Header list of 1raw.pdb file
Complete list - r 2 2 Bytes
HEADER RNA 17-JUL-96 1RAW
TITLE ATP BINDING RNA APTAMER IN COMPLEX WITH AMP, NMR, 10 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RNA APTAMER;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ATP-BINDING, RESIDUES 1 - 36;
COMPND 5 SYNONYM: RAB;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: CONSENSUS SEQUENCE OF THE ATP BINDING RNA APTAMER
COMPND 8 FLANKED BY A 6 BASE PAIR STEM AND A FOUR BASE PAIR STEM CAPPED BY A
COMPND 9 UUCG TETRALOOP. COMPLEXED WITH AMP.
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS RIBONUCLEIC ACID, UUCG TETRALOOP, RNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR T.DIECKMANN,J.FEIGON
REVDAT 3 02-MAR-22 1RAW 1 REMARK
REVDAT 2 24-FEB-09 1RAW 1 VERSN
REVDAT 1 27-JAN-97 1RAW 0
JRNL AUTH T.DIECKMANN,E.SUZUKI,G.K.NAKAMURA,J.FEIGON
JRNL TITL SOLUTION STRUCTURE OF AN ATP-BINDING RNA APTAMER REVEALS A
JRNL TITL 2 NOVEL FOLD
JRNL REF RNA V. 2 628 1996
JRNL REFN ISSN 1355-8382
JRNL PMID 8756406
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH M.SASSANFAR,J.W.SZOSTAK
REMARK 1 TITL AN RNA MOTIF THAT BINDS ATP
REMARK 1 REF NATURE V. 364 550 1993
REMARK 1 REFN ISSN 0028-0836
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 1RAW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000175981.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 6.0
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 : 500 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : AMX; DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XPLOR 3.0
REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 N3 G A 17 HO3' AMP A 37 1.20
REMARK 500 HO2' G A 17 O4' C A 18 1.30
REMARK 500 HO2' G A 7 O5' G A 8 1.33
REMARK 500 HO2' A A 9 O5' A A 10 1.38
REMARK 500 HO2' A A 5 OP1 G A 6 1.38
REMARK 500 O2' G A 25 H5' G A 26 1.45
REMARK 500 H2 A A 9 O2' U A 16 1.46
REMARK 500 O2' A A 10 H42 C A 15 1.48
REMARK 500 HO2' A A 12 OP2 A A 13 1.50
REMARK 500 HO2' G A 8 O5' A A 9 1.51
REMARK 500 O2' A A 5 H5' G A 6 1.53
REMARK 500 H21 G A 8 OP2 G A 11 1.56
REMARK 500 H3' U A 22 O2 U A 23 1.57
REMARK 500 O2 C A 18 H5'1 AMP A 37 1.60
REMARK 500 N3 G A 17 O3' AMP A 37 2.14
REMARK 500
REMARK 500 REMARK: NULL
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 9 C8 A A 9 N9 -0.050
REMARK 500 1 A A 10 C8 A A 10 N9 -0.055
REMARK 500 1 G A 25 C8 G A 25 N9 -0.088
REMARK 500 1 G A 26 C8 G A 26 N9 -0.046
REMARK 500 1 G A 30 N7 G A 30 C8 -0.037
REMARK 500 2 A A 10 C8 A A 10 N9 -0.054
REMARK 500 2 G A 17 C8 G A 17 N9 -0.042
REMARK 500 2 G A 25 C8 G A 25 N9 -0.084
REMARK 500 2 G A 26 C8 G A 26 N9 -0.042
REMARK 500 2 G A 30 N7 G A 30 C8 -0.038
REMARK 500 3 A A 9 C8 A A 9 N9 -0.049
REMARK 500 3 A A 10 C8 A A 10 N9 -0.049
REMARK 500 3 C A 21 N1 C A 21 C6 -0.037
REMARK 500 3 G A 25 C8 G A 25 N9 -0.090
REMARK 500 4 A A 9 C8 A A 9 N9 -0.050
REMARK 500 4 A A 10 C8 A A 10 N9 -0.053
REMARK 500 4 G A 25 C8 G A 25 N9 -0.088
REMARK 500 4 G A 26 C8 G A 26 N9 -0.047
