PDB Short entry for 1KOD HEADER RNA 28-MAR-96 1KOD TITLE RNA APTAMER COMPLEXED WITH CITRULLINE, NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(P*AP*GP*AP*AP*GP*GP*AP*GP*UP*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*GP*GP*UP*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 IN VITRO SELECTED RNA, RNA APTAMER, RNA EXPDTA SOLUTION NMR AUTHOR Y.S.YANG,M.KOCHOYAN,P.BURGSTALLER,E.WESTHOF,M.FAMULOK REVDAT 4 15-NOV-23 1KOD 1 ATOM REVDAT 3 23-FEB-22 1KOD 1 REMARK REVDAT 2 24-FEB-09 1KOD 1 VERSN REVDAT 1 08-NOV-96 1KOD 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 REMARK 3 AUTHORS : WESTHOF,DUMAS,MORAS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KOD 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_1000174468. 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 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 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 G A 6 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.6 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 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 10 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 A A 11 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 G A 12 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G A 14 N7 - C8 - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 U A 15 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 A B 27 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 A B 27 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G B 29 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 29 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 G B 30 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 G B 30 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 G B 30 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 U B 31 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 U B 32 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 A B 33 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G B 34 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 G B 34 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 G B 35 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 G B 35 N7 - C8 - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 G B 35 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 U B 36 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 38 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G B 38 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 C B 39 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 C B 39 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES 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 CIR B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KOC RELATED DB: PDB REMARK 900 1 STRUCTURE DBREF 1KOD A 5 15 PDB 1KOD 1KOD 5 15 DBREF 1KOD B 27 40 PDB 1KOD 1KOD 27 40 SEQRES 1 A 11 A G A A G G A G U G U SEQRES 1 B 14 A C G G U U A G G U C G C SEQRES 2 B 14 U HET CIR B 1 12 HETNAM CIR CITRULLINE FORMUL 3 CIR C6 H13 N3 O3 SITE 1 AC1 6 G A 12 U A 13 G B 30 U 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