1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 SER A 2 AND SER B 7 OF EACH MODEL ARE D-SERINE. CYS A 4 AND VAL A 5 OF EACH MODEL ARE METHYLATED. CYS B 9 AND VAL B 10 OF EACH MODEL ARE METHYLATED. Addess, K.J. Feigon, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C3 H7 N O3 105.093 D-SERINE D-peptide linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C6 H13 N O2 131.173 n N-METHYLVALINE L-peptide linking C4 H9 N O2 S 135.185 N-METHYLCYSTEINE L-peptide linking C9 H6 N2 O2 174.156 2-CARBOXYQUINOXALINE non-polymer US Biochemistry BICHAW 0033 0006-2960 33 12386 10.1021/BI00207A005 7918461 Sequence Specificity of Quinoxaline Antibiotics. 1. Solution Structure of a 1:1 Complex between Triostin a and [D(Gacgtc)]2 and Comparison with the Solution Structure of the [N-Mecys3,N-Mecys7]Tandem-[D(Gatatc)]2 Complex. 1994 US Biochemistry BICHAW 0033 0006-2960 32 2498 10.1021/BI00061A006 8448108 Solution Structure of a Complex between [N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2 1993 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 794.982 TRIOSTIN A 1 syn polymer 1809.217 DNA (5'-D(*GP*AP*CP*GP*TP*C)-3') 2 syn polymer 174.156 2-CARBOXYQUINOXALINE 2 syn non-polymer DEOXYRIBONUCLEIC ACID no yes (DSN)A(NCY)(MVA)(DSN)A(NCY)(MVA) SAXVSAXV A polypeptide(L) no no (DG)(DA)(DC)(DG)(DT)(DC) GACGTC C,D polydeoxyribonucleotide n n n n n n n n n n n n n n -14.370 1 19 C 11 D 22 -0.495 C_DG11:DC22_D 1 -3.264 -0.890 0.397 -0.526 9.008 1 20 C 12 D 21 4.495 C_DA12:DT21_D 2 8.738 -0.015 0.872 -0.315 -24.430 1 19 C 13 D 20 -5.477 C_DC13:DG20_D 3 -0.995 -0.057 0.983 -0.287 25.113 1 19 C 14 D 19 -6.480 C_DG14:DC19_D 4 -1.344 0.112 0.844 -0.214 -11.378 1 20 C 15 D 18 8.624 C_DT15:DA18_D 5 7.795 0.116 1.196 -0.481 -2.720 1 19 C 16 D 17 -11.682 C_DC16:DG17_D 6 -17.550 0.136 1.241 -0.607 2.591 44.367 C C 11 12 -5.373 D D 22 21 2.653 -4.047 0.508 -0.035 CC_DG11DA12:DT21DC22_DD 1 -4.114 5.462 44.009 0.256 -0.980 7.114 27.116 C C 12 13 6.445 D D 21 20 7.338 2.955 0.547 0.688 CC_DA12DC13:DG20DT21_DD 2 9.392 -20.484 25.296 -0.240 4.263 1.466 2.739 C C 13 14 70.488 D D 20 19 2.301 2.581 -0.376 0.733 CC_DC13DG14:DC19DG20_DD 3 -0.055 1.498 0.914 -40.350 6.690 3.120 42.825 C C 15 16 -5.926 D D 18 17 2.987 -4.314 -1.675 -0.102 CC_DT15DC16:DG17DA18_DD 4 -3.985 5.474 42.439 0.263 1.921 pdbx_database_status pdbx_struct_assembly pdbx_validate_polymer_linkage repository Initial release Version format compliance Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Other