1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Lentzen, G. Klinck, R. Matassova, N. Aboul-Ela, F. Murchie, A.I.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H5 N O2 S 119.142 n (2Z)-2-amino-3-sulfanylprop-2-enoic acid peptide linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C4 H7 N O2 101.104 n (2Z)-2-AMINOBUT-2-ENOIC ACID Z-DEHYDROBUTYRINE peptide linking C3 H7 N O2 S 121.158 D-CYSTEINE D-peptide linking C3 H5 N O2 87.077 n 2-AMINO-ACRYLIC ACID 2,3-DIDEHYDROALANINE peptide linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C3 H5 N O3 103.077 n 3-hydroxy-2-iminopropanoic acid peptide linking H2 N 16.023 AMINO GROUP non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C12 H13 N O4 235.236 8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID non-polymer C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C6 H13 N O4 163.172 n (2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Chem.Biol. CBOLE2 2050 1074-5521 10 769 10.1016/S1074-5521(03)00173-X 12954336 Structural Basis for Contrasting Activities of Ribosome Binding Thiazole Antibiotics 2003 US Cell(Cambridge,Mass.) CELLB5 0998 0092-8674 97 491 10.1016/S0092-8674(00)80759-X 10338213 A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex 1999 US Science SCIEAS 0038 0036-8075 284 1171 10.1126/SCIENCE.284.5417.1171 10325228 Crystal Structure of a Conserved Ribosomal Protein-RNA Complex 1999 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 14980.726 50S RIBOSOMAL PROTEIN L11 1 nat polymer 1805.985 THIOSTREPTON 1 nat polymer 18693.145 RNA RESIDUES 1051-1108 1 nat polymer ALANINAMIDE, BRYAMYCIN, THIACTIN no no AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKK AAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKK AAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD A polypeptide(L) no yes (QUA)IA(DHA)AS(BB9)T(DBU)(DCY)(TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2) XIASASCTTCICTCSCSSX B polypeptide(L) no no GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC C polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 2336 THERMOTOGA MARITIMA sample 146537 STREPTOMYCES AZUREUS sample 2336 THERMOTOGA MARITIMA -6.725 1 19 C 1051 C 1108 6.827 C_G1051:C1108_C 1 -8.819 -0.453 -0.068 0.102 -3.133 1 19 C 1052 C 1107 5.150 C_C1052:G1107_C 2 -17.311 0.367 0.141 -0.289 -6.222 1 20 C 1053 C 1106 9.602 C_U1053:A1106_C 3 -13.374 -0.887 0.105 -0.018 -2.780 1 19 C 1054 C 1105 5.038 C_G1054:C1105_C 4 -8.463 -0.457 0.085 -0.057 -13.474 1 19 C 1055 C 1104 2.434 C_G1055:C1104_C 5 -14.487 0.126 -0.448 -0.229 -17.709 10 11 C 1056 C 1103 -5.174 C_G1056:A1103_C 6 -10.873 6.768 -0.139 -4.215 -11.911 1 19 C 1087 C 1102 4.348 C_G1087:C1102_C 7 -0.941 -0.265 -0.387 0.011 -6.809 1 16 C 1090 C 1101 20.218 C_U1090:U1101_C 8 -5.982 -2.485 