data_5Y5E # _model_server_result.job_id zhSOln4_H9DouX08VXHXwA _model_server_result.datetime_utc '2024-11-27 02:18:40' _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 5y5e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":209}' # _entry.id 5Y5E # _exptl.entry_id 5Y5E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 282.334 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL _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 5Y5E _cell.length_a 48.726 _cell.length_b 61.063 _cell.length_c 63.356 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y5E _symmetry.cell_setting ? _symmetry.Int_Tables_number 17 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 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,H,I,J,K,L _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 6 _struct_asym.id J _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 25 A CYS 25 1_555 A SG CYS 116 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 27 A CYS 27 1_555 A SG CYS 43 A CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 A SG CYS 42 A CYS 42 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 A SG CYS 48 A CYS 48 1_555 A SG CYS 123 A CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 49 A CYS 49 1_555 A SG CYS 89 A CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 A SG CYS 58 A CYS 58 1_555 A SG CYS 82 A CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf7 A SG CYS 76 A CYS 76 1_555 A SG CYS 87 A CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc1 A O TYR 26 A TYR 26 1_555 I CA CA . A CA 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc2 A O GLY 28 A GLY 28 1_555 I CA CA . A CA 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 A O GLY 30 A GLY 30 1_555 I CA CA . A CA 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc4 A OD1 ASP 47 A ASP 47 1_555 I CA CA . A CA 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc5 A OD2 ASP 47 A ASP 47 1_555 I CA CA . A CA 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc6 A OG1 THR 81 A THR 81 1_555 K NA NA . A NA 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc7 C OAO 7W3 . A 7W3 202 1_555 I CA CA . A CA 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc8 C OAT 7W3 . A 7W3 202 1_555 I CA CA . A CA 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc9 K NA NA . A NA 210 1_555 L O HOH . A HOH 421 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? # _chem_comp.formula 'C11 H26 N2 O6' _chem_comp.formula_weight 282.334 _chem_comp.id B3P _chem_comp.mon_nstd_flag . _chem_comp.name 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL _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 C1 C2 B3P sing 120 n n C1 C3 B3P sing 121 n n C1 H11 B3P sing 122 n n C1 H12 B3P sing 123 n n C2 N2 B3P sing 124 n n C2 H21 B3P sing 125 n n C2 H22 B3P sing 126 n n C3 N1 B3P sing 127 n n C3 H31 B3P sing 128 n n C3 H32 B3P sing 129 n n N1 C4 B3P sing 130 n n N1 HN1 B3P sing 131 n n C4 C5 B3P sing 132 n n C4 C6 B3P sing 133 n n C4 C7 B3P sing 134 n n C5 O4 B3P sing 135 n n C5 H51 B3P sing 136 n n C5 H52 B3P sing 137 n n C6 O5 B3P sing 138 n n C6 H61 B3P sing 139 n n C6 H62 B3P sing 140 n n C7 O6 B3P sing 141 n n C7 H71 B3P sing 142 n n C7 H72 B3P sing 143 n n N2 C8 B3P sing 144 n n N2 HN2 B3P sing 145 n n C8 C9 B3P sing 146 n n C8 C10 B3P sing 147 n n C8 C11 B3P sing 148 n n C9 O1 B3P sing 149 n n C9 H91 B3P sing 150 n n C9 H92 B3P sing 