data_4YCM # _model_server_result.job_id FD-emt3HlNqrWg-xbWAF-w _model_server_result.datetime_utc '2024-11-24 17:41:45' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4ycm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1004}' # _entry.id 4YCM # _exptl.entry_id 4YCM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 604.771 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(4S,5E,8S,9E,11S,13E,15E,18R)-8-methoxy-9,11-dimethyl-18-[(1Z,4E)-2-methylhexa-1,4-dien-1-yl]-2-oxooxacyclooctadeca-5,9,13,15-tetraen-4-yl 3-O-methyl-beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4YCM _cell.length_a 71.666 _cell.length_b 71.666 _cell.length_c 585.235 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YCM _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 876 A CYS 876 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A C AME 1 A AME 1 1_555 A N GLU 2 A GLU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A O LEU 711 A LEU 711 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc2 A O LYS 712 A LYS 712 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc3 A O ALA 714 A ALA 714 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? metalc ? metalc4 A OE1 GLU 732 A GLU 732 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.15 ? metalc ? metalc5 A OE2 GLU 732 A GLU 732 1_555 B NA NA . A NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? # _chem_comp.formula 'C34 H52 O9' _chem_comp.formula_weight 604.771 _chem_comp.id 7BS _chem_comp.mon_nstd_flag . _chem_comp.name '(4S,5E,8S,9E,11S,13E,15E,18R)-8-methoxy-9,11-dimethyl-18-[(1Z,4E)-2-methylhexa-1,4-dien-1-yl]-2-oxooxacyclooctadeca-5,9,13,15-tetraen-4-yl 3-O-methyl-beta-D-glucopyranoside' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Biselyngbyaside # _atom_sites.entry_id 4YCM _atom_sites.fract_transf_matrix[1][1] 0.013954 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013954 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.001709 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NA A 1 1001 1001 NA NA . C 3 SO4 A 1 1002 1007 SO4 SO4 . D 3 SO4 A 1 1003 1008 SO4 SO4 . E 4 7BS A 1 1004 2 7BS 7BS . F 5 PTY A 1 1005 1012 PTY PTY . G 5 PTY A 1 1006 1013 PTY PTY . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C68 7BS . . . E 4 27.503 -19.361 64.546 1 80.42 ? C68 7BS 1004 A 1 HETATM 2 O O67 7BS . . . E 4 27.655 -18.122 63.86 1 76.5 ? O67 7BS 1004 A 1 HETATM 3 C C20 7BS . . . E 4 28.045 -18.297 62.489 1 75.63 ? C20 7BS 1004 A 1 HETATM 4 C C21 7BS . . . E 4 27.607 -16.973 61.845 1 81.82 ? C21 7BS 1004 A 1 HETATM 5 C C22 7BS . . . E 4 27.096 -16.984 60.437 1 85.79 ? C22 7BS 1004 A 1 HETATM 6 C C23 7BS . . . E 4 26.662 -15.818 59.953 1 86.41 ? C23 7BS 1004 A 1 HETATM 7 C C24 7BS . . . E 4 26.665 -15.568 58.478 1 81.91 ? C24 7BS 1004 A 1 HETATM 8 O O29 7BS . . . E 4 25.703 -16.521 57.963 1 80.62 ? O29 7BS 1004 A 1 HETATM 9 C C33 7BS . . . E 4 25.457 -16.943 56.599 1 78.9 ? C33 7BS 1004 A 1 HETATM 10 C C32 7BS . . . E 4 26.748 -17.516 55.947 1 110.44 ? C32 7BS 1004 A 1 HETATM 11 O O36 7BS . . . E 4 27.817 -16.557 55.884 1 110.94 ? O36 7BS 1004 A 1 HETATM 12 C C31 7BS . . . E 4 26.473 -17.995 54.493 1 86.53 ? C31 7BS 1004 A 1 HETATM 13 O O71 7BS . . . E 4 27.551 -18.807 53.976 1 87.6 ? O71 7BS 1004 A 1 HETATM 14 C C72 7BS . . . E 4 28.744 -18.131 53.525 1 88.79 ? C72 7BS 1004 A 1 HETATM 15 C C30 7BS . . . E 4 25.284 -18.981 54.48 1 81.08 ? C30 7BS 1004 A 1 HETATM 16 O O37 7BS . . . E 4 24.87 -19.193 53.111 1 80.34 ? O37 7BS 1004 A 1 HETATM 17 C C35 7BS . . . E 4 24.076 -18.427 55.276 1 79.01 ? C35 7BS 1004 A 1 HETATM 18 C C38 7BS . . . E 4 22.976 -19.519 55.378 1 119.67 ? C38 7BS 1004 A 1 HETATM 19 O O39 7BS . . . E 4 23.492 -20.715 55.989 1 118.12 ? O39 7BS 1004 A 1 HETATM 20 O O34 7BS . . . E 4 24.446 -17.969 56.603 1 76.69 ? O34 7BS 1004 A 1 HETATM 21 C C27 7BS . . . E 4 26.341 -14.083 58.147 1 73.01 ? C27 7BS 1004 A 1 HETATM 22 C C26 7BS . . . E 4 27.038 -13.753 56.861 1 75.8 ? C26 7BS 1004 A 1 HETATM 23 O O28 7BS . . . E 4 26.459 -13.54 55.807 1 85.47 ? O28 7BS 1004 A 1 HETATM 24 O O25 7BS . . . E 4 28.356 -13.626 57.049 1 72.42 ? O25 7BS 1004 A 1 HETATM 25 C C8 7BS . . . E 4 29.151 -13.644 55.855 1 73.52 ? C8 7BS 1004 A 1 HETATM 26 C C9 7BS . . . E 4 30.536 -14.066 56.401 1 71.51 ? C9 7BS 1004 A 1 HETATM 27 C C10 7BS . . . E 4 30.61 -15.519 56.808 1 77.43 ? C10 7BS 1004 A 1 HETATM 28 C C11 7BS . . . E 4 31.08 -15.961 57.982 1 80.52 ? C11 7BS 1004 A 1 HETATM 29 C C12 7BS . . . E 4 31.198 -17.401 58.3 1 77.73 ? C12 7BS 1004 A 1 HETATM 30 C C13 7BS . . . E 4 31.727 -17.874 59.438 1 76.77 ? C13 7BS 1004 A 1 HETATM 31 C C14 7BS . . . E 4 31.839 -19.351 59.75 1 80.03 ? C14 7BS 1004 A 1 HETATM 32 C C15 7BS . . . E 4 31.515 -19.671 61.236 1 78 ? C15 7BS 1004 A 1 HETATM 33 C C19 7BS . . . E 4 31.72 -21.178 61.544 1 61.54 ? C19 7BS 1004 A 1 HETATM 34 C C16 7BS . . . E 4 30.068 -19.311 