Header list of 1koc.pdb file
Complete list - 23 202 Bytes
HEADER RNA 28-MAR-96 1KOC
TITLE RNA APTAMER COMPLEXED WITH ARGININE, NMR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RNA (5'-R(P*AP*GP*AP*AP*GP*GP*AP*GP*CP*GP*U)-3');
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: RNA (5'-R(P*AP*CP*AP*GP*GP*UP*AP*GP*GP*UP*CP*GP*CP*U)-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 COMPLEX (RNA APTAMER-PEPTIDE), IN VITRO SELECTED RNA, RNA APTAMER,
KEYWDS 2 RNA
EXPDTA SOLUTION NMR
AUTHOR Y.S.YANG,M.KOCHOYAN,P.BURGSTALLER,E.WESTHOF,M.FAMULOK
REVDAT 3 23-FEB-22 1KOC 1 REMARK
REVDAT 2 24-FEB-09 1KOC 1 VERSN
REVDAT 1 17-AUG-96 1KOC 0
JRNL AUTH Y.YANG,M.KOCHOYAN,P.BURGSTALLER,E.WESTHOF,M.FAMULOK
JRNL TITL STRUCTURAL BASIS OF LIGAND DISCRIMINATION BY TWO RELATED RNA
JRNL TITL 2 APTAMERS RESOLVED BY NMR SPECTROSCOPY.
JRNL REF SCIENCE V. 272 1343 1996
JRNL REFN ISSN 0036-8075
JRNL PMID 8650546
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH P.BURGSTALLER,M.KOCHOYAN,M.FAMULOK
REMARK 1 TITL STRUCTURAL PROBING AND DAMAGE SELECTION OF CITRULLINE-AND
REMARK 1 TITL 2 ARGININE-SPECIFIC RNA APTAMERS IDENTIFY BASE POSITIONS
REMARK 1 TITL 3 REQUIRED FOR BINDING
REMARK 1 REF NUCLEIC ACIDS RES. V. 23 4769 1995
REMARK 1 REFN ISSN 0305-1048
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1KOC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000174467.
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 : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
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 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 G B 31 C8 G B 31 N9 -0.043
REMARK 500 G B 35 N7 G B 35 C8 -0.038
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 A A 5 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES
REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 A A 8 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES
REMARK 500 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 G A 10 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES
REMARK 500 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES
REMARK 500 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 C A 13 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES
REMARK 500 G A 14 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES
REMARK 500 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 U A 15 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES
REMARK 500 A B 27 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES
REMARK 500 A B 27 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES
REMARK 500 A B 27 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 A B 29 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 G B 30 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES
REMARK 500 G B 30 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 G B 30 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES
REMARK 500 G B 31 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES
REMARK 500 G B 31 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 U B 32 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 A B 33 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 G B 34 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 G B 34 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES
REMARK 500 G B 35 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES
REMARK 500 G B 35 N7 - C8 - N9 ANGL. DEV. = 5.5 DEGREES
REMARK 500 G B 35 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES
REMARK 500 U B 36 O4' - C1' - N1 ANGL. DEV. = 7.4 DEGREES
REMARK 500 C B 37 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 G B 38 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 G B 38 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 C B 39 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES
REMARK 500 U B 40 C3' - C2' - C1' ANGL. DEV. = 4.8 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 G B 35 0.09 SIDE CHAIN
REMARK 500 ARG B 1 0.18 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ARG B 1
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1KOD RELATED DB: PDB
REMARK 900 1 STRUCTURE
DBREF 1KOC A 5 15 PDB 1KOC 1KOC 5 15
DBREF 1KOC B 27 40 PDB 1KOC 1KOC 27 40
SEQRES 1 A 11 A G A A G G A G C G U
SEQRES 1 B 14 A C A G G U A G G U C G C
SEQRES 2 B 14 U
HET ARG B 1 14
HETNAM ARG ARGININE
FORMUL 3 ARG C6 H15 N4 O2 1+
SITE 1 AC1 6 G A 12 C A 13 G B 30 G B 31
SITE 2 AC1 6 A B 33 G B 35
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