0.037 -1.763 -2.787 1 19 C 1091 C 1100 7.170 C_G1091:C1100_C 9 0.730 -0.212 -0.356 -0.084 0.573 1 19 C 1092 C 1099 3.261 C_C1092:G1099_C 10 0.181 -0.037 -0.243 -0.275 -6.476 10 11 C 1093 C 1098 -5.736 C_G1093:A1098_C 11 0.815 6.806 -0.058 -4.083 18.891 2 21 C 1086 C 1082 168.228 C_A1086:U1082_C 12 -6.288 0.232 -0.283 1.405 -1.018 1 20 C 1057 C 1081 8.423 C_A1057:U1081_C 13 -19.131 0.092 0.123 -0.028 -15.671 1 20 C 1058 C 1080 6.802 C_U1058:A1080_C 14 -7.542 -0.197 0.082 -0.108 -7.401 1 19 C 1059 C 1079 -4.126 C_G1059:C1079_C 15 -4.623 -0.131 0.144 -0.257 -2.629 3 23 C 1060 C 1088 -67.855 C_U1060:A1088_C 16 5.058 -0.630 0.653 3.398 1.559 1 19 C 1062 C 1076 -3.633 C_G1062:C1076_C 17 -5.131 -0.273 -0.214 -0.151 -8.395 1 19 C 1063 C 1075 0.132 C_G1063:C1075_C 18 -16.562 -0.297 -0.472 -0.380 -4.999 1 19 C 1064 C 1074 4.496 C_C1064:G1074_C 19 -14.637 0.340 -0.118 -0.331 -9.754 C 1065 C 1073 6.689 C_U1065:A1073_C 20 -5.636 5.606 -0.137 -1.138 2.770 37.165 C C 1051 1052 12.357 C C 1108 1107 3.065 7.815 -0.428 -1.249 CC_G1051C1052:G1107C1108_CC 1 -2.682 4.242 36.267 -2.901 0.348 2.401 30.143 C C 1052 1053 24.763 C C 1107 1106 3.139 12.505 0.385 -1.138 CC_C1052U1053:A1106G1107_CC 2 -0.239 0.472 27.480 -4.454 -0.784 2.992 33.191 C C 1053 1054 8.926 C C 1106 1105 3.216 5.078 0.051 -1.230 CC_U1053G1054:C1105A1106_CC 3 -1.519 2.670 32.776 -2.967 -0.333 2.856 34.487 C C 1054 1055 19.262 C C 1105 1104 3.587 11.219 0.195 -1.744 CC_G1054G1055:C1104C1105_CC 4 1.714 -2.943 32.620 -4.708 -0.059 3.486 66.888 C C 1055 1056 9.838 C C 1104 1103 3.644 10.803 -0.498 -0.666 CC_G1055G1056:A1103C1104_CC 5 3.331 -3.034 66.035 -1.070 0.595 2.508 38.676 C C 1056 1087 5.102 C C 1103 1102 3.246 3.350 -3.406 0.612 CC_G1056G1087:C1102A1103_CC 6 8.328 -12.681 37.659 0.557 6.056 3.591 37.462 C C 1087 1090 -5.086 C C 1102 1101 3.388 -3.260 -0.921 -3.414 CC_G1087U1090:U1101C1102_CC 7 2.664 -4.156 37.233 -4.858 1.808 2.926 35.994 C C 1090 1091 7.745 C C 1101 1100 3.182 4.771 -0.808 -1.471 CC_U1090G1091:C1100U1101_CC 8 1.729 -2.807 35.646 -3.017 1.539 2.984 29.260 C C 1091 1092 4.831 C C 1100 1099 3.184 2.438 -0.024 -2.312 CC_G1091C1092:G1099C1100_CC 9 0.134 -0.266 29.161 -5.076 0.075 3.393 59.686 C C 1092 1093 5.042 C C 1099 1098 3.512 5.012 -0.235 -1.285 CC_C1092G1093:A1098G1099_CC 10 2.276 -2.290 59.455 -1.556 0.356 1.215 174.515 C C 1086 1057 -76.122 C C 1082 1081 0.742 -150.786 -2.601 -2.575 CC_A1086A1057:U1081U1082_CC 11 78.607 -39.684 113.056 -1.029 1.438 3.086 35.249 C C 1057 1058 11.930 C C 1081 1080 3.531 7.170 -0.644 -2.099 CC_A1057U1058:A1080U1081_CC 12 -2.744 4.566 34.429 -4.556 0.646 2.518 29.400 C C 1058 1059 13.085 C C 1080 1079 3.114 6.573 -1.017 -1.756 CC_U1058G1059:C1079A1080_CC 13 3.393 -6.755 28.474 -4.695 2.642 -1.670 -179.473 C C 1059 