Header list of 2a5p.pdb file
Complete list - 9 20 Bytes
HEADER DNA 30-JUN-05 2A5P
TITLE MONOMERIC PARALLEL-STRANDED DNA TETRAPLEX WITH SNAP-BACK 3+1 3' G-
TITLE 2 TETRAD, SINGLE-RESIDUE CHAIN REVERSAL LOOPS, GAG TRIAD IN THE CONTEXT
TITLE 3 OF GAAG DIAGONAL LOOP, NMR, 8 STRUCT.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*IP*GP*AP*GP*GP*GP*TP*GP*GP
COMPND 3 *GP*GP*AP*AP*GP*G)-3';
COMPND 4 CHAIN: A
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 OTHER_DETAILS: C-MYC GENE
KEYWDS MONOMERIC PARALLEL-STRANDED QUADRUPLEX; C-MYC PROMOTER 3+1 G-TETRAD;
KEYWDS 2 SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP; GAG TRIAD; GAAG LOOP, DNA
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR A.T.PHAN,V.V.KURYAVYI,H.Y.GAW,D.J.PATEL
REVDAT 3 09-MAR-22 2A5P 1 REMARK
REVDAT 2 24-FEB-09 2A5P 1 VERSN
REVDAT 1 26-JUL-05 2A5P 0
JRNL AUTH A.T.PHAN,V.KURYAVYI,H.Y.GAW,D.J.PATEL
JRNL TITL SMALL-MOLECULE INTERACTION WITH A FIVE-GUANINE-TRACT
JRNL TITL 2 G-QUADRUPLEX STRUCTURE FROM THE HUMAN MYC PROMOTER.
JRNL REF NAT.CHEM.BIOL. V. 1 167 2005
JRNL REFN ISSN 1552-4450
JRNL PMID 16408022
JRNL DOI 10.1038/NCHEMBIO723
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XPLOR 3.851
REMARK 3 AUTHORS : AT BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2A5P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-05.
REMARK 100 THE DEPOSITION ID IS D_1000033519.
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 : 90 MM
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 70 MM KCL 20 MM POTASSIUM
REMARK 210 PHOSPHATE, 90% H2O, 10% D2O; 70
REMARK 210 MM KCL 20 MM POTASSIUM PHOSPHATE,
REMARK 210 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-1H NOESY; 1H-1H TOCSY; 1H-31P
REMARK 210 COSY; 1H-1H COSY; 1H-15N JRHMQC;
REMARK 210 1H-15N HMBC; 1H-13C JRHM 1H-13C
REMARK 210 HMBC; 1H-13C HSQC; 1H-13C SHMBC;
REMARK 210 1H-31P TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : VARIAN UNITY INOVA; AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.0, FELIX 2000
REMARK 210 METHOD USED : DISTANCE GEOMETRY AND SIMULATED
REMARK 210 ANNEALING, DISTANCE RESTRAINED
REMARK 210 MOLECULAR DYNAMICS REFINEMENT
REMARK 210 AND RELAXATION MATRIX INTENSITY
REMARK 210 REFINEMENT
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING
REMARK 210 THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL WITH THE
REMARK 210 EXPERIMENTAL DISTANCE RESTRAINTS SPECIFIED WITH THE R-6
REMARK 210 AVERAGING OPTION. EIGHT BEST STRUCTURES SELECTED ON THE BASIS OF
REMARK 210 GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND
REMARK 210 FAVOURABLE NON-BONDED ENERGY TERMS WERE FURTHER OPTIMIZED WITH
REMARK 210 RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND
REMARK 210 RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS
REMARK 210 FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE
REMARK 210 WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE
REMARK 210 CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE
REMARK 210 PROPORTION 1:4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE,
REMARK 210 NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE
REMARK 210 THEN SLOWLY COOLED TO 300K IN 14 PS AND EQUILIBRATED AT 300K FOR
REMARK 210 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS
REMARK 210 WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO
REMARK 210 MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/
REMARK 210 MOL. SOFT PLANARITY RESTRAINTS IMPOSED ON TETRADS AND TRIAD
REMARK 210 BEFORE HEATING WERE EXCLUDED AT THE EQUILIBRATION STAGE. THE
REMARK 210 DIHEDRAL AND HYDROGEN-BONDING RESTRAINTS FOR TETRADS, WERE
REMARK 210 MAINTAINED THROUGHOUT. ALL EIGHT STRUCTURES WERE SUBJECTED TO
REMARK 210 RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES OF
REMARK 210 NON-EXCHANGEABLE PROTONS WERE USED AS RESTRAINTS WITH
REMARK 210 EXCHANGEABLE PROTONS REPLACED BY DEUTERONS. DYNAMICS STARTED AT
REMARK 210 5K AND THE SYSTEM WAS HEATHED UP TO 300 K IN 0.6 PSEC. THE FORCE
REMARK 210 CONSTANT FOR NOE INTENSITIES WAS GRADUALLY INCREASED FROM 0 TO
REMARK 210 400 KCAL*MOL-1*A-2 WITH SIMULTANEOUS DECREASE OF THE DISTANCE
REMARK 210 FORCE CONSTANTS FOR NON-EXCHANGEABLE PROTONS FROM 32 TO 16.