REMARK 500 4 G A 30 N7 G A 30 C8 -0.037
REMARK 500 5 A A 9 C8 A A 9 N9 -0.053
REMARK 500 5 A A 10 C8 A A 10 N9 -0.048
REMARK 500 5 G A 17 C8 G A 17 N9 -0.068
REMARK 500 5 G A 25 C8 G A 25 N9 -0.080
REMARK 500 5 G A 26 C8 G A 26 N9 -0.042
REMARK 500 6 A A 10 C8 A A 10 N9 -0.049
REMARK 500 6 G A 17 N3 G A 17 C4 -0.043
REMARK 500 6 G A 25 C8 G A 25 N9 -0.085
REMARK 500 7 A A 10 C2' A A 10 C1' -0.050
REMARK 500 7 G A 11 C8 G A 11 N9 -0.043
REMARK 500 7 G A 17 C8 G A 17 N9 -0.066
REMARK 500 7 G A 25 C8 G A 25 N9 -0.091
REMARK 500 7 G A 26 C8 G A 26 N9 -0.045
REMARK 500 8 A A 9 C8 A A 9 N9 -0.049
REMARK 500 8 G A 17 C8 G A 17 N9 -0.068
REMARK 500 8 G A 25 N7 G A 25 C8 -0.038
REMARK 500 8 G A 25 C8 G A 25 N9 -0.082
REMARK 500 8 G A 26 C8 G A 26 N9 -0.045
REMARK 500 9 G A 17 C8 G A 17 N9 -0.060
REMARK 500 9 G A 25 C8 G A 25 N9 -0.103
REMARK 500 10 A A 9 C8 A A 9 N9 -0.048
REMARK 500 10 A A 10 C8 A A 10 N9 -0.053
REMARK 500 10 G A 17 N3 G A 17 C4 -0.046
REMARK 500 10 G A 25 N7 G A 25 C8 -0.036
REMARK 500 10 G A 25 C8 G A 25 N9 -0.073
REMARK 500 10 G A 26 C8 G A 26 N9 -0.043
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 1 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 G A 2 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 G A 3 C5 - N7 - C8 ANGL. DEV. = -4.1 DEGREES
REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 6.9 DEGREES
REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 A A 4 C5 - N7 - C8 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 A A 4 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES
REMARK 500 1 A A 4 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES
REMARK 500 1 A A 5 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 A A 5 N7 - C8 - N9 ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 A A 5 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES
REMARK 500 1 G A 6 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 7.0 DEGREES
REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 G A 7 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 G A 7 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 6.6 DEGREES
REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 G A 8 C5 - N7 - C8 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 A A 9 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 A A 9 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES
REMARK 500 1 A A 10 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 A A 10 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES
REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 A A 10 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 1 G A 11 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 G A 11 N7 - C8 - N9 ANGL. DEV. = 6.9 DEGREES
REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES
REMARK 500 1 A A 12 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 A A 12 N7 - C8 - N9 ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 A A 12 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES
REMARK 500 1 A A 13 C5 - N7 - C8 ANGL. DEV. = -3.8 DEGREES
REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 6.0 DEGREES
REMARK 500 1 A A 13 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 A A 14 C5 - N7 - C8 ANGL. DEV. = -3.6 DEGREES
REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 A A 14 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES
REMARK 500 1 G A 17 C5 - N7 - C8 ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 7.2 DEGREES
REMARK 500 1 G A 17 C8 - N9 - C4 ANGL. DEV. = -4.3 DEGREES
REMARK 500 1 G A 19 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES
REMARK 500 1 G A 19 N7 - C8 - N9 ANGL. DEV. = 6.8 DEGREES
REMARK 500 1 G A 19 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 653 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 1 G A 8 0.10 SIDE CHAIN
REMARK 500 1 A A 9 0.10 SIDE CHAIN
REMARK 500 1 U A 23 0.15 SIDE CHAIN
REMARK 500 2 G A 8 0.10 SIDE CHAIN
REMARK 500 2 A A 9 0.10 SIDE CHAIN
REMARK 500 2 C A 24 0.08 SIDE CHAIN
REMARK 500 3 G A 8 0.09 SIDE CHAIN
REMARK 500 3 A A 9 0.09 SIDE CHAIN
REMARK 500 3 C A 21 0.07 SIDE CHAIN
REMARK 500 3 G A 25 0.09 SIDE CHAIN
REMARK 500 4 G A 8 0.10 SIDE CHAIN
REMARK 500 4 A A 9 0.09 SIDE CHAIN
REMARK 500 4 U A 23 0.15 SIDE CHAIN
REMARK 500 5 G A 8 0.10 SIDE CHAIN
REMARK 500 5 A A 9 0.09 SIDE CHAIN
REMARK 500 5 G A 11 0.07 SIDE CHAIN
REMARK 500 5 G A 17 0.08 SIDE CHAIN
REMARK 500 5 C A 24 0.06 SIDE CHAIN
REMARK 500 6 G A 8 0.09 SIDE CHAIN
REMARK 500 6 A A 9 0.09 SIDE CHAIN
REMARK 500 6 G A 11 0.06 SIDE CHAIN
REMARK 500 6 U A 22 0.10 SIDE CHAIN
REMARK 500 6 G A 25 0.06 SIDE CHAIN
REMARK 500 7 A A 9 0.07 SIDE CHAIN
REMARK 500 7 A A 10 0.08 SIDE CHAIN
REMARK 500 7 G A 11 0.07 SIDE CHAIN
REMARK 500 7 A A 12 0.06 SIDE CHAIN
REMARK 500 7 G A 17 0.09 SIDE CHAIN
REMARK 500 7 U A 23 0.06 SIDE CHAIN
REMARK 500 7 G A 25 0.06 SIDE CHAIN
REMARK 500 8 G A 8 0.10 SIDE CHAIN
REMARK 500 8 A A 9 0.08 SIDE CHAIN
REMARK 500 8 A A 10 0.05 SIDE CHAIN
REMARK 500 8 G A 11 0.06 SIDE CHAIN
REMARK 500 8 G A 17 0.07 SIDE CHAIN
REMARK 500 8 U A 22 0.09 SIDE CHAIN
REMARK 500 8 U A 23 0.07 SIDE CHAIN
REMARK 500 8 G A 25 0.09 SIDE CHAIN
REMARK 500 9 A A 9 0.08 SIDE CHAIN
REMARK 500 9 A A 10 0.06 SIDE CHAIN
REMARK 500 9 G A 11 0.05 SIDE CHAIN
REMARK 500 9 G A 17 0.10 SIDE CHAIN
REMARK 500 9 U A 23 0.15 SIDE CHAIN
REMARK 500 10 G A 8 0.10 SIDE CHAIN
REMARK 500 10 A A 9 0.09 SIDE CHAIN
REMARK 500 10 U A 22 0.10 SIDE CHAIN
REMARK 500 10 U A 23 0.07 SIDE CHAIN
REMARK 500 10 G A 25 0.14 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 AMP A 37
DBREF 1RAW A 1 36 PDB 1RAW 1RAW 1 36
SEQRES 1 A 36 G G G A A G G G A A G A A
SEQRES 2 A 36 A C U G C G G C U U C G G
SEQRES 3 A 36 C C G G C U U C C C
HET AMP A 37 36
HETNAM AMP ADENOSINE MONOPHOSPHATE
FORMUL 2 AMP C10 H14 N5 O7 P
SITE 1 AC1 9 G A 7 G A 8 A A 10 G A 11
SITE 2 AC1 9 A A 12 G A 17 C A 18 G A 19
SITE 3 AC1 9 G A 30
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 - r 2 2 Bytes