0.063545 -0.023304 -0.003039 0.000000 0.067044 -0.003447 0.000000 0.000000 0.039893 0.00000 0.00000 0.00000 Schafer, M. Sheldrick, G.M. Bahner, I. Lackner, H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 3 85.93 86.19 69.86 15.737 15.887 25.156 C5 H11 N O2 117.146 D-VALINE D-peptide linking C4 H8 O2 88.105 ETHYL ACETATE non-polymer C H4 O 32.042 METHANOL non-polymer C6 H13 N O2 131.173 n N-METHYLVALINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C16 H12 N2 O4 296.277 2-AMINO-1,9-DICARBONYL-4,6-DIMETHYL-10-DEHYDRO-PHENOXAZIN-3-ONE PHENOXAZINE non-polymer C3 H7 N O2 89.093 n SARCOSINE peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking N 1 N N N 2 R C N 3 N C N 4 N C N 5 N C N 6 N C N 7 N O N 8 N O N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N C N 21 N C N 22 N O N 23 N O N 24 N C N 25 N C N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N C N 35 N O N 36 N H N 37 N H N 38 N H N 39 N H N 40 N N N 41 N C N 42 S C N 43 N C N 44 N C N 45 N C N 46 N C N 47 N O N 48 N O N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N N N 63 S C N 64 N C N 65 N O N 66 N C N 67 N C N 68 N C N 69 N O N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H Y 79 N C N 80 N C N 81 N O Y 82 N C N 83 N N Y 84 N C N 85 N O Y 86 N C Y 87 N O Y 88 N C Y 89 N C Y 90 N C Y 91 N C N 92 N C N 93 N O Y 94 N N Y 95 N C Y 96 N C Y 97 N C Y 98 N C N 99 N C N 100 N C N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N N N 114 N C N 115 N C N 116 N O N 117 N C N 118 N O N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N N N 127 S C N 128 N C N 129 N O N 130 R C N 131 N O N 132 N C N 133 N O N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N doub N 17 N sing N 18 N sing N 19 N sing N 20 N doub N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N doub N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing Y 76 N doub Y 77 N sing N 78 N doub N 79 N sing N 80 N sing Y 81 N sing N 82 N sing N 83 N sing N 84 N doub Y 85 N sing Y 86 N doub N 87 N sing Y 88 N sing Y 89 N sing Y 90 N doub Y 91 N sing N 92 N sing Y 93 N sing N 94 N sing Y 95 N doub N 96 N sing N 97 N sing Y 98 N sing N 99 N doub N 100 N sing Y 101 N doub Y 102 N sing Y 103 N sing Y 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N doub N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing GE Angew.Chem.Int.Ed.Engl. ACIEAY 0179 1521-3773 37 2381 2384 10.1002/(SICI)1521-3773(19980918)37:17<2381::AID-ANIE2381>3.0.CO;2-L 29710967 Crystal Structures of Actinomycin D and Actinomycin Z3. 