61.49 1 76.28 ? C16 7BS 1004 A 1 HETATM 35 C C17 7BS . . . E 4 29.554 -18.459 62.397 1 76.39 ? C17 7BS 1004 A 1 HETATM 36 C C18 7BS . . . E 4 30.356 -17.66 63.413 1 76.86 ? C18 7BS 1004 A 1 HETATM 37 C C4 7BS . . . E 4 29.149 -12.276 55.205 1 74.62 ? C4 7BS 1004 A 1 HETATM 38 C C1 7BS . . . E 4 29.558 -11.871 53.981 1 71.83 ? C1 7BS 1004 A 1 HETATM 39 C C3 7BS . . . E 4 29.306 -10.432 53.571 1 74.52 ? C3 7BS 1004 A 1 HETATM 40 C C2 7BS . . . E 4 30.231 -12.652 52.861 1 64.08 ? C2 7BS 1004 A 1 HETATM 41 C C5 7BS . . . E 4 30.707 -14.075 52.995 1 64.29 ? C5 7BS 1004 A 1 HETATM 42 C C6 7BS . . . E 4 31.937 -14.475 52.655 1 63.15 ? C6 7BS 1004 A 1 HETATM 43 C C7 7BS . . . E 4 32.474 -15.796 53.115 1 68.95 ? C7 7BS 1004 A 1 HETATM 44 H H1 7BS . . . E 4 27.204 -19.169 65.587 1 96.5 ? H1 7BS 1004 A 1 HETATM 45 H H2 7BS . . . E 4 28.457 -19.907 64.532 1 96.5 ? H2 7BS 1004 A 1 HETATM 46 H H3 7BS . . . E 4 26.728 -19.963 64.047 1 96.5 ? H3 7BS 1004 A 1 HETATM 47 H H4 7BS . . . E 4 27.535 -19.159 62.033 1 90.76 ? H4 7BS 1004 A 1 HETATM 48 H H5 7BS . . . E 4 28.475 -16.297 61.869 1 98.18 ? H5 7BS 1004 A 1 HETATM 49 H H6 7BS . . . E 4 27.214 -17.857 59.797 1 102.95 ? H6 7BS 1004 A 1 HETATM 50 H H7 7BS . . . E 4 26.618 -14.961 60.624 1 103.7 ? H7 7BS 1004 A 1 HETATM 51 H H9 7BS . . . E 4 27.668 -15.792 58.086 1 98.29 ? H9 7BS 1004 A 1 HETATM 52 H H10 7BS . . . E 4 25.123 -16.072 56.022 1 94.69 ? H10 7BS 1004 A 1 HETATM 53 H H11 7BS . . . E 4 27.089 -18.371 56.549 1 132.53 ? H11 7BS 1004 A 1 HETATM 54 H H12 7BS . . . E 4 28.487 -16.789 56.516 1 133.13 ? H12 7BS 1004 A 1 HETATM 55 H H13 7BS . . . E 4 26.286 -17.127 53.844 1 103.83 ? H13 7BS 1004 A 1 HETATM 56 H H14 7BS . . . E 4 29.472 -18.87 53.161 1 106.55 ? H14 7BS 1004 A 1 HETATM 57 H H15 7BS . . . E 4 29.183 -17.565 54.36 1 106.55 ? H15 7BS 1004 A 1 HETATM 58 H H16 7BS . . . E 4 28.489 -17.438 52.711 1 106.55 ? H16 7BS 1004 A 1 HETATM 59 H H17 7BS . . . E 4 25.6 -19.936 54.922 1 97.3 ? H17 7BS 1004 A 1 HETATM 60 H H18 7BS . . . E 4 25.606 -19.044 52.531 1 96.4 ? H18 7BS 1004 A 1 HETATM 61 H H19 7BS . . . E 4 23.665 -17.567 54.725 1 94.81 ? H19 7BS 1004 A 1 HETATM 62 H H20 7BS . . . E 4 22.61 -19.759 54.369 1 143.6 ? H20 7BS 1004 A 1 HETATM 63 H H21 7BS . . . E 4 22.144 -19.134 55.981 1 143.6 ? H21 7BS 1004 A 1 HETATM 64 H H22 7BS . . . E 4 22.846 -21.406 55.923 1 141.75 ? H22 7BS 1004 A 1 HETATM 65 H H23 7BS . . . E 4 26.7 -13.426 58.952 1 87.61 ? H23 