Header list of 1bp8.pdb file
Complete list - 29 20 Bytes
HEADER DNA 13-AUG-98 1BP8
TITLE 4:2:1 MITHRAMYCIN:MG++:D(ACCCGGGT)2 COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*AP*CP*CP*CP*GP*GP*GP*T)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: FOUR MOLECULES OF MITHRAMYCIN (PLICAMYCIN) (RESIDUES
COMPND 6 DDA-DDA-DXB-DDA-DDL-DDB, CHAINS C, D, E, F) BOUND IN THE MINOR
COMPND 7 GROOVE. OXYGENS OF THE MITHRAMYCIN CHROMOPHORE (RESIDUE DXB) ARE
COMPND 8 COMPLEXED WITH MG++
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS MITHRAMYCIN, DNA, OLIGONUCLEOTIDE
EXPDTA SOLUTION NMR
AUTHOR M.A.KENIRY,E.A.OWEN,R.H.SHAFER
REVDAT 6 29-JUL-20 1BP8 1 COMPND REMARK HETNAM LINK
REVDAT 6 2 1 SITE ATOM
REVDAT 5 02-OCT-19 1BP8 1 REMARK LINK ATOM
REVDAT 4 24-FEB-09 1BP8 1 VERSN
REVDAT 3 29-MAR-05 1BP8 1 JRNL SOURCE REMARK
REVDAT 2 01-APR-03 1BP8 1 JRNL
REVDAT 1 16-AUG-99 1BP8 0
JRNL AUTH M.A.KENIRY,E.A.OWEN,R.H.SHAFER
JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE 4:1
JRNL TITL 2 MITHRAMYCIN:D(ACCCGGGT)2 COMPLEX: EVIDENCE FOR AN
JRNL TITL 3 INTERACTION BETWEEN THE E SACCHARIDES
JRNL REF BIOPOLYMERS V. 54 104 2000
JRNL REFN ISSN 0006-3525
JRNL PMID 10861371
JRNL DOI 10.1002/1097-0282(200008)54:2<104::AID-BIP3>3.0.CO;2-2
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CHARMM 23.2
REMARK 3 AUTHORS : MSI, WALTHAM , MA
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JOURNAL CITATION ABOVE
REMARK 4
REMARK 4 1BP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-99.
REMARK 100 THE DEPOSITION ID IS D_1000007303.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : 7.2
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; PCOSY; TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA 600
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR, MARDIGRAS, CORMA CHARMM
REMARK 210 CHARMM
REMARK 210 METHOD USED : FULL RELAXATION MATRIX ANALYSIS
REMARK 210 AND RESTRAINED MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 7
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR TWO
REMARK 210 DIMENSIONAL NMR SPECTROSCOPY
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, C, D, E, F, G, H, I, J
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 DA A 1 O5' DA A 1 C5' -0.642
REMARK 500 DC A 2 C4 DC A 2 C5 -0.060
REMARK 500 DC A 3 C5' DC A 3 C4' 0.045
REMARK 500 DC A 3 N1 DC A 3 C6 -0.084
REMARK 500 DC A 3 C4 DC A 3 C5 -0.053
REMARK 500 DC A 4 N1 DC A 4 C6 -0.058
REMARK 500 DG A 5 N1 DG A 5 C2 -0.070
REMARK 500 DG A 5 N7 DG A 5 C8 0.045
REMARK 500 DG A 5 C8 DG A 5 N9 -0.068
REMARK 500 DG A 6 N1 DG A 6 C2 -0.077
REMARK 500 DG A 6 N7 DG A 6 C8 0.044
REMARK 500 DG A 6 C8 DG A 6 N9 -0.044
REMARK 500 DG A 7 N1 DG A 7 C2 -0.085
REMARK 500 DG A 7 N7 DG A 7 C8 0.040
REMARK 500 DG A 7 C8 DG A 7 N9 -0.049
REMARK 500 DT A 8 C3' DT A 8 C2' -0.179
REMARK 500 DT A 8 O3' DT A 8 C3' -0.221
REMARK 500 DT A 8 C2 DT A 8 N3 -0.051
REMARK 500 DT A 8 N3 DT A 8 C4 -0.050
REMARK 500 DT A 8 C6 DT A 8 N1 -0.064
REMARK 500 DC B 2 C4 DC B 2 C5 -0.062
REMARK 500 DC B 3 C2' DC B 3 C1' -0.062
REMARK 500 DC B 3 N1 DC B 3 C6 -0.074
REMARK 500 DC B 3 C4 DC B 3 C5 -0.053
REMARK 500 DC B 4 N1 DC B 4 C6 -0.059
