Header list of 1rmx.pdb file
Complete list - 2 202 Bytes
HEADER DNA 28-NOV-03 1RMX TITLE A SHORT LEXITROPSIN THAT RECOGNIZES THE DNA MINOR GROOVE AT 5'-ACTAGT- TITLE 2 3': UNDERSTANDING THE ROLE OF ISOPROPYL-THIAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS MINOR-GROOVE-DNA COMPLEX, SIDE-BY-SIDE BINDING, DNA RECOGNITION, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR N.G.ANTHONY,B.F.JOHNSTON,A.I.KHALAF,S.P.MACKAY,J.A.PARKINSON, AUTHOR 2 C.J.SUCKLING,R.D.WAIGH REVDAT 4 02-MAR-22 1RMX 1 REMARK REVDAT 3 24-FEB-09 1RMX 1 VERSN REVDAT 2 05-OCT-04 1RMX 1 JRNL REVDAT 1 24-AUG-04 1RMX 0 JRNL AUTH N.G.ANTHONY,B.F.JOHNSTON,A.I.KHALAF,S.P.MACKAY, JRNL AUTH 2 J.A.PARKINSON,C.J.SUCKLING,R.D.WAIGH JRNL TITL SHORT LEXITROPSIN THAT RECOGNIZES THE DNA MINOR GROOVE AT JRNL TITL 2 5'-ACTAGT-3': UNDERSTANDING THE ROLE OF ISOPROPYL-THIAZOLE. JRNL REF J.AM.CHEM.SOC. V. 126 11338 2004 JRNL REFN ISSN 0002-7863 JRNL PMID 15355117 JRNL DOI 10.1021/JA030658N REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SYBYL 6.3, SYBYL 6.3 REMARK 3 AUTHORS : TRIPOS INC. (SYBYL), TRIPOS INC. (SYBYL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RMX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020892. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.4MM DNA DUPLEX WITH 2 REMARK 210 EQUIVALENTS OF AIK13/20 LIGAND, REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE; AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.0, VNMR 6, SPARKY REMARK 210 3.105 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR REMARK 210 TECHNIQUES 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: 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 DC A 1 C2 DC A 1 N3 0.088 REMARK 500 DC A 1 N3 DC A 1 C4 -0.067 REMARK 500 DC A 1 C4 DC A 1 C5 0.049 REMARK 500 DG A 2 C2 DG A 2 N3 -0.055 REMARK 500 DG A 2 N3 DG A 2 C4 0.086 REMARK 500 DG A 2 C4 DG A 2 C5 -0.051 REMARK 500 DG A 2 C5 DG A 2 N7 0.054 REMARK 500 DG A 2 N7 DG A 2 C8 -0.044 REMARK 500 DG A 2 C8 DG A 2 N9 -0.074 REMARK 500 DG A 2 N9 DG A 2 C4 -0.070 REMARK 500 DA A 3 C5 DA A 3 N7 -0.046 REMARK 500 DA A 3 N7 DA A 3 C8 -0.044 REMARK 500 DA A 3 C8 DA A 3 N9 -0.065 REMARK 500 DC A 4 C2 DC A 4 N3 0.088 REMARK 500 DC A 4 N3 DC A 4 C4 -0.066 REMARK 500 DA A 6 C5 DA A 6 N7 -0.046 REMARK 500 DA A 6 N7 DA A 6 C8 -0.044 REMARK 500 DA A 6 C8 DA A 6 N9 -0.068 REMARK 500 DG A 7 N3 DG A 7 C4 0.100 REMARK 500 DG A 7 C4 DG A 7 C5 -0.046 REMARK 500 DG A 7 C6 DG A 7 N1 -0.048 REMARK 500 DG A 7 C5 DG A 7 N7 0.047 REMARK 500 DG A 7 N7 DG A 7 C8 -0.050 REMARK 500 DG A 7 C8 DG A 7 N9 -0.070 REMARK 500 DG A 7 N9 DG A 7 C4 -0.052 REMARK 500 DC A 9 C2 DC A 9 N3 0.088 REMARK 500 DC A 9 N3 DC A 9 C4 -0.068 REMARK 500 DG A 10 C2 DG A 10 N3 -0.053 REMARK 500 DG A 10 N3 DG A 10 C4 0.089 REMARK 500 DG A 10 C4 DG A 10 C5 -0.048 REMARK 500 DG A 10 C5 DG A 10 N7 0.053 REMARK 500 DG A 10 N7 DG A 10 C8 -0.046 REMARK 500 DG A 10 C8 DG A 10 N9 -0.075 REMARK 500 DG A 10 N9 DG A 10 C4 -0.068 REMARK 500 DC B 11 C2 DC B 11 N3 0.087 REMARK 500 DC B 11 N3 DC B 11 C4 -0.067 REMARK 500 DC B 11 C4 DC B 11 C5 0.049 REMARK 500 DG B 12 C2 DG B 12 N3 -0.053 REMARK 500 DG B 12 N3 DG B 12 C4 0.089 REMARK 500 DG B 12 C4 DG B 12 C5 -0.050 REMARK 500 DG B 12 C5 DG B 12 N7 0.054 REMARK 500 DG B 12 N7 DG B 12 C8 -0.045 REMARK 500 DG B 12 C8 DG B 12 N9 -0.072 REMARK 500 DG B 12 N9 DG B 12 C4 -0.066 REMARK 500 DA B 13 C5 DA B 13 N7 -0.045 REMARK 500 DA B 13 N7 DA B 13 C8 -0.044 REMARK 500 DA B 13 C8 DA B 13 N9 -0.066 REMARK 500 DC B 14 C2 DC B 14 N3 0.087 REMARK 500 DC B 14 N3 DC B 14 C4 -0.067 REMARK 500 DC B 14 C4 DC B 