Header list of 1cx5.pdb file
Complete list - 16 202 Bytes
HEADER DNA-RNA HYBRID 28-AUG-99 1CX5
TITLE ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*TP*T*(MMT)P*TP*GP*CP*GP*C);
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: C3* OF THYMINE T 6 A BINDS DIRECTLY TO CO3* OF MMT;
COMPND 6 O3* OF T 6 A IS MISSING;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: 5'-R(*GP*CP*GP*CP*AP*AP*AP*AP*CP*GP*CP*G);
COMPND 9 CHAIN: B;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS ANTISENSE, DNA/RNA HYBRID, MODIFIED BACKBONE LINKER, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
AUTHOR X.YANG,X.HAN,C.CROSS,Y.SANGHVI,X.GAO
REVDAT 5 16-FEB-22 1CX5 1 REMARK LINK
REVDAT 4 24-FEB-09 1CX5 1 VERSN
REVDAT 3 01-APR-03 1CX5 1 JRNL
REVDAT 2 07-APR-00 1CX5 1 JRNL
REVDAT 1 14-SEP-99 1CX5 0
JRNL AUTH X.YANG,X.HAN,C.CROSS,S.BARE,Y.SANGHVI,X.GAO
JRNL TITL NMR STRUCTURE OF AN ANTISENSE DNA.RNA HYBRID DUPLEX
JRNL TITL 2 CONTAINING A 3'-CH(2)N(CH(3))-O-5' OR AN MMI BACKBONE
JRNL TITL 3 LINKER.
JRNL REF BIOCHEMISTRY V. 38 12586 1999
JRNL REFN ISSN 0006-2960
JRNL PMID 10504227
JRNL DOI 10.1021/BI990456X
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1CX5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-99.
REMARK 100 THE DEPOSITION ID IS D_1000009601.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1-2 MM HYBRID DUPLEX IN 0.1 M
REMARK 210 NACL, 10 MM SODIUM PHOSPHATE AND
REMARK 210 0.1 MM SODIUM EDTA.
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : UXNMR, FELIX 2.3/95/97,
REMARK 210 MARDIGRAS, QUANTA 4/98
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 9
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED,BACK CALCULATED DATA
REMARK 210 AGREE WITH EXPERIMENTAL NOESY
REMARK 210 SPECTRUM
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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 DC A 1 C2 - N3 - C4 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DG A 2 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DC A 3 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES
REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 DC A 3 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DC A 3 N3 - C2 - O2 ANGL. DEV. = -6.2 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG A 4 C6 - N1 - C2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DG A 4 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DG A 4 N1 - C6 - O6 ANGL. DEV. = -5.0 DEGREES
REMARK 500 DT A 5 C4' - C3' - C2' ANGL. DEV. = -6.8 DEGREES
REMARK 500 DT A 5 C3' - C2' - C1' ANGL. DEV. = 9.1 DEGREES
REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = -5.2 DEGREES
REMARK 500 DT A 5 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 DT A 5 N3 - C4 - O4 ANGL. DEV. = -4.8 DEGREES
REMARK 500 DT A 5 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DT A 6 O4' - C4' - C3' ANGL. DEV. = 8.1 DEGREES
REMARK 500 DT A 6 C4' - C3' - C2' ANGL. DEV. = -10.3 DEGREES
REMARK 500 DT A 6 C3' - C2' - C1' ANGL. DEV. = 10.1 DEGREES
REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DT A 6 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 DT A 6 N1 - C2 - N3 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DT A 6 C2 - N3 - C4 ANGL. DEV. = -6.3 DEGREES
REMARK 500 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES
REMARK 500 DT A 8 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 DT A 8 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DT A 8 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DG A 9 C5' - C4' - O4' ANGL. DEV. = 8.5 DEGREES
REMARK 500 DG A 9 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DG A 9 N1 - C6 - O6 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DC A 10 C2 - N3 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DC A 10 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 11 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DG A 11 N1 - C6 - O6 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC A 12 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES
REMARK 500 G B 101 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 G B 101 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 G B 101 N1 - C6 - O6 ANGL. DEV. = -4.9 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 77 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 DC A 1 0.07 SIDE CHAIN
REMARK 500 DG A 2 0.08 SIDE CHAIN
REMARK 500 DG A 4 0.09 SIDE CHAIN
REMARK 500 DT A 5 0.13 SIDE CHAIN
REMARK 500 DT A 6 0.16 SIDE CHAIN
REMARK 500 DT A 8 0.13 SIDE CHAIN
REMARK 500 DG A 9 0.15 SIDE CHAIN
REMARK 500 DC A 10 0.08 SIDE CHAIN
REMARK 500 DG A 11 0.06 SIDE CHAIN
REMARK 500 C B 102 0.10 SIDE CHAIN
REMARK 500 G B 103 0.08 SIDE CHAIN
REMARK 500 A B 105 0.09 SIDE CHAIN
REMARK 500 C B 109 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1CX5 A 1 12 PDB 1CX5 1CX5 1 12
DBREF 1CX5 B 101 112 PDB 1CX5 1CX5 101 112
SEQRES 1 A 12 DC DG DC DG DT DT MMT DT DG DC DG DC
SEQRES 1 B 12 G C G C A A A A C G C G
MODRES 1CX5 MMT A 7 DT 5'-O-(DIMETHYLAMINO)-THYMIDINE
HET MMT A 7 37
HETNAM MMT 5'-O-(DIMETHYLAMINO)-THYMIDINE
FORMUL 1 MMT C12 H19 N3 O5
LINK C3' DT A 6 C3X MMT A 7 1555 1555 1.53
LINK O3' MMT A 7 P DT A 8 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
Complete list - 16 202 Bytes