Advisory Derived calculations Other 1 0 1995-02-07 1 1 2011-06-14 1 2 2011-07-13 1 3 2011-07-27 1 4 2013-02-27 1 5 2017-11-01 _pdbx_database_status.process_site _pdbx_struct_assembly.method_details SOLUTION STRUCTURE OF D(ACACGTGT) COMPLEXED WITH QUINOMYCIN UK-6305 CRYSTAL STRUCTURE OF D(GCGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P6322 CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632 CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP C21 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P42212 SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN A AT POSITIONS 4 AND 8 CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P41212 Y BNL 1994-08-10 REL QUI 2-CARBOXYQUINOXALINE 1931 STREPTOMYCINEAE sample TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, TRIOSTIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) QUI Anticancer TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. TRIOSTIN A Cyclic depsipeptide TRIOSTIN A CONTAINS TWO PLANAR AROMATIC QUINOXALINE RINGS THAT ARE COVALENTLY ATTACHED TO A CYCLIC OCTADEPSIPEPTIDE RING REPRESENTED BY CHAINS A AND B IN THIS ENTRY. THERE IS A DISULFIDE BRIDGE LINKING CYS A 4 TO CYS B 9. BOTH CYS AND VAL RESIDUES CONTAIN METHYLATED AMIDE NITROGENS; THE TWO D-SER RESIDUES ARE AMIDE BONDED TO THE TWO QUINOXALINE RINGS. 5 NUMBER OF ATOMS PRESENT IN ENTRY. NUMBER OF PROTEIN ATOMS 328 NUMBER OF NUCLEIC ACID ATOMS 48 NUMBER OF SOLVENT ATOMS 240 NUMBER OF HETEROGEN ATOMS 40 AVERAGE PAIRWISE RMSD BOND DISTANCES FOR HEAVY ATOM POSITIONS FOR 5 STRUCTURES: 1.37 ANGSTROMS. DISTANCE GEOMETRY, MOLECULAR DYNAMICS BRUNGER refinement X-PLOR QUI 0 3 QUI QUI 0 A QUI 9 3 QUI QUI 9 A DSN 1 n 1 DSN 1 A ALA 2 n 2 ALA 2 A NCY 3 n 3 NCY 3 A MVA 4 n 4 MVA 4 A DSN 5 n 5 DSN 5 A ALA 6 n 6 ALA 6 A NCY 7 n 7 NCY 7 A MVA 8 n 8 MVA 8 A DG 11 n 1 DG 11 C DA 12 n 2 DA 12 C DC 13 n 3 DC 13 C DG 14 n 4 DG 14 C DT 15 n 5 DT 15 C DC 16 n 6 DC 16 C DG 17 n 1 DG 17 D DA 18 n 2 DA 18 D DC 19 n 3 DC 19 D DG 20 n 4 DG 20 D DT 21 n 5 DT 21 D DC 22 n 6 DC 22 D software_defined_assembly PISA 3 trimeric 2080 -3 2840 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 4 A A C N MVA DSN 4 5 2.81 5 A A C N MVA DSN 4 5 2.88 1 1.94 0.30 108.30 110.24 C C C O4' C1' N9 DG DG DG 11 11 11 N 1 3.28 0.50 113.10 116.38 C C C N7 C8 N9 DG DG DG 11 11 11 N 1 -6.21 1.00 110.10 103.89 C C C C1' O4' C4' DC DC DC 13 13 13 N 1 3.77 0.60 118.90 122.67 C C C N1 C2 O2 DC DC DC 13 13 13 N 1 -5.50 0.80 105.90 100.40 C