data_7DAD # _model_server_result.job_id aFNvisJN4gs9iRnVDnRRjA _model_server_result.datetime_utc '2024-11-05 08:28:26' _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 7dad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":502}' # _entry.id 7DAD # _exptl.entry_id 7DAD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 491.683 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'EPOTHILONE D' _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 7DAD _cell.length_a 105.163 _cell.length_b 158.506 _cell.length_c 181.605 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DAD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 11 _struct_asym.id V _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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc11 B OE1 GLU 111 B GLU 111 1_555 N CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc12 B OE2 GLU 111 B GLU 111 1_555 N CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc13 L O1A GDP . B GDP 501 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc14 C OD1 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc15 C OD2 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc16 C O THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc17 C OG1 THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc18 C O GLY 44 C GLY 44 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc19 C OE1 GLU 55 C GLU 55 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc20 C OE2 GLU 55 C GLU 55 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc21 R O1G GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc22 R O1B GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc23 F OE1 GLU 331 F GLU 331 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc24 F OE2 GLU 331 F GLU 331 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc25 F OD1 ASN 333 F ASN 333 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc26 W O2G ACP . F ACP 401 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc27 W O2B ACP . F ACP 401 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? # _chem_comp.formula 'C27 H41 N O5 S' _chem_comp.formula_weight 491.683 _chem_comp.id EPD _chem_comp.mon_nstd_flag . _chem_comp.name 'EPOTHILONE D' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C51 C5 EPD sing 134 n n C51 H511 EPD sing 135 n n C51 H512 EPD sing 136 n n C51 H513 EPD sing 137 n n C5 C4 EPD doub 138 z n C5 C6 EPD sing 139 n n C4 C3 EPD sing 140 n n C4 H4 EPD sing 141 n n C3 C2 EPD sing 142 n n C3 H31 EPD sing 143 n n C3 H32 EPD sing 144 n n C2 C20 EPD sing 145 n n C2 O1 EPD sing 146 n n C2 H2 EPD sing 147 n n C20 C21 EPD sing 148 n n C20 C22 EPD doub 149 e n C21 H211 EPD sing 150 n n C21 H212 EPD sing 151 n n C21 H213 EPD sing 152 n n C22 C23 EPD sing 153 n n C22 H22 EPD sing 154 n n C23 C24 EPD doub 155 n y C23 N26 EPD sing 156 n y C24 S1 EPD sing 157 n y C24 H24 EPD sing 158 n n S1 C25 EPD sing 159 n y C25 C27 EPD sing 160 n n C25 N26 EPD doub 161 n y C27 H271 EPD sing 162 n n C27 H272 EPD sing 163 n n C27 H273 EPD sing 164 n n C6 C7 EPD sing 165 n n C6 H61 EPD sing 166 n n C6 H62 EPD sing 167 n n C7 C8 EPD sing 168 n n C7 H71 EPD sing 169 n n C7 H72 EPD sing 170 n n C8 C9 EPD sing 171 n n C8 H81 EPD sing 172 n n C8 H82 EPD sing 173 n n C9 C91 EPD sing 174 n n C9 C10 EPD sing 175 n n C9 H9 EPD sing 176 n n C91 H911 EPD sing 177 n n C91 H912 EPD sing 178 n n C91 H913 EPD sing 179 n n C10 O10 EPD sing 180 n n C10 C11 EPD sing 181 n n C10 H10 EPD sing 182 n n O10 H3 EPD sing 183 n n C11 C28 EPD sing 184 n n C11 C12 EPD sing 185 n n C11 H11 EPD sing 186 n n C28 H281 EPD sing 187 n n C28 H282 EPD sing 188 n n C28 H283 EPD sing 189 n n C12 O12 EPD doub 190 n n C12 C13 EPD sing 191 n n C13 C30 EPD sing 192 n n C13 C29 EPD sing 193 n n C13 C14 EPD sing 194 n n C30 H301 EPD sing 