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 5 22-MAY-24 2ARG 1 REMARK 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