1998 10.2210/pdb1a7y/pdb pdb_00001a7y 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 133 1 COLLIMATOR AREA DETECTOR 1997-11-03 SIEMENS HI-STAR GRAPHITE(002) M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE SIEMENS 1259.447 ACTINOMYCIN D 3 nat polymer 88.105 ETHYL ACETATE 7 syn non-polymer 32.042 METHANOL 1 syn non-polymer DACTINOMYCIN no yes T(DVA)P(SAR)(MVA)(PXZ)T(DVA)P(SAR)(MVA) TVPGVXTVPGV A,B,C polypeptide(L) n n n n n n n n n n n sample 1890 STREPTOMYCES ANTIBIOTICUS 1 1.50 18.00 5.0 PH 5.0 diffrn_source pdbx_database_status pdbx_validate_polymer_linkage citation citation_author struct_conn atom_site atom_site_anisotrop chem_comp_atom chem_comp_bond database_2 struct_conn struct_site repository Initial release Version format compliance Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Other Advisory Data collection Other Database references Derived calculations Atomic model Data collection Database references Derived calculations 1 0 1999-03-23 1 1 2011-06-14 1 2 2011-07-13 1 3 2011-07-27 1 4 2012-12-12 1 5 2018-03-07 1 6 2019-11-13 2 0 2023-11-15 _diffrn_source.source _pdbx_database_status.process_site _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.page_last _citation.pdbx_database_id_PubMed _citation.title _citation_author.name _struct_conn.pdbx_leaving_atom_flag _atom_site.auth_atom_id _atom_site.label_atom_id _atom_site_anisotrop.pdbx_auth_atom_id _atom_site_anisotrop.pdbx_label_atom_id _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id CRYSTAL STRUCTURE OF ACTINOMYCIN Z3 CRYSTAL STRUCTURE OF N8-ACTINOMYCIN D COMPLEXED WITH D(GAAGCTTC)2 CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D COMPLEXED WITH NON-COMPLEMENTARY DNA CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CGATCGATCG)2 SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (AAGCGCTT)2 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 SOLUTION STRUCTURE OF ACTNIOMYCIN D COMPLEXED WITH MISMATCHED DNA (GTCACCGAC) CRYSTAL STRUCTURE OF F8-ACTINOMYCIN D COMPLEXED WITH DNA (GAAGCTTC)2 SOLUTION STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (GATGCTTC)2 CRYSTAL STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (ATGCTGCAT)2 CRYSTAL STRUCTURE OF 7-AMINO-ACTINOMYCIN D COMPLEXED WITH A NON-COMPLEMENTARY DNA (TTAGT)2 SOLUTIOM STRUCTURE OF ACTINOMYCIN D COMPLEXED WITH DNA (CCGTTTTGTGG)2 CRYSTAL STRUCTURE OF ACTINOMYCIN X2 Y BNL 1998-03-19 REL REL EEE ETHYL ACETATE MOH METHANOL ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES) Antibiotic ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ) Actinomycin D Polypeptide EEE 104 2 EEE EEE 104 A EEE 105 2 EEE EEE 105 A EEE 106 2 EEE EEE 106 A EEE 107 2 EEE EEE 107 A EEE 101 2 EEE EEE 101 C EEE 102 2 EEE EEE 102 C EEE 103 2 EEE EEE 103 C MOH 108 3 MOH MOH 108 C THR 1 n 1 THR 1 A DVA 2 n 2 DVA 2 A PRO 3 n 3 PRO 3 A SAR 4 n 4 SAR 4 A MVA 5 n 5 MVA 5 A PXZ 6 n 6 PXZ 6 A THR 7 n 7 THR 7 A DVA 8 n 8 DVA 8 A PRO 9 n 9 PRO 9 A SAR 10 n 10 SAR 10 A MVA 11 n 11 MVA 11 A THR 1 n 1 THR 1 B DVA 2 n 2 DVA 2 B PRO 3 n 3 PRO 3 B SAR 4 n 4 SAR 4 B MVA 5 n 5 MVA 5 B PXZ 6 n 6 PXZ 6 B THR 7 n 7 THR 7 B DVA 8 n 8 DVA 8 B PRO 9 n 9 PRO 9 B SAR 10 n 10 SAR 10 B MVA 11 n 11 MVA 11 B THR 1 n 1 THR 1 C DVA 2 n 2 DVA 2 C PRO 3 n 3 PRO 3 C SAR 4 n 4 SAR 4 C MVA 5 n 5 MVA 5 C PXZ 6 n 6 PXZ 6 C THR 7 n 7 THR 7 C DVA 8 n 8 DVA 8 C PRO 9 n 9 PRO 9 C SAR 10 n 10 SAR 10 C MVA 11 n 11 MVA 11 C 0.054 0.057 0.055 0.058 0.066 0.068 1334 1401 10.000 9.900 13362 author_defined_assembly 1 monomeric author_defined_assembly 1 monomeric author_defined_assembly 1 monomeric 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 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.039 0.068 0.057 0.058 0.94 2875 1401 14126 3689 9.900 95.1 RANDOM 1 FREE R 0.000 AB INITIO NO RESTRAINTS ON DISTANCES AND ANGLES 0 318.00 314.00 0.94 0 314 44 0 270 0.000 0.000 0.024 0.163 0.000 0.000 0.000 0.006 0.027 0.000 0.940 999.000 1A7Y 14126 0.04400 1 25.9000 4.380 95.1 0.07200 0.94 1.05 11.900 1 2.85 90.5 model building SHELXL-97 refinement SHELXL-97 data reduction SAINT data scaling SADABS phasing SHELXL-97 CRYSTAL STRUCTURE OF ACTINOMYCIN D 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N covale 1.342 both A THR 1 A C THR 1 1_555 A DVA 2 A N DVA 2 1_555 covale 1.345 one A THR 1 A OG1 THR 1 1_555 A MVA 5 A C MVA 5 1_555 covale 1.359 one A THR 1 A N THR 1 1_555 A PXZ 6 A C0 PXZ 6 1_555 covale 1.348 both A DVA 2 A C DVA 2 1_555 A PRO 3 A N PRO 3 1_555 covale 1.342 both A PRO 3 A C PRO 3 1_555 A SAR 4 A N SAR 4 1_555 covale 1.350 both A SAR 4 A C SAR 4 1_555 A MVA 5 A N MVA 5 1_555 covale 1.347 one A PXZ 6 A C0' PXZ 6 1_555 A THR 7 A N THR 7 1_555 covale 1.329 both A THR 7 A C THR 7 1_555 A DVA 8 A N DVA 8 1_555 covale 1.357 one A THR 7 A OG1 THR 7 1_555 A MVA 11 A C MVA 11 1_555 covale 1.360 both A DVA 8 A C DVA 8 1_555 A PRO 9 A N PRO 9 1_555 covale 1.340 both A PRO 9 A C PRO 9 1_555 A SAR 10 A N SAR 10 1_555 covale 1.348 both A SAR 10 A C SAR 10 1_555 A MVA 11 A N MVA 11 1_555 covale 1.346 both B THR 1 B C THR 1 1_555 B DVA 2 B N DVA 2 