C C O4' C1' C2' DG DG DG 14 14 14 N 1 3.23 0.50 113.10 116.33 C C C N7 C8 N9 DG DG DG 14 14 14 N 1 -6.50 1.00 110.10 103.60 D D D C1' O4' C4' DG DG DG 17 17 17 N 1 3.26 0.50 113.10 116.36 D D D N7 C8 N9 DG DG DG 17 17 17 N 1 -6.82 1.00 110.10 103.28 D D D C1' O4' C4' DC DC DC 19 19 19 N 1 2.72 0.30 108.30 111.02 D D D O4' C1' N1 DC DC DC 19 19 19 N 1 3.73 0.60 118.90 122.63 D D D N1 C2 O2 DC DC DC 19 19 19 N 1 3.14 0.50 113.10 116.24 D D D N7 C8 N9 DG DG DG 20 20 20 N 1 -4.88 0.80 105.90 101.02 D D D O4' C1' C2' DT DT DT 21 21 21 N 1 2.77 0.30 108.30 111.07 D D D O4' C1' N1 DC DC DC 22 22 22 N 2 -5.31 0.80 105.90 100.59 C C C O4' C1' C2' DG DG DG 11 11 11 N 2 4.53 0.30 108.30 112.83 C C C O4' C1' N9 DG DG DG 11 11 11 N 2 3.07 0.50 113.10 116.17 C C C N7 C8 N9 DG DG DG 11 11 11 N 2 1.83 0.30 108.30 110.13 C C C O4' C1' N1 DC DC DC 13 13 13 N 2 -5.86 0.80 105.90 100.04 C C C O4' C1' C2' DG DG DG 14 14 14 N 2 3.91 0.30 108.30 112.21 C C C O4' C1' N9 DG DG DG 14 14 14 N 2 3.27 0.50 113.10 116.37 C C C N7 C8 N9 DG DG DG 14 14 14 N 2 3.36 0.30 108.30 111.66 C C C O4' C1' N1 DC DC DC 16 16 16 N 2 3.47 0.50 113.10 116.57 D D D N7 C8 N9 DG DG DG 17 17 17 N 2 -6.18 1.00 110.10 103.92 D D D C1' O4' C4' DG DG DG 20 20 20 N 2 -6.79 0.80 105.90 99.11 D D D O4' C1' C2' DG DG DG 20 20 20 N 2 4.38 0.30 108.30 112.68 D D D O4' C1' N9 DG DG DG 20 20 20 N 2 3.27 0.50 113.10 116.37 D D D N7 C8 N9 DG DG DG 20 20 20 N 3 2.01 0.30 108.30 110.31 C C C O4' C1' N9 DG DG DG 11 11 11 N 3 3.35 0.50 113.10 116.45 C C C N7 C8 N9 DG DG DG 11 11 11 N 3 2.55 0.30 108.30 110.85 C C C O4' C1' N9 DA DA DA 12 12 12 N 3 3.50 0.30 108.30 111.80 C C C O4' C1' N1 DC DC DC 13 13 13 N 3 2.16 0.30 108.30 110.46 C C C O4' C1' N9 DG DG DG 14 14 14 N 3 3.19 0.50 113.10 116.29 C C C N7 C8 N9 DG DG DG 14 14 14 N 3 -6.75 0.80 105.90 99.15 C C C O4' C1' C2' DT DT DT 15 15 15 N 3 3.11 0.30 108.30 111.41 C C C O4' C1' N1 DC DC DC 16 16 16 N 3 3.35 0.50 113.10 116.45 D D D N7 C8 N9 DG DG DG 17 17 17 N 3 9.22 1.20 119.70 128.92 D D D C3' O3' P DG DG DA 17 17 18 Y 3 -4.91 0.80 105.90 100.99 D D D O4' C1' C2' DA DA DA 18 18 18 N 3 -4.57 0.70 102.20 97.63 D D D C4' C3' C2' DC DC DC 19 19 19 N 3 4.04 0.30 108.30 112.34 D D D O4' C1' N1 DC DC DC 19 19 19 N 3 -5.54 0.80 105.90 100.36 D D D O4' C1' C2' DG DG DG 20 20 20 N 3 3.63 0.30 108.30 111.93 D D D O4' C1' N9 DG DG DG 20 20 20 N 3 3.23 0.50 113.10 116.33 D D D N7 C8 N9 DG DG DG 20 20 20 N 3 4.11 0.30 108.30 112.41 D D D O4' C1' N1 DC DC DC 22 22 