REMARK 210 AFTER EQUILIBRATION AT 300 K FOR 3 PSEC THE RESULTING STRUCTURES
REMARK 210 WERE SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS
REMARK 210 LESS THAN 0.1KCAL/MOL. THE DISTANCE RESTRAINTS FOR EXCHANGEABLE
REMARK 210 PROTONS HYDROGEN BONDS AND DIHEDRAL ANGLE RESTRAINTS WERE
REMARK 210 MAINTAINED. SOFT PLANARITY RESTRAINTS WEERE SET FOR TETRAD (1
REMARK 210 KCAL*MOL-1*A-2) AND TRIAD (0.5 KCAL*MOL-1*A-2).
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 DA A 3 C5' DA A 3 C4' 0.046
REMARK 500 1 DG A 20 C5' DG A 20 C4' 0.053
REMARK 500 1 DG A 23 C5' DG A 23 C4' 0.058
REMARK 500 2 DG A 2 C5' DG A 2 C4' 0.051
REMARK 500 2 DA A 3 C5' DA A 3 C4' 0.055
REMARK 500 2 DG A 20 C5' DG A 20 C4' 0.052
REMARK 500 2 DG A 23 C5' DG A 23 C4' 0.052
REMARK 500 3 DA A 3 C5' DA A 3 C4' 0.047
REMARK 500 3 DG A 20 C5' DG A 20 C4' 0.053
REMARK 500 3 DG A 23 C5' DG A 23 C4' 0.056
REMARK 500 4 DG A 2 C5' DG A 2 C4' 0.053
REMARK 500 4 DA A 3 C5' DA A 3 C4' 0.053
REMARK 500 4 DG A 20 C5' DG A 20 C4' 0.050
REMARK 500 4 DG A 23 C5' DG A 23 C4' 0.055
REMARK 500 5 DG A 2 C5' DG A 2 C4' 0.044
REMARK 500 5 DA A 3 C5' DA A 3 C4' 0.043
REMARK 500 5 DG A 20 C5' DG A 20 C4' 0.051
REMARK 500 5 DG A 23 C5' DG A 23 C4' 0.058
REMARK 500 6 DG A 2 C5' DG A 2 C4' 0.045
REMARK 500 6 DA A 3 C5' DA A 3 C4' 0.046
REMARK 500 6 DG A 20 C5' DG A 20 C4' 0.054
REMARK 500 6 DG A 23 C5' DG A 23 C4' 0.058
REMARK 500 7 DG A 2 C5' DG A 2 C4' 0.043
REMARK 500 7 DA A 3 C5' DA A 3 C4' 0.043
REMARK 500 7 DG A 20 C5' DG A 20 C4' 0.050
REMARK 500 7 DG A 23 C5' DG A 23 C4' 0.050
REMARK 500 8 DA A 3 C5' DA A 3 C4' 0.045
REMARK 500 8 DG A 20 C5' DG A 20 C4' 0.051
REMARK 500 8 DG A 23 C5' DG A 23 C4' 0.054
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' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES
REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 1 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 2 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 3 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 3 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 3 DG A 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 3 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 3 DT A 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES
REMARK 500 3 DG A 17 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 3 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 3 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 3 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 4 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 4 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 4 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 4 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 4 DA A 12 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 4 DG A 13 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 4 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 4 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 4 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 4 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 5 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 5 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 5 DG A 6 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES
REMARK 500 5 DA A 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 5 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 5 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 5 DG A 19 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 5 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 5 DG A 23 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES
REMARK 500 6 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 6 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 6 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500 6 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 6 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 6 DG A 17 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 68 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1EEG RELATED DB: PDB
REMARK 900 A(GGGG)A HEXAD
REMARK 900 RELATED ID: 1JJP RELATED DB: PDB
REMARK 900 A(GGGG) PENTAD, 5' 3+1 TETRAD
REMARK 900 RELATED ID: 1Y8D RELATED DB: PDB
REMARK 900 A(GGGG) PENTAD, 5' 3+1 TETRAD
REMARK 900 RELATED ID: 1D6D RELATED DB: PDB
REMARK 900 AAT TRIAD IN DIAGONAL LOOP
REMARK 900 RELATED ID: 2A5R RELATED DB: PDB
DBREF 2A5P A 1 24 PDB 2A5P 2A5P 1 24
SEQRES 1 A 24 DT DG DA DG DG DG DT DG DG DI DG DA DG
SEQRES 2 A 24 DG DG DT DG DG DG DG DA DA DG DG
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 - 9 20 Bytes