AN EQUILIBRIUM WITH DUPLEX
JRNL        REF    NUCLEIC ACIDS RES.            V.  33  1749 2005
JRNL        REFN                   ISSN 0305-1048
JRNL        PMID   15788747
JRNL        DOI    10.1093/NAR/GKI318
REMARK   1
REMARK   2
REMARK   2 RESOLUTION. NOT APPLICABLE.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : AMBER 6
REMARK   3   AUTHORS     : KOLLMAN ET AL.
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: STRUCTURES WERE REFINED BY NMR
REMARK   3  RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A
REMARK   3  GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING
REMARK   3  STRUCTURES WERE SUBJECTED TO ENERGY MINIMIZATION. 2',5'
REMARK   3  PHOSPHODIESTER LINKAGES BETWEEN RESIDUES, O3* OF EACH RIBOSE
REMARK   3  MODIFIED BY METHOXYETHYL.
REMARK   4
REMARK   4 1XV6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-04.
REMARK 100 THE RCSB ID CODE IS RCSB030800.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210  EXPERIMENT TYPE                : NMR
REMARK 210  TEMPERATURE           (KELVIN) : 303
REMARK 210  PH                             : 7.4
REMARK 210  IONIC STRENGTH                 : 50MM NACL
REMARK 210  PRESSURE                       : AMBIENT
REMARK 210  SAMPLE CONTENTS                : 0.9MM HAIRPIN, 100% D2O, 50MM
REMARK 210                                   NACL
REMARK 210
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D NOESY, DQF-COSY
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ
REMARK 210  SPECTROMETER MODEL             : INOVA
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN
REMARK 210
REMARK 210  STRUCTURE DETERMINATION.
REMARK 210   SOFTWARE USED                 : VNMR 6.1B, FELIX 2000
REMARK 210   METHOD USED                   : SIMULATED ANNEALING, ENERGY
REMARK 210                                   MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 30
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 30
REMARK 210 CONFORMERS, SELECTION CRITERIA  : ALL CALCULATED STRUCTURES
REMARK 210                                   SUBMITTED
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 18
REMARK 210
REMARK 210 REMARK: STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND
REMARK 210  HETERONUCLEAR TECHNIQUES.
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.
DBREF  1XV6 A    1    12  PDB    1XV6     1XV6             1     12
SEQRES   1 A   12  C2L G2L C2L G2L A2L A2L U2L U2L C2L G2L C2L G2L
MODRES 1XV6 C2L A    1    C
MODRES 1XV6 G2L A    2    G
MODRES 1XV6 C2L A    3    C
MODRES 1XV6 G2L A    4    G
MODRES 1XV6 A2L A    5    A
MODRES 1XV6 A2L A    6    A
MODRES 1XV6 U2L A    7    U
MODRES 1XV6 U2L A    8    U
MODRES 1XV6 C2L A    9    C
MODRES 1XV6 G2L A   10    G
MODRES 1XV6 C2L A   11    C
MODRES 1XV6 G2L A   12    G
HET    C2L  A   1      42
HET    G2L  A   2      44
HET    C2L  A   3      44
HET    G2L  A   4      44
HET    A2L  A   5      43
HET    A2L  A   6      43
HET    U2L  A   7      43
HET    U2L  A   8      43
HET    C2L  A   9      44
HET    G2L  A  10      44
HET    C2L  A  11      44
HET    G2L  A  12      45
HETNAM     C2L 5-METHYL-3'-O-METHOXYETHYL CYTIDINE 5'-MONOPHOSPHATE
HETNAM     G2L 3'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE
HETNAM     A2L 3'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE
HETNAM     U2L 5-METHYL-3'-O-METHOXYETHYL URIDINE-5'-MONOPHOSPHATE
FORMUL   1  C2L    4(C13 H22 N3 O9 P)
FORMUL   1  G2L    4(C13 H20 N5 O9 P)
FORMUL   1  A2L    2(C13 H20 N5 O8 P)
FORMUL   1  U2L    2(C13 H21 N2 O10 P)
LINK         O2' C2L A   1                 P   G2L A   2     1555   1555  1.63
LINK         O2' G2L A   2                 P   C2L A   3     1555   1555  1.60
LINK         O2' C2L A   3                 P   G2L A   4     1555   1555  1.62
LINK         O2' G2L A   4                 P   A2L A   5     1555   1555  1.63
LINK         O2' A2L A   5                 P   A2L A   6     1555   1555  1.61
LINK         O2' A2L A   6                 P   U2L A   7     1555   1555  1.62
LINK         O2' U2L A   7                 P   U2L A   8     1555   1555  1.65
LINK         O2' U2L A   8                 P   C2L A   9     1555   1555  1.62
LINK         O2' C2L A   9                 P   G2L A  10     1555   1555  1.61
LINK         O2' G2L A  10                 P   C2L A  11     1555   1555  1.61
LINK         O2' C2L A  11                 P   G2L A  12     1555   1555  1.61
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
      
 References