1060 84.329 C C 1079 1088 -1.653 -168.644 2.880 -0.799 CC_G1059U1060:A1088C1079_CC 14 -26.651 -13.327 -173.467 0.353 1.448 3.088 36.833 C C 1062 1063 12.526 C C 1076 1075 3.516 7.856 -0.429 -1.765 CC_G1062G1063:C1075C1076_CC 15 -1.132 1.804 35.996 -3.883 0.522 3.099 35.470 C C 1063 1064 3.798 C C 1075 1074 3.189 2.312 0.878 -1.623 CC_G1063C1064:G1074C1075_CC 16 0.800 -1.315 35.389 -2.990 -1.328 3.297 51.703 C C 1064 1065 7.547 C C 1074 1073 3.425 6.551 0.331 -1.004 CC_C1064U1065:A1073G1074_CC 17 6.517 -7.508 50.927 -1.610 0.077 pdbx_database_related database_PDB_rev database_PDB_rev_record entity_poly pdbx_seq_map_depositor_info struct_conn pdbx_nmr_software repository Initial release Atomic model Database references Derived calculations Structure summary Version format compliance Other Database references Data collection Derived calculations Polymer sequence Data collection 1 0 2003-09-11 1 1 2011-07-13 1 2 2012-11-30 1 3 2017-11-15 2 0 2019-04-24 2 1 2019-08-21 _pdbx_database_related.db_name _entity_poly.pdbx_seq_one_letter_code_can _pdbx_seq_map_depositor_info.one_letter_code _struct_conn.pdbx_leaving_atom_flag _pdbx_nmr_software.name CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-MGGDP COMPLEXED WITH THE THIOPEPTIDE GE2270A. CRYSTAL STRUCTURE OF THIOPEPTIDE THIOSTREPTON CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-GNP COMPLEXED WITH THIOPEPTIDE GE2270A. SOLUTION STRUCTURE OF THE COMPLEX OF THIOPEPTIDE THIOSTREPTON AND RIBOSOMAL L11-RNA CRYSTAL STRUCTURE OF NOSIHEPTIDE COMPLEXED WITH THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS CRYSTAL STRUCTURE OF RIBOSOMAL L11-RNA COMPLEXED WITH THE THIOPEPTIDE THIOSTREPTON CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN L11-RNA COMPLEX FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E. COLI 70S RIBOSOME CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5A RESOLUTIO FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (EF-G) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUND WITH EF-G,GDP AND FUSIDIC ACID FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (DOMAIN G'AND V) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUNDWITH EF-G AND GMPPCP FITTING OF L11 PROTEIN IN THE LOW RESOLUTION CRYO-EM MAP OFE.COLI 70S RIBOSOME COORDINATES OF S12, L11 PROTEINS AND P-TRNA, FROM THE 70S X-RAY STRUCTURE ALIGNED TO THE 70S CRYO-EM MAP OF E. COLIRIBOSOME COORDINATES OF S12, L11 PROTEINS AND E-SITE TRNA FROM 70S CRYSTAL STRUCTURE SEPARATELY FITTED INTO THE CRYO-EM MAPOF E.COLI 70S.EF-G.GDPNP COMPLEX. THE COORDINATESORIGINALLY FROM THE E-SITE TRNA WERE FITTED IN THEPOSITION OF THE HYBRID P /E-SITE TRNA. SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-EM MAP OF THE LARGE 50S SUBUNIT AT 7.5 A. PDBE Y PDBE 2003-08-08 REL THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: THIOSTREPTON CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 18 DESCRIPTION: THIOSTREPTON IS A HETEROCYCLIC THIOPEPTIDE, CONSISTING OF FOUR THIAZOLES ONE THIAZOLINE ONE PIPERIDEINE RINGS. A MODIFIED QUINOLINE LINKED TO MAIN-CHAIN RESIDUE 1 AND SIDE-CHAIN OF RESIDUE 12. THE OBSERVED C-TERMINAL AMINO GROUP NH2(18) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE. Antibiotic Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes. THIOSTREPTON Thiopeptide BEST OVERALL DOCKING SCORE AND LEAST RESTRAINT VIOLATION. THE NOES INCLUDED IN THE RESTRAINTED MODELING WERE OBTAINED FROM A FILTERED NOESY EXPERIMENT ON A COMPLEX OF UNLABELED THIOSTREPTON WITH THE RNA. AS ALL INTERNAL COORDINATES WERE HELD RIGID ACCORDING TO THE X-RAY STRUCTURES, ONLY INTERMOLECULAR NOES WERE INCLUDED. ASSIGNMENTS FOR RNA WERE CHOSEN FROM AN ITERATIVE DOCKING PROCESS (SEE LENTZEN ET AL AND MANUSCRIPT TO BE PUBLISHED) LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE 1 NOESY 100 MM NACL, 5 MM MGCL2 6.2 pH 1 atm 303 K THE COORDINATES OF THE PROTEIN, RNA AND THE ANTIBIOTIC WERE HELD RIGID DURING REFINEMENT. THE COORDINATES OF THE RIBOSOMAL L11 (CHAIN A) AND THE RNA (CHAIN C) WERE FROM PDB ENTRY 1MMS. THE COORDINATES OF THE ANTIBIOTIC THIOSTREPTON (CHAIN B) WERE FROM PDB ENTRY 1E9W. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION. DOCKING/MODELING DAVID MORLEY refinement rDOCK 600 Bruker DRX n 1 2 A n 2 3 A n 3 4 A n 4 5 A n 5 6 A n 6 7 A GLN 8 n 7 GLN 8 A ILE 9 n 8 ILE 9 A LYS 10 n 9 LYS 10 A LEU 11 n 10 LEU 11 A GLN 12 n 11 GLN 12 A LEU 13 n 12 LEU 13 A PRO 14 n 13 PRO 14 A ALA 15 n 14 ALA 15 A GLY 16 n 15 GLY 16 A LYS 17 n 16 LYS 17 A ALA 18 n 17 ALA 18 A THR 19 n 18 THR 19 A PRO 20 n 19 PRO 20 A ALA 21 n 20 ALA 21 A PRO 22 n 21 PRO 22 A PRO 23 n 22 PRO 23 A VAL 24 n 23 VAL 24 A GLY 25 n 24 GLY 25 A PRO 26 n 25 PRO 26 A ALA 27 n 26 ALA 27 A LEU 28 n 27 LEU 28 A GLY 29 n 28 GLY 29 A GLN 30 n 29 GLN 30 A HIS 31 n 30 HIS 31 A GLY 32 n 31 GLY 32 A VAL 33 n 32 VAL 33 A ASN 34 n 33 ASN 34 A ILE 35 n 34 ILE 35 A MET 36 n 35 MET 36 A GLU 37 n 36 GLU 37 A PHE 38 n 37 PHE 38 A CYS 39 n 38 CYS 39 A LYS 40 n 39 LYS 40 A ARG 41 n 40 ARG 41 A PHE 42 n 41 PHE 42 A ASN 43 n 42 ASN 43 A ALA 44 n 43 ALA 44 A GLU 45 n 44 GLU 45 A THR 46 n 45 THR 46 A ALA 47 n 46 ALA 47 A ASP 48 n 47 ASP 48 A LYS 49 n 48 LYS 49 A ALA 50 n 49 ALA 50 A GLY 51 n 50 GLY 51 A MET 52 n 51 MET 52 A ILE 53 n 52 ILE 53 A LEU 54 n 53 LEU 54 A PRO 55 n 54 PRO 55 A VAL 56 n 55 VAL 56 A VAL 57 n 56 VAL 57 A ILE 58 n 57 ILE 58 A THR 59 n 58 THR 59 A VAL 60 n 59 VAL 60 A TYR 61 n 60 TYR 61 A GLU 62 n 61 GLU 62 A ASP 63 n 62 ASP 63 A LYS 64 n 63 LYS 64 A SER 65 n 64 SER 65 A PHE 66 n 65 PHE 66 A THR 67 n 66 THR 67 A PHE 68 n 67 PHE 68 