22 N 4 -5.38 0.80 105.90 100.52 C C C O4' C1' C2' DG DG DG 11 11 11 N 4 4.41 0.30 108.30 112.71 C C C O4' C1' N9 DG DG DG 11 11 11 N 4 3.30 0.50 113.10 116.40 C C C N7 C8 N9 DG DG DG 11 11 11 N 4 -5.17 0.70 102.20 97.03 C C C C4' C3' C2' DC DC DC 13 13 13 N 4 5.15 0.30 108.30 113.45 C C C O4' C1' N1 DC DC DC 13 13 13 N 4 -5.38 0.80 105.90 100.52 C C C O4' C1' C2' DG DG DG 14 14 14 N 4 3.29 0.50 113.10 116.39 C C C N7 C8 N9 DG DG DG 14 14 14 N 4 -4.71 0.70 102.20 97.49 C C C C4' C3' C2' DC DC DC 16 16 16 N 4 5.70 0.30 108.30 114.00 C C C O4' C1' N1 DC DC DC 16 16 16 N 4 2.85 0.30 108.30 111.15 D D D O4' C1' N9 DG DG DG 17 17 17 N 4 3.54 0.50 113.10 116.64 D D D N7 C8 N9 DG DG DG 17 17 17 N 4 4.24 0.30 108.30 112.54 D D D O4' C1' N9 DA DA DA 18 18 18 N 4 2.03 0.30 108.30 110.33 D D D O4' C1' N1 DC DC DC 19 19 19 N 4 -5.74 0.80 105.90 100.16 D D D O4' C1' C2' DG DG DG 20 20 20 N 4 3.67 0.30 108.30 111.97 D D D O4' C1' N9 DG DG DG 20 20 20 N 4 3.38 0.50 113.10 116.48 D D D N7 C8 N9 DG DG DG 20 20 20 N 5 3.29 0.50 113.10 116.39 C C C N7 C8 N9 DG DG DG 11 11 11 N 5 3.58 0.30 108.30 111.88 C C C O4' C1' N1 DC DC DC 13 13 13 N 5 -5.23 0.80 105.90 100.67 C C C O4' C1' C2' DG DG DG 14 14 14 N 5 2.87 0.30 108.30 111.17 C C C O4' C1' N9 DG DG DG 14 14 14 N 5 3.03 0.50 113.10 116.13 C C C N7 C8 N9 DG DG DG 14 14 14 N 5 2.71 0.30 108.30 111.01 C C C O4' C1' N1 DC DC DC 16 16 16 N 5 -4.94 0.80 105.90 100.96 D D D O4' C1' C2' DG DG DG 17 17 17 N 5 3.44 0.50 113.10 116.54 D D D N7 C8 N9 DG DG DG 17 17 17 N 5 -5.16 0.70 102.20 97.04 D D D C4' C3' C2' DC DC DC 19 19 19 N 5 2.24 0.30 108.30 110.54 D D D O4' C1' N1 DC DC DC 19 19 19 N 5 -5.61 0.80 105.90 100.29 D D D O4' C1' C2' DG DG DG 20 20 20 N 5 2.53 0.30 108.30 110.83 D D D O4' C1' N9 DG DG DG 20 20 20 N 5 3.22 0.50 113.10 116.32 D D D N7 C8 N9 DG DG DG 20 20 20 N 1 C C C5 C7 DT DT 15 15 0.039 0.006 1.496 1.535 N 1 D D C5 C7 DT DT 21 21 0.043 0.006 1.496 1.539 N 2 C C C5 C7 DT DT 15 15 0.042 0.006 1.496 1.538 N 3 C C C5 C7 DT DT 15 15 0.038 0.006 1.496 1.534 N 4 C C C5 C7 DT DT 15 15 0.036 0.006 1.496 1.532 N 4 D D C5 C7 DT DT 21 21 0.036 0.006 1.496 1.532 N 5 C C C5 C7 DT DT 15 15 0.040 0.006 1.496 1.536 N 5 D D C5 C7 DT DT 21 21 0.037 0.006 1.496 1.533 N 5 A NCY 3 -98.73 -61.43 5 A NCY 7 -90.57 -62.43 model building X-PLOR refinement X-PLOR phasing X-PLOR TRIOSTIN A SEQUENCE SPECIFICITY OF QUINOXALINE ANTIBIOTICS. 