151 n n C10 O2 B3P sing 152 n n C10 H101 B3P sing 153 n n C10 H102 B3P sing 154 n n C11 O3 B3P sing 155 n n C11 H111 B3P sing 156 n n C11 H112 B3P sing 157 n n O1 HO1 B3P sing 158 n n O2 HO2 B3P sing 159 n n O3 HO3 B3P sing 160 n n O4 HO4 B3P sing 161 n n O5 HO5 B3P sing 162 n n O6 HO6 B3P sing 163 n n # _atom_sites.entry_id 5Y5E _atom_sites.fract_transf_matrix[1][1] 0.020523 _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] 0.016377 _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] 0.015784 _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 GOL A 1 201 1 GOL GOL . C 3 7W3 A 1 202 1 7W3 DRG . D 4 CL A 1 203 1 CL CL . E 4 CL A 1 204 2 CL CL . F 4 CL A 1 205 3 CL CL . G 4 CL A 1 206 4 CL CL . H 4 CL A 1 207 5 CL CL . I 5 CA A 1 208 1 CA CA . J 6 B3P A 1 209 1 B3P B3P . K 7 NA A 1 210 1 NA NA . L 8 HOH A 1 301 63 HOH HOH . L 8 HOH A 2 302 68 HOH HOH . L 8 HOH A 3 303 64 HOH HOH . L 8 HOH A 4 304 96 HOH HOH . L 8 HOH A 5 305 82 HOH HOH . L 8 HOH A 6 306 28 HOH HOH . L 8 HOH A 7 307 88 HOH HOH . L 8 HOH A 8 308 75 HOH HOH . L 8 HOH A 9 309 120 HOH HOH . L 8 HOH A 10 310 103 HOH HOH . L 8 HOH A 11 311 80 HOH HOH . L 8 HOH A 12 312 24 HOH HOH . L 8 HOH A 13 313 131 HOH HOH . L 8 HOH A 14 314 35 HOH HOH . L 8 HOH A 15 315 56 HOH HOH . L 8 HOH A 16 316 140 HOH HOH . L 8 HOH A 17 317 44 HOH HOH . L 8 HOH A 18 318 76 HOH HOH . L 8 HOH A 19 319 94 HOH HOH . L 8 HOH A 20 320 57 HOH HOH . L 8 HOH A 21 321 58 HOH HOH . L 8 HOH A 22 322 14 HOH HOH . L 8 HOH A 23 323 29 HOH HOH . L 8 HOH A 24 324 134 HOH HOH . L 8 HOH A 25 325 3 HOH HOH . L 8 HOH A 26 326 10 HOH HOH . L 8 HOH A 27 327 77 HOH HOH . L 8 HOH A 28 328 74 HOH HOH . L 8 HOH A 29 329 90 HOH HOH . L 8 HOH A 30 330 1 HOH HOH . L 8 HOH A 31 331 37 HOH HOH . L 8 HOH A 32 332 101 HOH HOH . L 8 HOH A 33 333 59 HOH HOH . L 8 HOH A 34 334 81 HOH HOH . L 8 HOH A 35 335 8 HOH HOH . L 8 HOH A 36 336 67 HOH HOH . L 8 HOH A 37 337 34 HOH HOH . L 8 HOH A 38 338 98 HOH HOH . L 8 HOH A 39 339 111 HOH HOH . L 8 HOH A 40 340 49 HOH HOH . L 8 HOH A 41 341 95 HOH HOH . L 8 HOH A 42 342 2 HOH HOH . L 8 HOH A 43 343 60 HOH HOH . L 8 HOH A 44 344 85 HOH HOH . L 8 HOH A 45 345 42 HOH HOH . L 8 HOH A 46 346 137 HOH HOH . L 8 HOH A 47 347 135 HOH HOH . L 8 HOH A 48 348 25 HOH HOH . L 8 HOH A 49 349 83 HOH HOH . L 8 HOH A 50 350 138 HOH HOH . L 8 HOH A 51 351 109 HOH HOH . L 8 HOH A 52 352 105 HOH HOH . L 8 HOH A 53 353 32 HOH HOH . L 8 HOH A 54 354 110 HOH HOH . L 8 HOH A 55 355 116 HOH HOH . L 8 HOH A 56 356 97 HOH HOH . L 8 HOH A 57 357 69 HOH HOH . L 8 HOH A 58 358 20 HOH HOH . L 8 HOH A 59 359 47 HOH HOH . L 8 HOH A 60 360 6 HOH HOH . L 8 HOH A 61 361 78 HOH HOH . L 8 HOH A 62 362 18 HOH HOH . L 8 HOH A 63 363 133 HOH HOH . L 8 HOH A 64 364 62 HOH HOH . L 8 HOH A 65 365 48 HOH HOH . L 8 HOH A 66 366 26 HOH HOH . L 8 HOH A 67 367 72 HOH HOH . L 8 HOH A 68 368 43 HOH HOH . L 8 HOH A 69 369 5 HOH HOH . L 8 HOH A 70 370 33 HOH HOH . L 8 HOH A 71 371 11 HOH HOH . L 8 HOH A 72 372 12 HOH HOH . L 8 HOH A 73 373 129 HOH HOH . L 8 HOH A 74 374 107 HOH HOH . L 8 HOH A 75 375 21 HOH HOH . L 8 HOH A 76 376 22 HOH HOH . L 8 HOH A 77 377 15 HOH HOH . L 8 HOH A 78 378 7 HOH HOH . L 8 HOH A 79 379 31 HOH HOH . L 8 HOH A 80 380 4 HOH HOH . L 8 HOH A 81 381 79 HOH HOH . L 8 HOH A 82 382 106 HOH HOH . L 8 HOH A 83 383 144 HOH HOH . L 8 HOH A 84 384 114 HOH HOH . L 8 HOH A 85 385 61 HOH HOH . L 8 HOH A 