A ILE 69 n 68 ILE 69 A ILE 70 n 69 ILE 70 A LYS 71 n 70 LYS 71 A THR 72 n 71 THR 72 A PRO 73 n 72 PRO 73 A PRO 74 n 73 PRO 74 A ALA 75 n 74 ALA 75 A SER 76 n 75 SER 76 A PHE 77 n 76 PHE 77 A LEU 78 n 77 LEU 78 A LEU 79 n 78 LEU 79 A LYS 80 n 79 LYS 80 A LYS 81 n 80 LYS 81 A ALA 82 n 81 ALA 82 A ALA 83 n 82 ALA 83 A GLY 84 n 83 GLY 84 A ILE 85 n 84 ILE 85 A GLU 86 n 85 GLU 86 A LYS 87 n 86 LYS 87 A GLY 88 n 87 GLY 88 A SER 89 n 88 SER 89 A SER 90 n 89 SER 90 A GLU 91 n 90 GLU 91 A PRO 92 n 91 PRO 92 A LYS 93 n 92 LYS 93 A ARG 94 n 93 ARG 94 A LYS 95 n 94 LYS 95 A ILE 96 n 95 ILE 96 A VAL 97 n 96 VAL 97 A GLY 98 n 97 GLY 98 A LYS 99 n 98 LYS 99 A VAL 100 n 99 VAL 100 A THR 101 n 100 THR 101 A ARG 102 n 101 ARG 102 A LYS 103 n 102 LYS 103 A GLN 104 n 103 GLN 104 A ILE 105 n 104 ILE 105 A GLU 106 n 105 GLU 106 A GLU 107 n 106 GLU 107 A ILE 108 n 107 ILE 108 A ALA 109 n 108 ALA 109 A LYS 110 n 109 LYS 110 A THR 111 n 110 THR 111 A LYS 112 n 111 LYS 112 A MET 113 n 112 MET 113 A PRO 114 n 113 PRO 114 A ASP 115 n 114 ASP 115 A LEU 116 n 115 LEU 116 A ASN 117 n 116 ASN 117 A ALA 118 n 117 ALA 118 A ASN 119 n 118 ASN 119 A SER 120 n 119 SER 120 A LEU 121 n 120 LEU 121 A GLU 122 n 121 GLU 122 A ALA 123 n 122 ALA 123 A ALA 124 n 123 ALA 124 A MET 125 n 124 MET 125 A LYS 126 n 125 LYS 126 A ILE 127 n 126 ILE 127 A ILE 128 n 127 ILE 128 A GLU 129 n 128 GLU 129 A GLY 130 n 129 GLY 130 A THR 131 n 130 THR 131 A ALA 132 n 131 ALA 132 A LYS 133 n 132 LYS 133 A SER 134 n 133 SER 134 A MET 135 n 134 MET 135 A GLY 136 n 135 GLY 136 A ILE 137 n 136 ILE 137 A GLU 138 n 137 GLU 138 A VAL 139 n 138 VAL 139 A VAL 140 n 139 VAL 140 A n 140 141 A QUA 0 n 1 QUA 0 B ILE 1 n 2 ILE 1 B ALA 2 n 3 ALA 2 B DHA 3 n 4 DHA 3 B ALA 4 n 5 ALA 4 B SER 5 n 6 SER 5 B BB9 6 n 7 BB9 6 B THR 7 n 8 THR 7 B DBU 8 n 9 DBU 8 B DCY 9 n 10 DCY 9 B TS9 10 n 11 TS9 10 B BB9 11 n 12 BB9 11 B THR 12 n 13 THR 12 B BB9 13 n 14 BB9 13 B MH6 14 n 15 MH6 14 B BB9 15 n 16 BB9 15 B DHA 16 n 17 DHA 16 B DHA 17 n 18 DHA 17 B NH2 18 n 19 NH2 18 B G 1051 n 1 G 1051 C C 1052 n 2 C 1052 C U 1053 n 3 U 1053 C G 1054 n 4 G 1054 C G 1055 n 5 G 1055 C G 1056 n 6 G 1056 C A 1057 n 7 A 1057 C U 1058 n 8 U 1058 C G 1059 n 9 G 1059 C U 1060 n 10 U 1060 C U 1061 n 11 U 1061 C G 1062 n 12 G 1062 C G 1063 n 13 G 1063 C C 1064 n 14 C 1064 C U 1065 n 15 U 1065 C U 1066 n 16 U 1066 C A 1067 n 17 A 1067 C G 1068 n 18 G 1068 C A 1069 n 19 A 1069 C A 1070 n 20 A 1070 C G 1071 n 21 G 1071 C C 1072 n 22 C 1072 C A 1073 n 23 A 1073 C G 1074 n 24 G 1074 C C 1075 n 25 C 1075 C C 1076 n 26 C 1076 C A 1077 n 27 A 1077 C U 1078 n 28 U 1078 C C 1079 n 29 C 1079 C A 1080 n 30 A 1080 C U 1081 n 31 U 1081 C U 1082 n 32 U 1082 C U 1083 n 33 U 1083 C A 1084 n 34 A 1084 C A 1085 n 35 A 1085 C A 1086 n 36 A 1086 C G 