1_555 covale 1.350 one B THR 1 B OG1 THR 1 1_555 B MVA 5 B C MVA 5 1_555 covale 1.350 one B THR 1 B N THR 1 1_555 B PXZ 6 B C0 PXZ 6 1_555 covale 1.351 both B DVA 2 B C DVA 2 1_555 B PRO 3 B N PRO 3 1_555 covale 1.349 both B PRO 3 B C PRO 3 1_555 B SAR 4 B N SAR 4 1_555 covale 1.351 both B SAR 4 B C SAR 4 1_555 B MVA 5 B N MVA 5 1_555 covale 1.330 one B PXZ 6 B C0' PXZ 6 1_555 B THR 7 B N THR 7 1_555 covale 1.338 both B THR 7 B C THR 7 1_555 B DVA 8 B N DVA 8 1_555 covale 1.339 one B THR 7 B OG1 THR 7 1_555 B MVA 11 B C MVA 11 1_555 covale 1.348 both B DVA 8 B C DVA 8 1_555 B PRO 9 B N PRO 9 1_555 covale 1.345 both B PRO 9 B C PRO 9 1_555 B SAR 10 B N SAR 10 1_555 covale 1.350 both B SAR 10 B C SAR 10 1_555 B MVA 11 B N MVA 11 1_555 covale 1.338 both C THR 1 C C THR 1 1_555 C DVA 2 C N DVA 2 1_555 covale 1.369 one C THR 1 C OG1 THR 1 1_555 C MVA 5 C C MVA 5 1_555 covale 1.356 one C THR 1 C N THR 1 1_555 C PXZ 6 C C0 PXZ 6 1_555 covale 1.342 both C DVA 2 C C DVA 2 1_555 C PRO 3 C N PRO 3 1_555 covale 1.356 both C PRO 3 C C PRO 3 1_555 C SAR 4 C N SAR 4 1_555 covale 1.354 both C SAR 4 C C SAR 4 1_555 C MVA 5 C N MVA 5 1_555 covale 1.342 one C PXZ 6 C C0' PXZ 6 1_555 C THR 7 C N THR 7 1_555 covale 1.347 both C THR 7 C C THR 7 1_555 C DVA 8 C N DVA 8 1_555 covale 1.354 one C THR 7 C OG1 THR 7 1_555 C MVA 11 C C MVA 11 1_555 covale 1.340 both C DVA 8 C C DVA 8 1_555 C PRO 9 C N PRO 9 1_555 covale 1.365 both C PRO 9 C C PRO 9 1_555 C SAR 10 C N SAR 10 1_555 covale 1.356 both C SAR 10 C C SAR 10 1_555 C MVA 11 C N MVA 11 1_555 ANTIBIOTIC ACTINOMYCIN, ANTIBIOTIC, ANTITUMOR, ANTICANCER, CHROMOPHORE, DEPSIPEPTIDE A DVA 2 A DVA 2 1 A PRO 3 A PRO 3 15.27 A PRO 3 A PRO 3 1 A SAR 4 A SAR 4 -4.60 A DVA 8 A DVA 8 1 A PRO 9 A PRO 9 19.55 A PRO 9 A PRO 9 1 A SAR 10 A SAR 10 -14.77 B DVA 2 B DVA 2 1 B PRO 3 B PRO 3 14.29 B PRO 3 B PRO 3 1 B SAR 4 B SAR 4 -7.25 B DVA 8 B DVA 8 1 B PRO 9 B PRO 9 18.82 B PRO 9 B PRO 9 1 B SAR 10 B SAR 10 -9.46 C DVA 2 C DVA 2 1 C PRO 3 C PRO 3 15.67 C PRO 3 C PRO 3 1 C SAR 4 C SAR 4 -17.54 C DVA 8 C DVA 8 1 C PRO 9 C PRO 9 10.99 C PRO 9 C PRO 9 1 C SAR 10 C SAR 10 -3.54 NOR00228 NOR 1 NOR00228 1 11 1A7Y 1 11 NOR00228 A 1 1 11 1 11 1A7Y 1 11 NOR00228 B 1 1 11 1 11 1A7Y 1 11 NOR00228 C 1 1 11 BINDING SITE FOR RESIDUE EEE A 104 A EEE 104 Software 5 BINDING SITE FOR RESIDUE EEE A 105 A EEE 105 Software 4 BINDING SITE FOR RESIDUE EEE A 106 A EEE 106 Software 3 BINDING SITE FOR RESIDUE EEE A 107 A EEE 107 Software 6 BINDING SITE FOR RESIDUE EEE C 101 C EEE 101 Software 