10 20 30 40 50 60 70 80 1NEM - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 15-MAR-99 1NEM
TITLE SACCHARIDE-RNA RECOGNITION IN THE NEOMYCIN B / RNA APTAMER TITLE 2 COMPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP*AP COMPND 4 *GP*UP*CP*C)-3'; COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: COMPLEXED WITH NEOMYCIN B; HETERO GROUPS COMPND 8 BDG (RING A), NEB (RING B), RIB (RING C), AND NED (RING D)
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS RNA APTAMER, AMINOGLYCOSIDE, ANTIBIOTIC
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR L.JIANG,A.MAJUMDAR,W.HU,T.J.JAISHREE,W.XU,D.J.PATEL
REVDAT 3 24-FEB-09 1NEM 1 VERSN REVDAT 2 19-SEP-06 1NEM 2 CONECT COMPND JRNL TITLE REVDAT 2 2 2 REMARK REVDAT 1 31-AUG-99 1NEM 0
JRNL AUTH L.JIANG,A.MAJUMDAR,W.HU,T.J.JAISHREE,W.XU,D.J.PATEL JRNL TITL SACCHARIDE-RNA RECOGNITION IN A COMPLEX FORMED JRNL TITL 2 BETWEEN NEOMYCIN B AND AN RNA APTAMER JRNL REF STRUCTURE FOLD.DES. V. 7 817 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10425683 JRNL DOI 10.1016/S0969-2126(99)80105-1
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1NEM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-99. REMARK 100 THE RCSB ID CODE IS RCSB000653.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : 10MM NA3PO4 REMARK 210 PRESSURE : 1 ATM 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 : DISTANCE RESTRAINED MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: EXPERIMENTS CONDUCTED IN D2O: 2D NOESY (50MS,120MS, REMARK 210 200MS,300MS) PHASE-SENSITIVE COSY, TOCSY, (1H)- (13)C HSQC 3D REMARK 210 (1H)-(13)C NOESY-HMQC (120MS, 300MS) 3D HCCH- COSY 3D HCCH- REMARK 210 TOCSY 2D (1H)-(13)C HCCH-TOCSY (65MS) 2D (1H)-(31)P REMARK 210 CORRELATION 3D (1H)-(13)C-(31)P CORRELATION
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 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 1 A A 6 N9 A A 6 C4 0.044 REMARK 500 1 A A 14 N9 A A 14 C4 0.042 REMARK 500 1 A A 17 N9 A A 17 C4 0.041 REMARK 500 1 U A 19 N1 U A 19 C2 0.055 REMARK 500 1 U A 20 N1 U A 20 C2 0.055 REMARK 500 1 U A 24 N1 U A 24 C2 0.061 REMARK 500 2 A A 6 N9 A A 6 C4 0.048 REMARK 500 2 A A 14 N9 A A 14 C4 0.040 REMARK 500 2 A A 17 N9 A A 17 C4 0.043 REMARK 500 2 U A 19 N1 U A 19 C2 0.056 REMARK 500 2 U A 20 N1 U A 20 C2 0.055 REMARK 500 2 U A 24 N1 U A 24 C2 0.063 REMARK 500 3 A A 6 N9 A A 6 C4 0.040 REMARK 500 3 U A 8 N1 U A 8 C2 0.055 REMARK 500 3 A A 14 N9 A A 14 C4 0.037 REMARK 500 3 A A 17 N9 A A 17 C4 0.038 REMARK 500 3 U A 24 N1 U A 24 C2 0.058 REMARK 500 4 C A 12 N1 C A 12 C2 0.064 REMARK 500 4 A A 14 N9 A A 14 C4 0.038 REMARK 500 4 A A 17 N9 A A 17 C4 0.040 REMARK 500 4 U A 19 N1 U A 19 C2 0.057 REMARK 500 4 U A 20 N1 U A 20 C2 0.055 REMARK 500 4 U A 21 N1 U A 21 C2 0.059 REMARK 500 4 U A 24 N1 U A 24 C2 0.060 REMARK 500 5 A A 6 N9 A A 6 C4 0.046 REMARK 500 5 C A 12 N1 C A 12 C2 0.062 REMARK 500 5 A A 14 N9 A A 14 C4 0.040 REMARK 500 5 A A 16 N9 A A 16 C4 0.038 REMARK 500 5 A A 17 N9 A A 17 C4 0.038 REMARK 500 5 U A 19 N1 U A 19 C2 0.056 REMARK 500 5 U A 24 N1 U A 24 C2 0.064 REMARK 500 6 C A 12 N1 C A 12 C2 0.062 REMARK 500 6 A A 14 N9 A A 14 C4 0.038 REMARK 500 6 A A 17 N9 A A 17 C4 0.046 REMARK 500 6 U A 19 N1 U A 19 C2 0.058 REMARK 500 6 U A 20 N1 U A 20 C2 0.062 REMARK 500 6 U A 21 N1 U A 21 C2 0.055 REMARK 500 6 U A 24 N1 U A 24 C2 0.061 REMARK 500 7 A A 6 N9 A A 6 C4 0.044 REMARK 500 7 A A 14 N9 A A 14 C4 0.038 REMARK 500 7 A A 17 N9 A A 17 C4 0.042 REMARK 500 7 U A 20 N1 U A 20 C2 0.057 REMARK 500 7 U A 21 N1 U A 21 C2 0.055 REMARK 500 7 U A 24 N1 U A 24 C2 0.057 REMARK 500 8 A A 6 N9 A A 6 C4 0.044 REMARK 500 8 U A 8 N1 U A 8 C2 0.054 REMARK 500 8 A A 14 N9 A A 14 C4 0.040 REMARK 500 8 A A 17 N9 A A 17 C4 0.042 REMARK 500 8 U A 19 N1 U A 19 C2 0.061 REMARK 500 8 U A 20 N1 U A 20 C2 0.056 REMARK 500 REMARK 500 THIS ENTRY HAS 56 BOND DEVIATIONS. 