1087 n 37 G 1087 C A 1088 n 38 A 1088 C G 1089 n 39 G 1089 C U 1090 n 40 U 1090 C G 1091 n 41 G 1091 C C 1092 n 42 C 1092 C G 1093 n 43 G 1093 C U 1094 n 44 U 1094 C A 1095 n 45 A 1095 C A 1096 n 46 A 1096 C C 1097 n 47 C 1097 C A 1098 n 48 A 1098 C G 1099 n 49 G 1099 C C 1100 n 50 C 1100 C U 1101 n 51 U 1101 C C 1102 n 52 C 1102 C A 1103 n 53 A 1103 C C 1104 n 54 C 1104 C C 1105 n 55 C 1105 C A 1106 n 56 A 1106 C G 1107 n 57 G 1107 C C 1108 n 58 C 1108 C author_defined_assembly 3 trimeric B DHA 3 2-AMINO-ACRYLIC ACID B DHA 4 SER B BB9 6 B BB9 7 CYS B DBU 8 (2Z)-2-AMINOBUT-2-ENOIC ACID B DBU 9 THR B TS9 10 B TS9 11 ILE B BB9 11 B BB9 12 CYS B BB9 13 B BB9 14 CYS B MH6 14 3-HYDROXY-2-IMINOPROPANOIC ACID B MH6 15 SER B BB9 15 B BB9 16 CYS B DHA 16 2-AMINO-ACRYLIC ACID B DHA 17 SER B DHA 17 2-AMINO-ACRYLIC ACID B DHA 18 SER 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 A N LEU 13 A N LEU 12 A O LEU 54 A O LEU 53 A N THR 59 A N THR 58 A O THR 67 A O THR 66 A N VAL 100 A N VAL 99 A O GLU 138 A O GLU 137 1 A ALA 2 A ALA 1 1 Y 1 A LYS 3 A LYS 2 1 Y 1 A LYS 4 A LYS 3 1 Y 1 A VAL 5 A VAL 4 1 Y 1 A ALA 6 A ALA 5 1 Y 1 A ALA 7 A ALA 6 1 Y 1 A ASP 141 A ASP 140 1 Y 1 C A 1069 0.061 SIDE CHAIN 1 B B C N BB9 MH6 13 14 0.138 0.023 1.336 1.474 Y 1 A ALA 15 -38.18 -99.29 1 A LYS 17 -176.59 140.91 1 A THR 19 95.17 -25.33 1 A VAL 24 -94.06 -92.82 1 A PRO 26 -28.71 -52.70 1 A ALA 27 -39.55 -89.24 1 A ILE 35 -27.29 -73.68 1 A GLU 62 -34.81 -34.92 1 A LYS 64 68.48 -9.28 1 A LYS 93 75.48 -42.99 1 B SER 5 71.83 80.85 1 B DCY 9 -147.29 -14.72 1 B TS9 10 -107.46 -65.50 50S RIBOSOMAL PROTEIN L11, THIOSTREPTON MINIMIZED AVERAGE Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA 1 N N 2 N N 3 N N A GLY 25 A GLY 24 HELX_P A GLN 30 A GLN 29 1 1 6 A ASN 34 A ASN 33 HELX_P A THR 46 A THR 45 1 2 13 A PRO 74 A PRO 73 HELX_P A GLY 84 A GLY 83 1 3 11 A ARG 102 A ARG 101 HELX_P A MET 113 A MET 112 1 4 12 A PRO 114 A PRO 113 HELX_P A LEU 116 A LEU 115 5 5 3 A SER 120 A SER 119 HELX_P A LYS 133 A LYS 132 1 6 14 covale 1.329 one B QUA 0 B C11 QUA 1 1_555 B THR 12 B OG1 THR 13 1_555 covale 1.499 one B QUA 0 B C7 QUA 1 1_555 B ILE 1 B N ILE 2 1_555 covale 1.383 both B ALA 2 B C ALA 3 1_555 B DHA 3 B N DHA 4 1_555 covale 1.348 both B DHA 3 B C DHA 4 1_555 B ALA 4 B N ALA 5 1_555 covale 1.752 one B SER 5 B C SER 6 1_555 B BB9 6 B SG BB9 7 1_555 covale 1.575 one B SER 5 B CA SER 6 1_555 B BB9 13 B C BB9 14 1_555 covale 1.524 one B SER 5 B CB SER 6 1_555 B MH6 14 B CB MH6 15 1_555 covale 1.306 both B SER 5 B C SER 6 1_555 B BB9 6 B N BB9 7 1_555 covale 1.323 both B BB9 6 B C BB9 7 1_555 B THR 7 B N THR 8 1_555 covale 1.352 both B THR 7 B C THR 8 1_555 B DBU 8 B N DBU 9 1_555 covale 1.294 both B DBU 8 B C DBU 9 1_555 B DCY 9 B N DCY 10 1_555 covale 1.749 