1. SOLUTION STRUCTURE OF A 1:1 COMPLEX BETWEEN TRIOSTIN A AND [D(GACGTC)]2 AND COMPARISON WITH THE SOLUTION STRUCTURE OF THE [N-MECYS3, N-MECYS7]TANDEM-[D(GATATC)]2 COMPLEX 1 N N 2 N N 2 N N 3 N N 3 N N disulf 2.021 A NCY 3 A SG NCY 3 1_555 A NCY 7 A SG NCY 7 1_555 covale 1.329 A QUI 0 D C QUI 1_555 A DSN 1 A N DSN 1 1_555 covale 1.305 A DSN 1 A C DSN 1 1_555 A ALA 2 A N ALA 2 1_555 covale 1.331 A DSN 1 A OG DSN 1 1_555 A MVA 8 A C MVA 8 1_555 covale 1.323 A ALA 2 A C ALA 2 1_555 A NCY 3 A N NCY 3 1_555 covale 1.329 A NCY 3 A C NCY 3 1_555 A MVA 4 A N MVA 4 1_555 covale 1.333 A MVA 4 A C MVA 4 1_555 A DSN 5 A OG DSN 5 1_555 covale 1.303 A DSN 5 A C DSN 5 1_555 A ALA 6 A N ALA 6 1_555 covale 1.327 A DSN 5 A N DSN 5 1_555 A QUI 9 E C QUI 1_555 covale 1.326 A ALA 6 A C ALA 6 1_555 A NCY 7 A N NCY 7 1_555 covale 1.327 A NCY 7 A C NCY 7 1_555 A MVA 8 A N MVA 8 1_555 hydrog DG-DT MISPAIR C DG 11 B O6 DG 1 1_555 D DT 21 C N3 DT 5 1_555 hydrog WATSON-CRICK C DG 11 B N1 DG 1 1_555 D DC 22 C N3 DC 6 1_555 hydrog WATSON-CRICK C DG 11 B N2 DG 1 1_555 D DC 22 C O2 DC 6 1_555 hydrog WATSON-CRICK C DG 11 B O6 DG 1 1_555 D DC 22 C N4 DC 6 1_555 hydrog WATSON-CRICK C DA 12 B N1 DA 2 1_555 D DT 21 C N3 DT 5 1_555 hydrog WATSON-CRICK C DA 12 B N6 DA 2 1_555 D DT 21 C O4 DT 5 1_555 hydrog WATSON-CRICK C DC 13 B N3 DC 3 1_555 D DG 20 C N1 DG 4 1_555 hydrog WATSON-CRICK C DC 13 B N4 DC 3 1_555 D DG 20 C O6 DG 4 1_555 hydrog WATSON-CRICK C DC 13 B O2 DC 3 1_555 D DG 20 C N2 DG 4 1_555 hydrog WATSON-CRICK C DG 14 B N1 DG 4 1_555 D DC 19 C N3 DC 3 1_555 hydrog WATSON-CRICK C DG 14 B N2 DG 4 1_555 D DC 19 C O2 DC 3 1_555 hydrog WATSON-CRICK C DG 14 B O6 DG 4 1_555 D DC 19 C N4 DC 3 1_555 hydrog DT-DG MISPAIR C DT 15 B N3 DT 5 1_555 D DG 17 C O6 DG 1 1_555 hydrog WATSON-CRICK C DT 15 B N3 DT 5 1_555 D DA 18 C N1 DA 2 1_555 hydrog WATSON-CRICK C DT 15 B O4 DT 5 1_555 D DA 18 C N6 DA 2 1_555 hydrog WATSON-CRICK C DC 16 B N3 DC 6 1_555 D DG 17 C N1 DG 1 1_555 hydrog WATSON-CRICK C DC 16 B N4 DC 6 1_555 D DG 17 C O6 DG 1 1_555 hydrog WATSON-CRICK C DC 16 B O2 DC 6 1_555 D DG 17 C N2 DG 1 1_555 DNA/ANTIBIOTIC BISINTERCALATOR, DEPSIPEPTIDE, QUINOXALINE, ANTIBIOTIC, ANTITUMOR, DNA-ANTIBIOTIC COMPLEX NOR01129 NOR 1 NOR01129 185D PDB 2 185D 1 8 185D 1 8 NOR01129 A 1 1 8 1 6 185D 11 16 185D C 2 1 6 1 6 185D 17 22 185D D 2 1 6 BINDING SITE FOR CHAIN A OF TRIOSTIN A Software 8 C DA 12 B DA 2 8 1_555 C DC 13 B DC 3 8 1_555 C DG 14 B DG 4 8 1_555 C DT 15 B DT 5 8 1_555 D DA 18 C DA 2 8 1_555 D DC 19 C DC 3 8 1_555 D DG 20 C DG 4 8 1_555 D DT 21 C DT 5 8 1_555 1 P 1