REMARK 500 DG B 5 N1 DG B 5 C2 -0.070
REMARK 500 DG B 5 N7 DG B 5 C8 0.042
REMARK 500 DG B 5 C8 DG B 5 N9 -0.064
REMARK 500 DG B 6 N1 DG B 6 C2 -0.077
REMARK 500 DG B 6 N7 DG B 6 C8 0.043
REMARK 500 DG B 6 C8 DG B 6 N9 -0.046
REMARK 500 DG B 7 N1 DG B 7 C2 -0.089
REMARK 500 DG B 7 N7 DG B 7 C8 0.042
REMARK 500 DT B 8 C2 DT B 8 N3 -0.058
REMARK 500 DT B 8 C6 DT B 8 N1 -0.067
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 DA A 1 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DA A 1 C2 - N3 - C4 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 DA A 1 C6 - C5 - N7 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DC A 2 C5' - C4' - O4' ANGL. DEV. = 9.4 DEGREES
REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC A 2 N1 - C2 - N3 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = 8.5 DEGREES
REMARK 500 DC A 3 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES
REMARK 500 DC A 3 C5' - C4' - O4' ANGL. DEV. = 12.1 DEGREES
REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DC A 4 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DG A 5 N3 - C4 - C5 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DG A 5 C4 - C5 - N7 ANGL. DEV. = -2.4 DEGREES
REMARK 500 DG A 5 C6 - C5 - N7 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 5 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DG A 6 N9 - C1' - C2' ANGL. DEV. = 12.7 DEGREES
REMARK 500 DG A 6 N3 - C4 - C5 ANGL. DEV. = -4.0 DEGREES
REMARK 500 DG A 6 C4 - C5 - N7 ANGL. DEV. = -2.7 DEGREES
REMARK 500 DG A 6 C6 - C5 - N7 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 6 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES
REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG A 7 N3 - C4 - C5 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DG A 7 C4 - C5 - N7 ANGL. DEV. = -2.8 DEGREES
REMARK 500 DG A 7 C6 - C5 - N7 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DG A 7 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DT A 8 C4' - C3' - C2' ANGL. DEV. = 8.3 DEGREES
REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DA B 1 N1 - C2 - N3 ANGL. DEV. = -3.5 DEGREES
REMARK 500 DA B 1 C2 - N3 - C4 ANGL. DEV. = 4.5 DEGREES
REMARK 500 DA B 1 C5 - C6 - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 DA B 1 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DA B 1 C6 - C5 - N7 ANGL. DEV. = 5.0 DEGREES
REMARK 500 DC B 2 C5' - C4' - O4' ANGL. DEV. = 8.6 DEGREES
REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DC B 2 N1 - C2 - N3 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DC B 2 N1 - C2 - O2 ANGL. DEV. = 8.3 DEGREES
REMARK 500 DC B 3 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES
REMARK 500 DC B 3 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 DC B 4 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DC B 4 C6 - N1 - C2 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DC B 4 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DG B 5 N3 - C4 - C5 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DG B 5 N3 - C4 - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DG B 5 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES
REMARK 500 DG B 6 N9 - C1' - C2' ANGL. DEV. = 12.1 DEGREES
REMARK 500 DG B 6 N3 - C4 - C5 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DG B 6 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 57 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 DC A 3 0.07 SIDE CHAIN
REMARK 500 DG A 6 0.07 SIDE CHAIN
REMARK 500 DC B 3 0.08 SIDE CHAIN
REMARK 500 DG B 6 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 17 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DXB A 21 O9
REMARK 620 2 DXB A 21 O1 83.4
REMARK 620 3 DXB B 19 O9 174.1 97.6
REMARK 620 4 DXB B 19 O1 111.0 84.9 74.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 18 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DXB A 22 O9
REMARK 620 2 DXB A 22 O1 74.4
REMARK 620 3 DXB B 20 O1 95.7 89.0
REMARK 620 4 DXB B 20 O9 177.6 104.2 86.2
REMARK 620 N 1 2 3
DBREF 1BP8 A 1 8 PDB 1BP8 1BP8 1 8
DBREF 1BP8 B 1 8 PDB 1BP8 1BP8 1 8
SEQRES 1 A 8 DA DC DC DC DG DG DG DT
SEQRES 1 B 8 DA DC DC DC DG DG DG DT
HET DDA C 1 20
HET DDA C 2 20
HET DDA D 1 20
HET DDL D 2 19
HET MDA D 3 23
HET DDA E 1 20
HET DDA E 2 20
HET DDA F 1 20
HET DDL F 2 19
HET MDA F 3 23
HET DDA G 1 20
HET DDL G 2 19
HET MDA G 3 23
HET DDA H 1 20
HET DDA H 2 20
HET DDA I 1 20
HET DDA I 2 19
HET DDA J 1 20
HET DDL J 2 19
HET MDA J 3 23
HET MG A 17 1
HET MG A 18 1
HET DXB A 21 49
HET DXB A 22 49
HET DXB B 19 49
HET DXB B 20 49
HETNAM DDA BETA-D-OLIVOPYRANOSE
HETNAM DDL 2,6-DIDEOXY-BETA-D-GALACTOPYRANOSE
HETNAM MDA 2,6-DIDEOXY-3-C-METHYL-BETA-D-RIBO-HEXOPYRANOSE
HETNAM MG MAGNESIUM ION
HETNAM DXB 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-
HETNAM 2 DXB DIHYDROXYPENTYL)-8,9-DIHYDROXY-7-METHYL-ANTHRACENE
HETSYN DDA 2,6-DIDEOXY-BETA-D-MANNOSE
HETSYN DDL 2,6-DIDEOXY-BETA-D-TALOSE
FORMUL 3 DDA 12(C6 H12 O4)
FORMUL 4 DDL 4(C6 H12 O4)
FORMUL 4 MDA 4(C7 H14 O4)
FORMUL 11 MG 2(MG 2+)
FORMUL 13 DXB 4(C21 H24 O7)
LINK C6 DXB A 21 O1 DDA C 1 1555 1555 1.34
LINK C2 DXB A 21 O1 DDA D 1 1555 1555 1.42
LINK C6 DXB A 22 O1 DDA E 1 1555 1555 1.36
LINK C2 DXB A 22 O1 DDA F 1 1555 1555 1.43
LINK C2 DXB B 19 O1 DDA G 1 1555 1555 1.43
LINK C6 DXB B 19 O1 DDA H 1 1555 1555 1.36
LINK C6 DXB B 20 O1 DDA I 1 1555 1555 1.35
LINK C2 DXB B 20 O1 DDA J 1 1555 1555 1.41
LINK O3 DDA C 1 C1 DDA C 2 1555 1555 1.39
LINK O3 DDA D 1 C1 DDL D 2 1555 1555 1.40
LINK O3 DDL D 2 C1 MDA D 3 1555 1555 1.41
LINK O3 DDA E 1 C1 DDA E 2 1555 1555 1.35
LINK O3 DDA F 1 C1 DDL F 2 1555 1555 1.41
LINK O3 DDL F 2 C1 MDA F 3 1555 1555 1.42
LINK O3 DDA G 1 C1 DDL G 2 1555 1555 1.41
LINK O3 DDL G 2 C1 MDA G 3 1555 1555 1.43
LINK O3 DDA H 1 C1 DDA H 2 1555 1555 1.40
LINK O3 DDA I 1 C1 DDA I 2 1555 1555 1.40
LINK O3 DDA J 1 C1 DDL J 2 1555 1555 1.40
LINK O3 DDL J 2 C1 MDA J 3 1555 1555 1.41
LINK MG MG A 17 O9 DXB A 21 1555 1555 1.65
LINK MG MG A 17 O1 DXB A 21 1555 1555 2.13
LINK MG MG A 17 O9 DXB B 19 1555 1555 2.26
LINK MG MG A 17 O1 DXB B 19 1555 1555 2.07
LINK MG MG A 18 O9 DXB A 22 1555 1555 2.31
LINK MG MG A 18 O1 DXB A 22 1555 1555 2.03
LINK MG MG A 18 O1 DXB B 20 1555 1555 2.11
LINK MG MG A 18 O9 DXB B 20 1555 1555 1.66
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 - 29 20 Bytes