one B DBU 8 B C DBU 9 1_555 B DCY 9 B SG DCY 10 1_555 covale 1.328 both B DCY 9 B C DCY 10 1_555 B TS9 10 B N TS9 11 1_555 covale 1.750 one B TS9 10 B C TS9 11 1_555 B BB9 11 B SG BB9 12 1_555 covale 1.279 both B TS9 10 B C TS9 11 1_555 B BB9 11 B N BB9 12 1_555 covale 1.359 both B BB9 11 B C BB9 12 1_555 B THR 12 B N THR 13 1_555 covale 1.708 one B THR 12 B C THR 13 1_555 B BB9 13 B SG BB9 14 1_555 covale 1.292 both B THR 12 B C THR 13 1_555 B BB9 13 B N BB9 14 1_555 covale 1.474 both B BB9 13 B C BB9 14 1_555 B MH6 14 B N MH6 15 1_555 covale 1.650 one B MH6 14 B C MH6 15 1_555 B BB9 15 B SG BB9 16 1_555 covale 1.301 both B MH6 14 B C MH6 15 1_555 B BB9 15 B N BB9 16 1_555 covale 1.380 both B BB9 15 B C BB9 16 1_555 B DHA 16 B N DHA 17 1_555 covale 1.229 both B DHA 16 B C DHA 17 1_555 B DHA 17 B N DHA 18 1_555 covale 1.350 both B DHA 17 B C DHA 18 1_555 B NH2 18 B N NH2 19 1_555 hydrog WATSON-CRICK C G 1051 C N1 G 1 1_555 C C 1108 C N3 C 58 1_555 hydrog WATSON-CRICK C G 1051 C N2 G 1 1_555 C C 1108 C O2 C 58 1_555 hydrog WATSON-CRICK C G 1051 C O6 G 1 1_555 C C 1108 C N4 C 58 1_555 hydrog WATSON-CRICK C C 1052 C N3 C 2 1_555 C G 1107 C N1 G 57 1_555 hydrog WATSON-CRICK C C 1052 C N4 C 2 1_555 C G 1107 C O6 G 57 1_555 hydrog WATSON-CRICK C C 1052 C O2 C 2 1_555 C G 1107 C N2 G 57 1_555 hydrog WATSON-CRICK C U 1053 C N3 U 3 1_555 C A 1106 C N1 A 56 1_555 hydrog WATSON-CRICK C U 1053 C O4 U 3 1_555 C A 1106 C N6 A 56 1_555 hydrog WATSON-CRICK C G 1054 C N1 G 4 1_555 C C 1105 C N3 C 55 1_555 hydrog WATSON-CRICK C G 1054 C N2 G 4 1_555 C C 1105 C O2 C 55 1_555 hydrog WATSON-CRICK C G 1054 C O6 G 4 1_555 C C 1105 C N4 C 55 1_555 hydrog G-A MISPAIR C G 1055 C N2 G 5 1_555 C A 1085 C N3 A 35 1_555 hydrog WATSON-CRICK C G 1055 C N1 G 5 1_555 C C 1104 C N3 C 54 1_555 hydrog WATSON-CRICK C G 1055 C N2 G 5 1_555 C C 1104 C O2 C 54 1_555 hydrog WATSON-CRICK C G 1055 C O6 G 5 1_555 C C 1104 C N4 C 54 1_555 hydrog TYPE_11_PAIR C G 1056 C N2 G 6 1_555 C A 1103 C N7 A 53 1_555 hydrog TYPE_11_PAIR C G 1056 C N3 G 6 1_555 C A 1103 C N6 A 53 1_555 hydrog WATSON-CRICK C A 1057 C N1 A 7 1_555 C U 1081 C N3 U 31 1_555 hydrog WATSON-CRICK C A 1057 C N6 A 7 1_555 C U 1081 C O4 U 31 1_555 hydrog WATSON-CRICK C U 1058 C N3 U 8 1_555 C A 1080 C N1 A 30 1_555 hydrog WATSON-CRICK C U 1058 C O4 U 8 1_555 C A 1080 C N6 A 30 1_555 hydrog WATSON-CRICK C G 1059 C N1 G 9 1_555 C C 1079 C N3 C 29 1_555 hydrog WATSON-CRICK C G 1059 C N2 G 9 1_555 C C 1079 C O2 C 29 1_555 hydrog WATSON-CRICK C G 1059 C O6 G 9 1_555 C C 1079 C N4 C 29 1_555 hydrog HOOGSTEEN C U 1060 C N3 U 10 1_555 C A 1088 C N7 A 38 1_555 hydrog HOOGSTEEN C U 1060 C O4 U 10 1_555 C A 1088 C N6 A 38 1_555 hydrog WATSON-CRICK C G 1062 C N1 G 12 1_555 C C 1076 C N3 C 26 1_555 hydrog WATSON-CRICK