Header list of 1nem.pdb file
Complete list - 29 20 Bytes
HEADER RNA 15-MAR-99 1NEM
TITLE SACCHARIDE-RNA RECOGNITION IN THE NEOMYCIN B / RNA APTAMER COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP
COMPND 3 *AP*GP*UP*CP*C)-3';
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: COMPLEXED WITH NEOMYCIN B; HETERO GROUPS BDG (RING A),
COMPND 7 NEB (RING B), RIB (RING C), AND NED (RING D)
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS RNA APTAMER, AMINOGLYCOSIDE, ANTIBIOTIC, RNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR L.JIANG,A.MAJUMDAR,W.HU,T.J.JAISHREE,W.XU,D.J.PATEL
REVDAT 4 29-JUL-20 1NEM 1 COMPND REMARK HETNAM LINK
REVDAT 4 2 1 SITE ATOM
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 BETWEEN
JRNL TITL 2 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 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 DEPOSITION ID IS D_1000000653.
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:
REMARK 210 EXPERIMENTS CONDUCTED IN D2O: 2D NOESY (50MS,120MS,200MS,300MS)
REMARK 210 PHASE-SENSITIVE
REMARK 210 COSY, TOCSY, (1H)- (13)C HSQC 3D (1H)-(13)C NOESY-HMQC (120MS,
REMARK 210 300MS) 3D HCCH-
REMARK 210 COSY 3D HCCH-TOCSY 2D (1H)-(13)C HCCH-TOCSY (65MS) 2D (1H)-(31)P
REMARK 210 CORRELATION
REMARK 210 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 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: MONOMERIC
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 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 U A 21 C3' - O3' - P ANGL. DEV. = 12.9 DEGREES
REMARK 500 1 A A 22 N1 - C6 - N6 ANGL. DEV. = 5.0 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 G A 11 C3' - O3' - P ANGL. DEV. = 16.8 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 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
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 B 1 17
HET IDG B 2 26
HET BDG A 27 26
HET NEB A 28 24
HETNAM BDR BETA-D-RIBOFURANOSE
HETNAM IDG 2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE
HETNAM BDG 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 C1 BDG A 27 O4 NEB A 28 1555 1555 1.40
LINK O5 NEB A 28 C1 BDR B 1 1555 1555 1.43
LINK O3 BDR B 1 C1 IDG B 2 1555 1555 1.40
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
MODEL 1
Complete list - 29 20 Bytes