Header list of 1aul.pdb file
Complete list - 16 202 Bytes
HEADER DNA 29-AUG-97 1AUL TITLE SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED TO A MINOR TITLE 2 GROOVE BINDER, NMR, MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*THXP*GP*AP*TP*TP*AP*TP*CP*TP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA COMPND 6 RESIDUE WITH A HEXAMETHYLENE LINKER; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*GP*AP*TP*AP*AP*TP*CP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: TRIPEPTIDE CDPI3 IS COVALENTLY LINKED TO THE T1 DNA COMPND 12 RESIDUE WITH A HEXAMETHYLENE LINKER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A SOURCE 4 WITH A HEXAMETHYLENE LINKER; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: CDPI3 COVALENTLY LINKED TO 5' END OF DNA STRAND A SOURCE 8 WITH A HEXAMETHYLENE LINKER KEYWDS DEOXYRIBONUCLEIC ACID, CDPI3, DNA EXPDTA SOLUTION NMR AUTHOR S.KUMAR,M.W.REED,H.B.GAMPER JUNIOR,V.V.GORN,E.A.LUKHTANOV,M.FOTI, AUTHOR 2 J.WEST,R.B.MEYER JUNIOR,B.I.SCHWEITZER REVDAT 4 16-FEB-22 1AUL 1 REMARK HETNAM LINK REVDAT 3 24-FEB-09 1AUL 1 VERSN REVDAT 2 01-APR-03 1AUL 1 JRNL REVDAT 1 24-DEC-97 1AUL 0 JRNL AUTH S.KUMAR,M.W.REED,H.B.GAMPER JR.,V.V.GORN,E.A.LUKHTANOV, JRNL AUTH 2 M.FOTI,J.WEST,R.B.MEYER JR.,B.I.SCHWEITZER JRNL TITL SOLUTION STRUCTURE OF A HIGHLY STABLE DNA DUPLEX CONJUGATED JRNL TITL 2 TO A MINOR GROOVE BINDER. JRNL REF NUCLEIC ACIDS RES. V. 26 831 1998 JRNL REFN ISSN 0305-1048 JRNL PMID 9443977 JRNL DOI 10.1093/NAR/26.3.831 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: CANONICAL B-TYPE STRUCTURE USED IN REMARK 3 RESTRAINED MOLECULAR DYNAMICS CALCULATIONS GENERATING SIX REMARK 3 STRUCTURES FROM DIFFERENT RANDOM NUMBER SEEDS. THE SIX REMARK 3 STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX REFINEMENT TO REMARK 3 GENERATE THE SIX FINAL STRUCTURES. THESE SIX STRUCTURES WERE REMARK 3 AVERAGED AND MINIMIZED TO GIVE THE FINAL STRUCTURE PRESENTED REMARK 3 HERE. REMARK 4 REMARK 4 1AUL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171277. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.15 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 : NOESY; DQF-COSY; HETEROTOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : RESTRAINED MOLECULAR REMARK 210 DYNAMICS/RELAXATION MATRIX REMARK 210 REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 6 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION 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: DIMERIC 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: 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 O4 THX A 1 H61 DA B 20 1.39 REMARK 500 H3 THX A 1 N1 DA B 20 1.57 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 THX A 1 O3' DG A 2 P 0.127 REMARK 500 DG A 2 P DG A 2 O5' 0.149 REMARK 500 DG A 2 O3' DA A 3 P 0.123 REMARK 500 DA A 3 P DA A 3 O5' 0.133 REMARK 500 DA A 3 N9 DA A 3 C4 -0.042 REMARK 500 DA A 3 O3' DT A 4 P 0.124 REMARK 500 DT A 4 P DT A 4 O5' 0.140 REMARK 500 DT A 4 O3' DT A 5 P 0.118 REMARK 500 DT A 5 P DT A 5 O5' 0.123 REMARK 500 DT A 5 O3' DA A 6 P 0.115 REMARK 500 DA A 6 P DA A 6 O5' 0.134 REMARK 500 DA A 6 C3' DA A 6 C2' 0.134 REMARK 500 DA A 6 O3' DT A 7 P 0.122 REMARK 500 DT A 7 P DT A 7 O5' 0.137 REMARK 500 DT A 7 O3' DC A 8 P 0.127 REMARK 500 DC A 8 P DC A 8 O5' 0.140 REMARK 500 DC A 8 O3' DT A 9 P 0.123 REMARK 500 DT A 9 P DT A 9 O5' 0.133 REMARK 500 DT A 9 C2' DT A 9 C1' 0.070 REMARK 500 DT A 9 O3' DG A 10 P 0.125 REMARK 500 DG A 10 P DG A 10 O5' 0.139 REMARK 500 DC B 11 C2' DC B 11 C1' 0.065 REMARK 500 DC B 11 O3' DA B 12 P 0.130 REMARK 500 DA B 12 P DA B 12 O5' 0.140 REMARK 500 DA B 12 O3' DG B 13 P 0.119 REMARK 500 DG B 13 P DG B 13 O5' 0.134 REMARK 500 DG B 13 O3' DA B 14 P 0.121 REMARK 500 DA B 14 P DA B 14 O5' 0.133 REMARK 500 DA B 14 O3' DT B 15 P 0.124 REMARK 500 DT B 15 P DT B 15 O5' 0.143 REMARK 500 DT B 15 O3' DA B 16 P 0.121 REMARK 500 DA B 16 P DA B 16 O5' 0.137 REMARK 500 DA B 16 C2' DA B 16 C1' 0.062 REMARK 500 DA B 16 O3' DA B 17 P 0.116 REMARK 500 DA B 17 P DA B 17 O5' 0.125 REMARK 500 DA B 17 O3' DT B 18 P 0.117 REMARK 500 DT B 18 P DT B 18 O5' 0.151 REMARK 500 DT B 18 O3' DC B 19 P 0.145 REMARK 500 DC B 19 P DC B 19 O5' 0.145 REMARK 500 DC B 19 C2' DC B 19 C1' 0.082 REMARK 500 DC B 19 O3' DA B 20 P 0.129 REMARK 500 DA B 20 P DA B 20 O5' 0.133 REMARK 500 DA B 20 C3' DA B 20 C2' 0.075 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 DG A 10 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 13 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES 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 DC B 19 0.07 SIDE CHAIN REMARK 500 DA B 20 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1AUL A 1 10 PDB 1AUL 1AUL 1 10 DBREF 1AUL B 11 20 PDB 1AUL 1AUL 11 20 SEQRES 1 A 10 THX DG DA DT DT DA DT DC DT DG SEQRES 1 B 10 DC DA DG DA DT DA DA DT DC DA HET THX A 1 124 HETNAM THX PHOSPHONIC ACID 6-({6-[6-(6-CARBAMOYL-3,6,7,8- HETNAM 2 THX TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONYL)-3,6,7,8- HETNAM 3 THX TETRAHYDRO-3,6-DIAZA-AS-INDOCENE-2-CA RBONYL]-3,6,7,8- HETNAM 4 THX TETRAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBONL}-AMINO)- HETNAM 5 THX HEXYL ESTER 5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H- HETNAM 6 THX PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL ESTER HETSYN THX CDPI3 FORMUL 1 THX C50 H53 N10 O12 P LINK O3' THX A 1 P DG A 2 1555 1555 1.73 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
Complete list - 16 202 Bytes