14 C5 0.048 REMARK 500 REMARK 500 THIS ENTRY HAS 69 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 DC A 1 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG A 2 OP1 - P - OP2 ANGL. DEV. = -11.7 DEGREES REMARK 500 DG A 2 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = 8.9 DEGREES REMARK 500 DG A 2 N3 - C4 - C5 ANGL. DEV. = -8.3 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = -9.5 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES REMARK 500 DG A 2 N9 - C4 - C5 ANGL. DEV. = 6.1 DEGREES REMARK 500 DG A 2 C6 - C5 - N7 ANGL. DEV. = 10.2 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -8.0 DEGREES REMARK 500 DA A 3 OP1 - P - OP2 ANGL. DEV. = -11.8 DEGREES REMARK 500 DA A 3 O4' - C1' - C2' ANGL. DEV. = -7.3 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA A 3 C2 - N3 - C4 ANGL. DEV. = 7.7 DEGREES REMARK 500 DA A 3 N3 - C4 - C5 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA A 3 C4 - C5 - C6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 3 C4 - C5 - N7 ANGL. DEV. = -5.3 DEGREES REMARK 500 DA A 3 C5 - N7 - C8 ANGL. DEV. = 5.8 DEGREES REMARK 500 DA A 3 N3 - C4 - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA A 3 C3' - O3' - P ANGL. DEV. = 14.0 DEGREES REMARK 500 DC A 4 OP1 - P - OP2 ANGL. DEV. = -11.5 DEGREES REMARK 500 DC A 4 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DC A 4 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 4 N3 - C4 - C5 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC A 4 N3 - C2 - O2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DC A 4 N3 - C4 - N4 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC A 4 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DT A 5 OP1 - P - OP2 ANGL. DEV. = -13.7 DEGREES REMARK 500 DT A 5 P - O5' - C5' ANGL. DEV. = 13.1 DEGREES REMARK 500 DT A 5 O4' - C1' - C2' ANGL. DEV. = -7.7 DEGREES REMARK 500 DT A 5 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT A 5 C2 - N3 - C4 ANGL. DEV. = -5.7 DEGREES REMARK 500 DT A 5 N3 - C4 - C5 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT A 5 C5 - C4 - O4 ANGL. DEV. = -6.0 DEGREES REMARK 500 DA A 6 OP1 - P - OP2 ANGL. DEV. = -12.5 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 6 N1 - C2 - N3 ANGL. DEV. = -7.1 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = 7.5 DEGREES REMARK 500 DA A 6 N3 - C4 - C5 ANGL. DEV. = -6.5 DEGREES REMARK 500 DA A 6 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 183 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 DA A 6 0.09 SIDE CHAIN REMARK 500 DA B 13 0.07 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 AIK A 11 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AIK B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RN9 RELATED DB: PDB REMARK 900 A SHORT LEXITROPSIN THAT RECOGNIZES THE DNA MINOR GROOVE AT 5'- REMARK 900 ACTAGT-3': UNDERSTANDING THE ROLE OF ISOPROPYL-THIAZOLE DBREF 1RMX A 1 10 PDB 1RMX 1RMX 1 10 DBREF 1RMX B 11 20 PDB 1RMX 1RMX 11 20 SEQRES 1 A 10 DC DG DA DC DT DA DG DT DC DG SEQRES 1 B 10 DC DG DA DC DT DA DG DT DC DG HET AIK A 11 72 HET AIK B 2 72 HETNAM AIK N-[3-(DIMETHYLAMINO)PROPYL]-2-({[4-({[4-(FORMYLAMINO)- HETNAM 2 AIK 1-METHYL-1H-PYRROL-2-YL]CARBONYL}AMINO)-1-METHYL-1H- HETNAM 3 AIK PYRROL-2-YL]CARBONYL}AMINO)-5-ISOPROPYL-1,3-THIAZOLE- HETNAM 4 AIK 4-CARBOXAMIDE FORMUL 3 AIK 2(C25 H34 N8 O4 S) SITE 1 AC1 8 DT A 5 DA A 6 DG A 7 DT A 8 SITE 2 AC1 8 DC A 9 AIK B 2 DA B 13 DG B 17 SITE 1 AC2 8 DG A 7 AIK A 11 DT B 15 DA B 16 SITE 2 AC2 8 DG B 17 DT B 18 DC B 19 DG B 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
Complete list - 2 202 Bytes