2 BINDING SITE FOR RESIDUE EEE C 102 C EEE 102 Software 6 BINDING SITE FOR RESIDUE EEE C 103 C EEE 103 Software 6 BINDING SITE FOR CHAIN A OF ACTINOMYCIN D Software 17 BINDING SITE FOR CHAIN B OF ACTINOMYCIN D Software 20 BINDING SITE FOR CHAIN C OF ACTINOMYCIN D Software 21 A DVA 8 A DVA 8 5 1_555 A EEE 105 E EEE 5 1_655 C PRO 3 C PRO 3 5 1_555 C PXZ 6 C PXZ 6 5 1_545 C EEE 101 H EEE 5 1_545 A THR 1 A THR 1 4 1_555 A THR 7 A THR 7 4 1_545 A EEE 104 D EEE 4 1_455 B SAR 10 B SAR 10 4 1_555 A MVA 5 A MVA 5 3 1_555 A THR 7 A THR 7 3 1_545 C PXZ 6 C PXZ 6 3 1_545 A PRO 3 A PRO 3 6 1_555 B DVA 2 B DVA 2 6 1_564 B PRO 3 B PRO 3 6 1_564 C THR 1 C THR 1 6 1_455 C PXZ 6 C PXZ 6 6 1_455 C PRO 9 C PRO 9 6 1_455 A EEE 104 D EEE 2 1_565 C MVA 5 C MVA 5 2 1_555 A SAR 10 A SAR 10 6 1_554 B THR 1 B THR 1 6 1_554 B MVA 5 B MVA 5 6 1_554 B PXZ 6 B PXZ 6 6 1_654 C PRO 3 C PRO 3 6 1_555 C EEE 103 J EEE 6 1_555 B MVA 5 B MVA 5 6 1_554 B PXZ 6 B PXZ 6 6 1_554 B DVA 8 B DVA 8 6 1_564 C PRO 9 C PRO 9 6 1_455 C MVA 11 C MVA 11 6 1_555 C EEE 102 I EEE 6 1_555 A EEE 104 D EEE 17 1_555 A EEE 105 E EEE 17 1_565 A EEE 105 E EEE 17 1_555 A EEE 106 F EEE 17 1_555 A EEE 106 F EEE 17 1_565 A EEE 107 G EEE 17 1_555 B THR 1 B THR 1 17 1_555 B PXZ 6 B PXZ 6 17 1_555 B THR 7 B THR 7 17 1_555 B PRO 9 B PRO 9 17 1_555 B PRO 9 B PRO 9 17 1_565 B MVA 11 B MVA 11 17 1_655 C PRO 3 C PRO 3 17 1_555 C SAR 4 C SAR 4 17 1_555 C MVA 5 C MVA 5 17 1_455 C PXZ 6 C PXZ 6 17 1_545 C EEE 102 I EEE 17 1_556 A THR 1 A THR 1 20 1_555 A PXZ 6 A PXZ 6 20 1_555 A THR 7 A THR 7 20 1_555 A PRO 9 A PRO 9 20 1_455 A PRO 9 A PRO 9 20 1_555 A MVA 11 A MVA 11 20 1_555 A MVA 11 A MVA 11 20 1_545 A EEE 105 E EEE 20 1_555 A EEE 107 G EEE 20 1_546 C DVA 2 C DVA 2 20 1_456 C PXZ 6 C PXZ 6 20 1_446 C DVA 8 C DVA 8 20 1_456 C PRO 9 C PRO 9 20 1_446 C SAR 10 C SAR 10 20 1_446 C SAR 10 C SAR 10 20 1_456 C MVA 11 C MVA 11 20 1_546 C EEE 102 I EEE 20 1_456 C EEE 102 I EEE 20 1_556 C EEE 103 J EEE 20 1_546 C EEE 103 J EEE 20 1_556 A DVA 2 A DVA 2 21 1_555 A PRO 3 A PRO 3 21 1_555 A SAR 4 A SAR 4 21 1_655 A SAR 4 A SAR 4 21 1_565 A MVA 5 A MVA 5 21 1_655 A PXZ 6 A PXZ 6 21 1_655 A EEE 104 D EEE 21 1_565 A EEE 104 D EEE 21 1_555 A EEE 106 F EEE 21 1_565 A EEE 107 G EEE 21 1_655 B PRO 3 B PRO 3 21 1_654 B PRO 3 B PRO 3 21 1_664 B MVA 5 B MVA 5 21 1_564 B PXZ 6 B PXZ 6 21 1_654 B DVA 8 B DVA 8 21 1_664 B DVA 8 B DVA 8 21 1_564 B MVA 11 B MVA 11 21 1_664 C EEE 101 H EEE 21 1_555 C EEE 102 I EEE 21 1_555 C EEE 103 J EEE 21 1_555 C EEE 103 J EEE 21 1_655 1 P 1