C G 1062 C N2 G 12 1_555 C C 1076 C O2 C 26 1_555 hydrog WATSON-CRICK C G 1062 C O6 G 12 1_555 C C 1076 C N4 C 26 1_555 hydrog WATSON-CRICK C G 1063 C N1 G 13 1_555 C C 1075 C N3 C 25 1_555 hydrog WATSON-CRICK C G 1063 C N2 G 13 1_555 C C 1075 C O2 C 25 1_555 hydrog WATSON-CRICK C G 1063 C O6 G 13 1_555 C C 1075 C N4 C 25 1_555 hydrog WATSON-CRICK C C 1064 C N3 C 14 1_555 C G 1074 C N1 G 24 1_555 hydrog WATSON-CRICK C C 1064 C N4 C 14 1_555 C G 1074 C O6 G 24 1_555 hydrog WATSON-CRICK C C 1064 C O2 C 14 1_555 C G 1074 C N2 G 24 1_555 hydrog U-A PAIR C U 1065 C O2 U 15 1_555 C A 1073 C N6 A 23 1_555 hydrog TYPE_6_PAIR C G 1071 C N1 G 21 1_555 C G 1091 C O6 G 41 1_555 hydrog TYPE_6_PAIR C G 1071 C N2 G 21 1_555 C G 1091 C N7 G 41 1_555 hydrog G-C PAIR C G 1071 C O6 G 21 1_555 C C 1100 C N4 C 50 1_555 hydrog C-C MISPAIR C C 1072 C N3 C 22 1_555 C C 1092 C N4 C 42 1_555 hydrog C-G PAIR C C 1072 C N4 C 22 1_555 C G 1099 C O6 G 49 1_555 hydrog REVERSED WATSON-CRICK C U 1082 C N3 U 32 1_555 C A 1086 C N1 A 36 1_555 hydrog REVERSED WATSON-CRICK C U 1082 C O2 U 32 1_555 C A 1086 C N6 A 36 1_555 hydrog WATSON-CRICK C G 1087 C N1 G 37 1_555 C C 1102 C N3 C 52 1_555 hydrog WATSON-CRICK C G 1087 C N2 G 37 1_555 C C 1102 C O2 C 52 1_555 hydrog WATSON-CRICK C G 1087 C O6 G 37 1_555 C C 1102 C N4 C 52 1_555 hydrog G-U MISPAIR C G 1089 C N2 G 39 1_555 C U 1101 C O4 U 51 1_555 hydrog TYPE_16_PAIR C U 1090 C N3 U 40 1_555 C U 1101 C O2 U 51 1_555 hydrog TYPE_16_PAIR C U 1090 C O4 U 40 1_555 C U 1101 C N3 U 51 1_555 hydrog WATSON-CRICK C G 1091 C N1 G 41 1_555 C C 1100 C N3 C 50 1_555 hydrog WATSON-CRICK C G 1091 C N2 G 41 1_555 C C 1100 C O2 C 50 1_555 hydrog WATSON-CRICK C G 1091 C O6 G 41 1_555 C C 1100 C N4 C 50 1_555 hydrog WATSON-CRICK C C 1092 C N3 C 42 1_555 C G 1099 C N1 G 49 1_555 hydrog WATSON-CRICK C C 1092 C N4 C 42 1_555 C G 1099 C O6 G 49 1_555 hydrog WATSON-CRICK C C 1092 C O2 C 42 1_555 C G 1099 C N2 G 49 1_555 hydrog TYPE_11_PAIR C G 1093 C N2 G 43 1_555 C A 1098 C N7 A 48 1_555 hydrog TYPE_11_PAIR C G 1093 C N3 G 43 1_555 C A 1098 C N6 A 48 1_555 RIBOSOME/ANTIBIOTIC RIBOSOME-ANTIBIOTIC COMPLEX, THIOPEPTIDE, ANTIBACTERIAL, THIAZOLE, OXAZOLE, RIBOSOME, L11, TRANSLATION INHIBITION RL11_THEMA UNP 1 P29395 THCL_STRAJ UNP 2 P0C8P8 1OLN PDB 3 1OLN 2 141 1OLN 2 141 P29395 A 1 1 140 1 17 1OLN 1 17 P0C8P8 B 2 2 18 1051 1108 1OLN 1051 1108 1OLN C 3 1 58 3 2 anti-parallel anti-parallel parallel A ILE 9 A ILE 8 A PRO 14 A PRO 13 A ILE 53 A ILE 52 A VAL 60 A VAL 59 A PHE 66 A PHE 65 A ILE 70 A ILE 69 A GLY 98 A GLY 97 A THR 101 A THR 100 A ILE 137 A ILE 136 A VAL 140 A VAL 139 BINDING SITE FOR CHAIN B OF THIOSTREPTON Software 4 A PRO 22 A PRO 21 4 1_555 C A 1067 C A 17 4 1_555 C G 1068 C G 18 4 1_555 C A 1095 C A 45 4 1_555 1 P 1