Header list of 2arg.pdb file
Complete list - 19 20 Bytes
HEADER DNA 19-AUG-98 2ARG
TITLE FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-
TITLE 2 UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA APTAMER [5'-D
COMPND 3 (*TP*GP*AP*CP*CP*AP*GP*GP*GP*CP*AP*AP*AP*CP*GP*GP*TP*AP*
COMPND 4 GP*GP*TP*GP*AP*GP*TP*GP*GP*TP*CP*A)-3'];
COMPND 5 CHAIN: A;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHESIZED IN-HOUSE ON A 10 MICROMOLAR SCALE
SOURCE 4 SYNTHESIS USING APPLIED BIOSYSTEM 392 DNA/RNA SYNTHESIZER
KEYWDS ADAPTIVE DNA STRUCTURAL TRANSITIONS, L-ARGININAMIDE BINDING POCKET,
KEYWDS 2 MOLECULAR RECOGNITION OF AN AMINO ACID, MINOR GROOVE RECOGNITION,
KEYWDS 3 BASE ENCAPSULATION WITHIN MINOR GROOVE, DNA APTAMER,
KEYWDS 4 DEOXYRIBONUCLEIC ACID, DNA
EXPDTA SOLUTION NMR
NUMMDL 9
AUTHOR C.H.LIN,W.WANG,R.A.JONES,D.J.PATEL
REVDAT 4 06-JUL-22 2ARG 1 COMPND SOURCE REMARK DBREF
REVDAT 4 2 1 HET HETNAM FORMUL ATOM
REVDAT 3 09-MAR-22 2ARG 1 REMARK
REVDAT 2 24-FEB-09 2ARG 1 VERSN
REVDAT 1 23-MAR-99 2ARG 0
JRNL AUTH C.H.LIN,W.WANG,R.A.JONES,D.J.PATEL
JRNL TITL FORMATION OF AN AMINO-ACID-BINDING POCKET THROUGH ADAPTIVE
JRNL TITL 2 ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP.
JRNL REF CHEM.BIOL. V. 5 555 1998
JRNL REFN ISSN 1074-5521
JRNL PMID 9818148
JRNL DOI 10.1016/S1074-5521(98)90114-4
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: TWENTY STARTING STRUCTURES WERE
REMARK 3 GENERATED BY METRICMATRIX DISTANCE GEOMETRY (FROM X-PLOR) AND
REMARK 3 WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR
REMARK 3 DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED
REMARK 3 FROM THE 2-D NMR DATA SETS. NINE FIN AL NMR-DISTANCE REFINED
REMARK 3 STRUCTURES WERE SELECTED BASED ON THE CRITERION OF LOW TOTAL
REMARK 3 ENERGY AND LOW RESTRAINTS VIOLATIONS.
REMARK 4
REMARK 4 2ARG 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_1000177776.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 277
REMARK 210 PH : 6.35
REMARK 210 IONIC STRENGTH : 100 MM
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; ROESY; 1H-15N HMQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : VARIAN UNITY-PLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR
REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR
REMARK 210 DYNAMIC
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 20
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9
REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST NOE, VDW, AND BOND ANGLE
REMARK 210 VIOLATION, LEAST TOTAL ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE INTER-PROTON DISTANCE RESTRAINTS WERE DERIVED FROM 2-D
REMARK 210 NOE BUILD UP EXPERIMENTS RECORDED AT 50, 90, 150, AND 90 AND 135
REMARK 210 MIXING TIME FOR EXCHANGEABLE PROTONS 200 MS MIXING TIME FOR NON-
REMARK 210 EXCHANGEABLE PROTONS AND AT 600 MHZ
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: 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 DT A 1 C6 DT A 1 N1 -0.055
REMARK 500 1 DG A 2 N7 DG A 2 C8 0.051
REMARK 500 1 DA A 3 C3' DA A 3 C2' -0.074
REMARK 500 1 DC A 4 C3' DC A 4 C2' -0.067
REMARK 500 1 DC A 4 N1 DC A 4 C6 -0.037
REMARK 500 1 DG A 7 N7 DG A 7 C8 0.043
REMARK 500 1 DG A 8 N7 DG A 8 C8 0.045
REMARK 500 1 DG A 9 N7 DG A 9 C8 0.043
REMARK 500 1 DC A 10 N1 DC A 10 C6 -0.045
REMARK 500 1 DA A 11 C5 DA A 11 N7 -0.038
REMARK 500 1 DG A 15 N7 DG A 15 C8 0.041
REMARK 500 1 DG A 16 C3' DG A 16 C2' -0.053
REMARK 500 1 DG A 16 N7 DG A 16 C8 0.049
REMARK 500 1 DG A 16 C8 DG A 16 N9 -0.061
REMARK 500 1 DG A 20 C3' DG A 20 C2' -0.061
REMARK 500 1 DG A 20 N7 DG A 20 C8 0.056
REMARK 500 1 DG A 22 N7 DG A 22 C8 0.042
REMARK 500 1 DG A 24 C5 DG A 24 N7 -0.042
REMARK 500 1 DG A 24 C8 DG A 24 N9 -0.051
REMARK 500 1 DG A 26 N7 DG A 26 C8 0.043
REMARK 500 1 DG A 27 C3' DG A 27 C2' -0.052
REMARK 500 1 DG A 27 N7 DG A 27 C8 0.046
REMARK 500 1 DT A 28 C3' DT A 28 C2' -0.049
REMARK 500 2 DT A 1 C6 DT A 1 N1 -0.056
REMARK 500 2 DG A 2 N7 DG A 2 C8 0.050
REMARK 500 2 DA A 3 C3' DA A 3 C2' -0.075
REMARK 500 2 DC A 4 C3' DC A 4 C2' -0.068
REMARK 500 2 DC A 4 N1 DC A 4 C6 -0.038
REMARK 500 2 DG A 7 N7 DG A 7 C8 0.050
REMARK 500 2 DG A 8 N7 DG A 8 C8 0.046
REMARK 500 2 DG A 9 N7 DG A 9 C8 0.045
REMARK 500 2 DC A 10 N1 DC A 10 C6 -0.045
REMARK 500 2 DA A 11 C5 DA A 11 N7 -0.039