7BS 1004 A 1 HETATM 66 H H24 7BS . . . E 4 25.254 -13.956 58.029 1 87.61 ? H24 7BS 1004 A 1 HETATM 67 H H25 7BS . . . E 4 28.774 -14.386 55.136 1 88.22 ? H25 7BS 1004 A 1 HETATM 68 H H26 7BS . . . E 4 30.769 -13.445 57.278 1 85.81 ? H26 7BS 1004 A 1 HETATM 69 H H27 7BS . . . E 4 31.287 -13.885 55.618 1 85.81 ? H27 7BS 1004 A 1 HETATM 70 H H28 7BS . . . E 4 30.274 -16.263 56.088 1 92.91 ? H28 7BS 1004 A 1 HETATM 71 H H29 7BS . . . E 4 31.392 -15.233 58.729 1 96.63 ? H29 7BS 1004 A 1 HETATM 72 H H30 7BS . . . E 4 30.802 -18.118 57.583 1 93.28 ? H30 7BS 1004 A 1 HETATM 73 H H31 7BS . . . E 4 32.086 -17.16 60.176 1 92.12 ? H31 7BS 1004 A 1 HETATM 74 H H32 7BS . . . E 4 32.865 -19.681 59.533 1 96.03 ? H32 7BS 1004 A 1 HETATM 75 H H33 7BS . . . E 4 31.134 -19.902 59.108 1 96.03 ? H33 7BS 1004 A 1 HETATM 76 H H34 7BS . . . E 4 32.17 -19.074 61.889 1 93.6 ? H34 7BS 1004 A 1 HETATM 77 H H35 7BS . . . E 4 31.468 -21.373 62.597 1 73.85 ? H35 7BS 1004 A 1 HETATM 78 H H36 7BS . . . E 4 32.769 -21.451 61.361 1 73.85 ? H36 7BS 1004 A 1 HETATM 79 H H37 7BS . . . E 4 31.065 -21.777 60.894 1 73.85 ? H37 7BS 1004 A 1 HETATM 80 H H38 7BS . . . E 4 29.341 -19.818 60.858 1 91.53 ? H38 7BS 1004 A 1 HETATM 81 H H39 7BS . . . E 4 31.428 -17.869 63.281 1 92.23 ? H39 7BS 1004 A 1 HETATM 82 H H40 7BS . . . E 4 30.048 -17.946 64.429 1 92.23 ? H40 7BS 1004 A 1 HETATM 83 H H41 7BS . . . E 4 30.172 -16.586 63.263 1 92.23 ? H41 7BS 1004 A 1 HETATM 84 H H42 7BS . . . E 4 28.706 -11.488 55.814 1 89.55 ? H42 7BS 1004 A 1 HETATM 85 H H43 7BS . . . E 4 28.811 -9.897 54.395 1 89.43 ? H43 7BS 1004 A 1 HETATM 86 H H44 7BS . . . E 4 28.661 -10.412 52.68 1 89.43 ? H44 7BS 1004 A 1 HETATM 87 H H45 7BS . . . E 4 30.264 -9.943 53.34 1 89.43 ? H45 7BS 1004 A 1 HETATM 88 H H46 7BS . . . E 4 31.117 -12.065 52.578 1 76.9 ? H46 7BS 1004 A 1 HETATM 89 H H47 7BS . . . E 4 29.516 -12.654 52.026 1 76.9 ? H47 7BS 1004 A 1 HETATM 90 H H48 7BS . . . E 4 30.037 -14.801 53.456 1 77.15 ? H48 7BS 1004 A 1 HETATM 91 H H49 7BS . . . E 4 32.618 -13.759 52.196 1 75.78 ? H49 7BS 1004 A 1 HETATM 92 H H50 7BS . . . E 4 33.495 -15.931 52.729 1 82.74 ? H50 7BS 1004 A 1 HETATM 93 H H51 7BS . . . E 4 31.83 -16.604 52.741 1 82.74 ? H51 7BS 1004 A 1 HETATM 94 H H52 7BS . . . E 4 32.493 -15.82 54.215 1 82.74 ? H52 7BS 1004 A 1 HETATM 95 H H53 7BS . . . E 4 26.807 -16.557 62.476 1 98.18 ? H53 7BS 1004 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 95 #