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 1 G A 4 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 5 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 A A 6 N1 - C6 - N6 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 C A 7 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 C A 7 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 9 N3 - C2 - N2 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 10 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 G A 10 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 11 N3 - C2 - N2 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C A 12 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G A 13 N3 - C2 - N2 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 A A 14 N1 - C6 - N6 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 15 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 A A 16 N1 - C6 - N6 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 17 N1 - C6 - N6 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 18 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 G A 18 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 22 N1 - C6 - N6 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 21 C3' - O3' - P ANGL. DEV. = 12.9 DEGREES REMARK 500 1 G A 23 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 C A 25 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 C A 26 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 4 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 G A 5 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 A A 6 N1 - C6 - N6 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 C A 7 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 C A 7 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 9 N3 - C2 - N2 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 G A 9 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 G A 10 N3 - C2 - N2 ANGL. DEV. = 6.7 DEGREES REMARK 500 2 G A 10 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 G A 11 P - O5' - C5' ANGL. DEV. = 10.0 DEGREES REMARK 500 2 G A 11 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 11 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 C A 12 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 C A 12 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 11 C3' - O3' - P ANGL. DEV. = 16.8 DEGREES REMARK 500 2 G A 13 N3 - C2 - N2 ANGL. DEV. = 6.9 DEGREES REMARK 500 2 A A 14 N1 - C6 - N6 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 G A 15 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 A A 16 N1 - C6 - N6 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 A A 17 N1 - C6 - N6 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 18 N3 - C2 - N2 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 G A 18 N1 - C6 - O6 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 18 C5 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 A A 22 N1 - C6 - N6 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 G A 23 N3 - C2 - N2 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 C A 25 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 213 ANGLE DEVIATIONS. 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 BDR A 29 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IDG A 30 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BDG A 27 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NEB A 28
DBREF 1NEM A 4 26 PDB 1NEM 1NEM 4 26
SEQRES 1 A 23 G G A C U G G G C G A G A SEQRES 2 A 23 A G U U U A G U C C
HET BDR A 29 17 HET IDG A 30 26 HET BDG A 27 26 HET NEB A 28 24
HETNAM BDR BETA-D-RIBOFURANOSYL HETNAM IDG O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE HETNAM BDG O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM NEB 2-DEOXY-D-STREPTAMINE
FORMUL 2 BDR C5 H10 O5 FORMUL 2 IDG C6 H14 N2 O4 FORMUL 3 BDG C6 H14 N2 O4 FORMUL 4 NEB C6 H15 N2 O3 1+
LINK O3 BDR A 29 C1 IDG A 30 1555 1555 1.40 LINK C1 BDR A 29 O5 NEB A 28 1555 1555 1.43 LINK C1 BDG A 27 O4 NEB A 28 1555 1555 1.40
SITE 1 AC1 6 A A 16 G A 18 U A 19 BDG A 27 SITE 2 AC1 6 NEB A 28 IDG A 30 SITE 1 AC2 6 C A 7 U A 8 A A 16 A A 17 SITE 2 AC2 6 G A 18 BDR A 29 SITE 1 AC3 7 G A 9 G A 13 A A 16 G A 18 SITE 2 AC3 7 U A 19 NEB A 28 BDR A 29 SITE 1 AC4 10 U A 8 G A 9 G A 10 A A 16 SITE 2 AC4 10 U A 19 U A 20 U A 21 A A 22 SITE 3 AC4 10 BDG A 27 BDR A 29
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