REMARK 500 2 DG A 15 N7 DG A 15 C8 0.043
REMARK 500 2 DG A 16 C3' DG A 16 C2' -0.056
REMARK 500 2 DG A 16 N7 DG A 16 C8 0.046
REMARK 500 2 DG A 16 C8 DG A 16 N9 -0.063
REMARK 500 2 DG A 20 C3' DG A 20 C2' -0.058
REMARK 500 2 DG A 20 N7 DG A 20 C8 0.055
REMARK 500 2 DG A 22 N7 DG A 22 C8 0.041
REMARK 500 2 DG A 24 C5 DG A 24 N7 -0.040
REMARK 500 2 DG A 24 C8 DG A 24 N9 -0.048
REMARK 500 2 DG A 26 N7 DG A 26 C8 0.046
REMARK 500 2 DG A 27 C3' DG A 27 C2' -0.054
REMARK 500 2 DG A 27 N7 DG A 27 C8 0.048
REMARK 500 3 DT A 1 C6 DT A 1 N1 -0.055
REMARK 500 3 DG A 2 N7 DG A 2 C8 0.050
REMARK 500 3 DA A 3 C3' DA A 3 C2' -0.075
REMARK 500 3 DC A 4 C3' DC A 4 C2' -0.070
REMARK 500 3 DC A 4 N1 DC A 4 C6 -0.039
REMARK 500
REMARK 500 THIS ENTRY HAS 217 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 DT A 1 O4' - C4' - C3' ANGL. DEV. = 6.7 DEGREES
REMARK 500 1 DT A 1 C3' - C2' - C1' ANGL. DEV. = 11.6 DEGREES
REMARK 500 1 DT A 1 O4' - C1' - N1 ANGL. DEV. = 9.9 DEGREES
REMARK 500 1 DT A 1 C4 - C5 - C7 ANGL. DEV. = 6.7 DEGREES
REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -9.5 DEGREES
REMARK 500 1 DA A 3 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES
REMARK 500 1 DC A 4 O4' - C4' - C3' ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 DC A 4 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 1 DC A 5 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES
REMARK 500 1 DC A 5 N3 - C4 - C5 ANGL. DEV. = -2.4 DEGREES
REMARK 500 1 DC A 5 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DG A 7 O4' - C1' - C2' ANGL. DEV. = -5.5 DEGREES
REMARK 500 1 DG A 8 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES
REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES
REMARK 500 1 DC A 10 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 12.7 DEGREES
REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DA A 12 C3' - O3' - P ANGL. DEV. = 8.0 DEGREES
REMARK 500 1 DA A 13 O4' - C1' - C2' ANGL. DEV. = -7.4 DEGREES
REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DC A 14 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DG A 16 O4' - C4' - C3' ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DG A 16 C4' - C3' - O3' ANGL. DEV. = 15.6 DEGREES
REMARK 500 1 DG A 16 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DG A 16 C3' - C2' - C1' ANGL. DEV. = 9.4 DEGREES
REMARK 500 1 DG A 16 N9 - C1' - C2' ANGL. DEV. = -13.1 DEGREES
REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 14.4 DEGREES
REMARK 500 1 DT A 17 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DT A 17 O4' - C1' - C2' ANGL. DEV. = 3.6 DEGREES
REMARK 500 1 DT A 17 N1 - C1' - C2' ANGL. DEV. = -11.4 DEGREES
REMARK 500 1 DT A 17 C4 - C5 - C7 ANGL. DEV. = 9.1 DEGREES
REMARK 500 1 DT A 17 C6 - C5 - C7 ANGL. DEV. = -11.1 DEGREES
REMARK 500 1 DA A 18 P - O5' - C5' ANGL. DEV. = 11.0 DEGREES
REMARK 500 1 DA A 18 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES
REMARK 500 1 DA A 18 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES
REMARK 500 1 DA A 18 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES
REMARK 500 1 DG A 20 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 1 DG A 20 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DG A 20 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES
REMARK 500 1 DT A 21 C4 - C5 - C7 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 DT A 21 C6 - C5 - C7 ANGL. DEV. = -8.1 DEGREES
REMARK 500 1 DG A 22 O4' - C1' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 DA A 23 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 24 N9 - C1' - C2' ANGL. DEV. = 10.9 DEGREES
REMARK 500 1 DG A 24 O4' - C1' - N9 ANGL. DEV. = 11.2 DEGREES
REMARK 500 1 DT A 25 C5' - C4' - O4' ANGL. DEV. = -11.9 DEGREES
REMARK 500 1 DT A 25 O4' - C1' - N1 ANGL. DEV. = 8.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 501 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 AAR A 31
DBREF 2ARG A 1 30 PDB 2ARG 2ARG 1 30
SEQRES 1 A 30 DT DG DA DC DC DA DG DG DG DC DA DA DA
SEQRES 2 A 30 DC DG DG DT DA DG DG DT DG DA DG DT DG
SEQRES 3 A 30 DG DT DC DA
HET AAR A 31 28
HETNAM AAR ARGININEAMIDE
FORMUL 2 AAR C6 H16 N5 O 1+
SITE 1 AC1 6 DC A 10 DG A 15 DG A 16 DA A 18
SITE 2 AC1 6 DG A 19 DG A 20
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 - 19 20 Bytes