195 n n C30 H302 EPD sing 196 n n C30 H303 EPD sing 197 n n C29 H291 EPD sing 198 n n C29 H292 EPD sing 199 n n C29 H293 EPD sing 200 n n C14 O14 EPD sing 201 n n C14 C15 EPD sing 202 n n C14 H14 EPD sing 203 n n O14 H1 EPD sing 204 n n C15 C16 EPD sing 205 n n C15 H151 EPD sing 206 n n C15 H152 EPD sing 207 n n C16 O16 EPD doub 208 n n C16 O1 EPD sing 209 n n # _atom_sites.entry_id 7DAD _atom_sites.fract_transf_matrix[1][1] 0.009509 _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] 0.006309 _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] 0.005506 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 CL A 1 504 504 CL CL . K 7 CA A 1 505 505 CA CA . L 9 GDP B 1 501 499 GDP GDP . M 6 MG B 1 502 500 MG MG . N 7 CA B 1 503 501 CA CA . O 10 MES B 1 504 502 MES MES . P 10 MES B 1 505 503 MES MES . Q 6 MG B 1 506 504 MG MG . R 5 GTP C 1 501 501 GTP GTP . S 6 MG C 1 502 502 MG MG . T 7 CA C 1 503 503 CA CA . U 5 GTP D 1 501 499 GTP GTP . V 11 EPD D 1 502 1 EPD EPD . W 12 ACP F 1 401 703 ACP ACP . X 6 MG F 1 402 1 MG MG . # 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 C51 EPD . . . V 11 3.538 -1.952 -36.175 1 86.21 ? C51 EPD 502 D 1 HETATM 2 C C5 EPD . . . V 11 2.18 -1.912 -36.877 1 88.95 ? C5 EPD 502 D 1 HETATM 3 C C4 EPD . . . V 11 1.005 -1.143 -36.19 1 88.06 ? C4 EPD 502 D 1 HETATM 4 C C3 EPD . . . V 11 -0.311 -1.148 -36.921 1 84.46 ? C3 EPD 502 D 1 HETATM 5 C C2 EPD . . . V 11 -1.172 -2.25 -36.307 1 87.24 ? C2 EPD 502 D 1 HETATM 6 C C20 EPD . . . V 11 -2.517 -1.627 -36.017 1 83.18 ? C20 EPD 502 D 1 HETATM 7 C C21 EPD . . . V 11 -3.137 -0.77 -37.096 1 85.47 ? C21 EPD 502 D 1 HETATM 8 C C22 EPD . . . V 11 -3.065 -1.892 -34.844 1 80.62 ? C22 EPD 502 D 1 HETATM 9 C C23 EPD . . . V 11 -4.428 -1.435 -34.316 1 83.9 ? C23 EPD 502 D 1 HETATM 10 C C24 EPD . . . V 11 -5.301 -0.348 -34.765 1 86.73 ? C24 EPD 502 D 1 HETATM 11 S S1 EPD . . . V 11 -6.532 -0.35 -33.849 1 88.68 ? S1 EPD 502 D 1 HETATM 12 C C25 EPD . . . V 11 -6.385 -1.551 -32.922 1 72.82 ? C25 EPD 502 D 1 HETATM 13 C C27 EPD . . . V 11 -7.397 -1.976 -31.901 1 88.32 ? C27 EPD 502 D 1 HETATM 14 N N26 EPD . . . V 11 -5.156 -2.168 -33.156 1 74.58 ? N26 EPD 502 D 1 HETATM 15 C C6 EPD . . . V 11 1.968 -2.576 -38.243 1 87.08 ? C6 EPD 502 D 1 HETATM 16 C C7 EPD . . . V 11 2.373 -4.051 -38.177 1 77.5 ? C7 EPD 502 D 1 HETATM 17 C C8 EPD . . . V 11 2.345 -4.59 -39.595 1 82.07 ? C8 EPD 502 D 1 HETATM 18 C C9 EPD . . . V 11 2.096 -6.09 -39.57 1 80.81 ? C9 EPD 502 D 1 HETATM 19 C C91 EPD . . . V 11 3.314 -6.805 -38.994 1 67.59 ? C91 EPD 502 D 1 HETATM 20 C C10 EPD . . . V 11 1.86 -6.609 -40.996 1 81.58 ? C10 EPD 502 D 1 HETATM 21 O O10 EPD . . . V 11 2.658 -5.868 -41.881 1 80.03 ? O10 EPD 502 D 1 HETATM 22 C C11 EPD . . . V 11 0.397 -6.5 -41.431 1 87.65 ? C11 EPD 502 D 1 HETATM 23 C C28 EPD . . . V 11 0.306 -7.251 -42.76 1 89.19 ? C28 EPD 502 D 1 HETATM 24 C C12 EPD . . . V 11 -0.581 -7.115 -40.406 1 76.38 ? C12 EPD 502 D 1 HETATM 25 O O12 EPD . . . V 11 -0.403 -8.176 -39.897 1 77.51 ? O12 EPD 502 D 1 HETATM 26 C C13 EPD . . . V 11 -1.834 -6.27 -40.085 1 82.86 ? C13 EPD 502 D 1 HETATM 27 C C30 EPD . . . V 11 -2.914 -7.205 -39.527 1 82.14 ? C30 EPD 502 D 1 HETATM 28 C C29 EPD . . . V 11 -2.405 -5.573 -41.32 1 86.31 ? C29 EPD 502 D 1 HETATM 29 C C14 EPD . . . V 11 -1.488 -5.173 -39.077 1 83.23 ? C14 EPD 502 D 1 HETATM 30 O O14 EPD . . . V 11 -2.335 -4.073 -39.339 1 79.26 ? O14 EPD 502 D 1 HETATM 31 C C15 EPD . . . V 11 -1.612 -5.708 -37.643 1 83.46 ? C15 EPD 502 D 1 HETATM 32 C C16 EPD . . . V 11 -1.452 -4.584 -36.599 1 79.97 ? C16 EPD 502 D 1 HETATM 33 O O16 EPD . . . V 11 -1.391 -4.766 -35.425 1 69.16 ? O16 EPD 502 D 1 HETATM 34 O O1 EPD . . . V 11 -1.378 -3.297 -37.213 1 103.64 ? O1 EPD 502 D 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 34 #