86 386 51 HOH HOH . L 8 HOH A 87 387 92 HOH HOH . L 8 HOH A 88 388 9 HOH HOH . L 8 HOH A 89 389 52 HOH HOH . L 8 HOH A 90 390 38 HOH HOH . L 8 HOH A 91 391 17 HOH HOH . L 8 HOH A 92 392 71 HOH HOH . L 8 HOH A 93 393 66 HOH HOH . L 8 HOH A 94 394 19 HOH HOH . L 8 HOH A 95 395 93 HOH HOH . L 8 HOH A 96 396 117 HOH HOH . L 8 HOH A 97 397 46 HOH HOH . L 8 HOH A 98 398 27 HOH HOH . L 8 HOH A 99 399 23 HOH HOH . L 8 HOH A 100 400 132 HOH HOH . L 8 HOH A 101 401 45 HOH HOH . L 8 HOH A 102 402 126 HOH HOH . L 8 HOH A 103 403 40 HOH HOH . L 8 HOH A 104 404 112 HOH HOH . L 8 HOH A 105 405 91 HOH HOH . L 8 HOH A 106 406 104 HOH HOH . L 8 HOH A 107 407 73 HOH HOH . L 8 HOH A 108 408 65 HOH HOH . L 8 HOH A 109 409 102 HOH HOH . L 8 HOH A 110 410 13 HOH HOH . L 8 HOH A 111 411 119 HOH HOH . L 8 HOH A 112 412 41 HOH HOH . L 8 HOH A 113 413 53 HOH HOH . L 8 HOH A 114 414 113 HOH HOH . L 8 HOH A 115 415 100 HOH HOH . L 8 HOH A 116 416 118 HOH HOH . L 8 HOH A 117 417 125 HOH HOH . L 8 HOH A 118 418 121 HOH HOH . L 8 HOH A 119 419 115 HOH HOH . L 8 HOH A 120 420 128 HOH HOH . L 8 HOH A 121 421 30 HOH HOH . L 8 HOH A 122 422 139 HOH HOH . L 8 HOH A 123 423 143 HOH HOH . L 8 HOH A 124 424 122 HOH HOH . L 8 HOH A 125 425 36 HOH HOH . L 8 HOH A 126 426 54 HOH HOH . L 8 HOH A 127 427 99 HOH HOH . L 8 HOH A 128 428 89 HOH HOH . L 8 HOH A 129 429 70 HOH HOH . L 8 HOH A 130 430 124 HOH HOH . L 8 HOH A 131 431 55 HOH HOH . L 8 HOH A 132 432 108 HOH HOH . L 8 HOH A 133 433 16 HOH HOH . L 8 HOH A 134 434 87 HOH HOH . L 8 HOH A 135 435 50 HOH HOH . L 8 HOH A 136 436 39 HOH HOH . L 8 HOH A 137 437 130 HOH HOH . L 8 HOH A 138 438 142 HOH HOH . L 8 HOH A 139 439 123 HOH HOH . L 8 HOH A 140 440 127 HOH HOH . L 8 HOH A 141 441 86 HOH HOH . L 8 HOH A 142 442 141 HOH HOH . L 8 HOH A 143 443 136 HOH HOH . L 8 HOH A 144 444 84 HOH HOH . # 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 C1 B3P . . . J 6 -0.433 -19.876 -0.064 0.5 30.99 ? C1 B3P 209 A 1 HETATM 2 C C2 B3P . . . J 6 -0.618 -19.243 -1.449 0.5 31.24 ? C2 B3P 209 A 1 HETATM 3 C C3 B3P . . . J 6 0.73 -19.243 0.714 0.5 30.5 ? C3 B3P 209 A 1 HETATM 4 N N1 B3P . . . J 6 0.896 -17.826 0.393 0.5 29.32 ? N1 B3P 209 A 1 HETATM 5 C C4 B3P . . . J 6 0.672 -16.719 1.328 0.5 26.99 ? C4 B3P 209 A 1 HETATM 6 C C5 B3P . . . J 6 -0.752 -16.124 1.203 0.5 26.07 ? C5 B3P 209 A 1 HETATM 7 C C6 B3P . . . J 6 1.001 -17.177 2.75 0.5 27.98 ? C6 B3P 209 A 1 HETATM 8 C C7 B3P . . . J 6 1.67 -15.651 0.913 0.5 27.01 ? C7 B3P 209 A 1 HETATM 9 N N2 B3P . . . J 6 -1.219 -17.919 -1.338 0.5 30.97 ? N2 B3P 209 A 1 HETATM 10 C C8 B3P . . . J 6 -0.853 -16.782 -2.171 0.5 28.86 ? C8 B3P 209 A 1 HETATM 11 C C9 B3P . . . J 6 0.603 -16.324 -1.96 0.5 29.17 ? C9 B3P 209 A 1 HETATM 12 C C10 B3P . . . J 6 -1.783 -15.684 -1.691 0.5 30.36 ? C10 B3P 209 A 1 HETATM 13 C C11 B3P . . . J 6 -1.172 -17.154 -3.629 0.5 30.12 ? C11 B3P 209 A 1 HETATM 14 O O1 B3P . . . J 6 0.824 -14.877 -1.898 0.5 24.62 ? O1 B3P 209 A 1 HETATM 15 O O2 B3P . . . J 6 -2.732 -16.15 -0.715 0.5 28.52 ? O2 B3P 209 A 1 HETATM 16 O O3 B3P . . . J 6 -0.247 -16.648 -4.626 0.5 28.45 ? O3 B3P 209 A 1 HETATM 17 O O4 B3P . . . J 6 -0.907 -14.75 1.664 0.5 21.13 ? O4 B3P 209 A 1 HETATM 18 O O5 B3P . . . J 6 -0.044 -16.855 3.687 0.5 31.33 ? O5 B3P 209 A 1 HETATM 19 O O6 B3P . . . J 6 2.575 -16.078 -0.113 0.5 25.17 ? O6 B3P 209 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 19 #