data_1D6V # _model_server_result.job_id axwdbLg8y8VATsozEOOxTQ _model_server_result.datetime_utc '2024-10-11 01:22:06' _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 1d6v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 1D6V # _exptl.entry_id 1D6V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.465 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL _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 99.09 _cell.angle_gamma 90 _cell.entry_id 1D6V _cell.length_a 52.718 _cell.length_b 64.446 _cell.length_c 73.87 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D6V _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 G _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 23 L CYS 23 1_555 A SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? disulf ? disulf2 A SG CYS 134 L CYS 134 1_555 A SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf4 B SG CYS 147 H CYS 140 1_555 B SG CYS 203 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc1 A OE1 GLU 79 L GLU 79 1_555 C CD CD . L CD 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.149 ? metalc ? metalc2 A OE2 GLU 79 L GLU 79 1_555 C CD CD . L CD 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc3 A OE2 GLU 81 L GLU 81 1_555 F CD CD . L CD 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc4 A OE1 GLU 81 L GLU 81 1_555 F CD CD . L CD 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc5 A OD1 ASN 138 L ASN 138 1_555 D CD CD . L CD 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc6 C CD CD . L CD 501 1_555 H O HOH . L HOH 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc7 D CD CD . L CD 502 1_555 H O HOH . L HOH 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc8 D CD CD . L CD 502 1_555 B NE2 HIS 171 H HIS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc9 E CD CD . L CD 503 1_555 H O HOH . L HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc10 E CD CD . L CD 503 1_555 H O HOH . L HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc11 F CD CD . L CD 504 1_555 H O HOH . L HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc12 F CD CD . L CD 504 1_555 H O HOH . L HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? # _chem_comp.formula 'C23 H27 N O4' _chem_comp.formula_weight 381.465 _chem_comp.id HOP _chem_comp.mon_nstd_flag . _chem_comp.name (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms OXY-COPE-HAPTEN # 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 HOP sing 152 n y C1 C6 HOP doub 153 n y C1 H1 HOP sing 154 n n C2 C3 HOP doub 155 n y C2 H2 HOP sing 156 n n C6 C5 HOP sing 157 n y C6 H6 HOP sing 158 n n C5 C4 HOP doub 159 n y C5 H5 HOP sing 160 n n C4 C3 HOP sing 161 n y C4 C7 HOP sing 162 n n C3 H3 HOP sing 163 n n C7 C12 HOP sing 164 n n C7 C8 HOP sing 165 n n C7 H7 HOP sing 166 n n C12 C11 HOP sing 167 n n C12 H121 HOP sing 168 n n C12 H122 HOP sing 169 n n C11 C10 HOP sing 170 n n C11 O19 HOP sing 171 n n C11 H11 HOP sing 172 n n C10 C9 HOP sing 173 n n C10 C13 HOP sing 174 n n C10 H10 HOP sing 175 n n C9 C8 HOP sing 176 n n C9 H91 HOP sing 177 n n C9 H92 HOP sing 178 n n C8 H81 HOP sing 179 n n C8 H82 HOP sing 180 n n C13 C14 HOP doub 181 n y C13 C18 HOP sing 182 n y C14 C15 HOP sing 183 n y C14 H14 HOP sing 184 n n C15 C16 HOP doub 185 n y C15 H15 HOP sing 186 n n C16 C17 HOP sing 187 n y C16 C20 HOP sing 188 n n C17 C18 HOP doub 189 n y C17 H17 HOP sing 190 n n C18 H18 HOP sing 191 n n O19 HO9 HOP sing 192 n n C20 O21 HOP doub 193 n n C20 N22 HOP sing 194 n n N22 C23 HOP sing 195 n n N22 HN2 HOP sing 196 n n C23 C24 HOP sing 197 n n C23 H231 HOP sing 198 n n C23 H232 HOP sing 199 n n C24 C25 HOP sing 200 n n C24 H241 HOP sing 201 n n C24 H242 HOP sing 202 n n C25 C26 HOP sing 203 n n C25 H251 HOP sing 204 n n C25 H252 HOP sing 205 n n C26 O27 HOP doub 206 n n C26 O28 HOP sing 207 n n O28 HO8 HOP sing 208 n n # _atom_sites.entry_id 1D6V _atom_sites.fract_transf_matrix[1][1] 0.018969 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003035 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015517 _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] 0.013709 _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 C 3 CD L 1 501 501 CD CD . D 3 CD L 1 502 502 CD CD . E 3 CD L 1 503 503 CD CD . F 3 CD L 1 504 504 CD CD . G 4 HOP H 1 401 401 HOP HOP . H 5 HOH L 1 505 1 HOH HOH . H 5 HOH L 2 506 2 HOH HOH . H 5 HOH L 3 507 3 HOH HOH . H 5 HOH L 4 508 4 HOH HOH . H 5 HOH L 5 509 7 HOH HOH . H 5 HOH L 6 510 11 HOH HOH . H 5 HOH L 7 511 13 HOH HOH . H 5 HOH L 8 512 14 HOH HOH . H 5 HOH L 9 513 15 HOH HOH . H 5 HOH L 10 514 16 HOH HOH . H 5 HOH L 11 515 17 HOH HOH . H 5 HOH L 12 516 19 HOH HOH . H 5 HOH L 13 517 21 HOH HOH . H 5 HOH L 14 518 22 HOH HOH . H 5 HOH L 15 519 24 HOH HOH . H 5 HOH L 16 520 25 HOH HOH . H 5 HOH L 17 521 27 HOH HOH . H 5 HOH L 18 522 31 HOH HOH . H 5 HOH L 19 523 32 HOH HOH . H 5 HOH L 20 524 34 HOH HOH . H 5 HOH L 21 525 35 HOH HOH . H 5 HOH L 22 526 36 HOH HOH . H 5 HOH L 23 527 38 HOH HOH . H 5 HOH L 24 528 39 HOH HOH . H 5 HOH L 25 529 40 HOH HOH . H 5 HOH L 26 530 41 HOH HOH . H 5 HOH L 27 531 43 HOH HOH . H 5 HOH L 28 532 45 HOH HOH . H 5 HOH L 29 533 46 HOH HOH . H 5 HOH L 30 534 48 HOH HOH . H 5 HOH L 31 535 49 HOH HOH . H 5 HOH L 32 536 50 HOH HOH . H 5 HOH L 33 537 52 HOH HOH . H 5 HOH L 34 538 54 HOH HOH . H 5 HOH L 35 539 55 HOH HOH . H 5 HOH L 36 540 57 HOH HOH . H 5 HOH L 37 541 58 HOH HOH . H 5 HOH L 38 542 60 HOH HOH . H 5 HOH L 39 543 61 HOH HOH . H 5 HOH L 40 544 64 HOH HOH . H 5 HOH L 41 545 65 HOH HOH . H 5 HOH L 42 546 66 HOH HOH . H 5 HOH L 43 547 69 HOH HOH . H 5 HOH L 44 548 71 HOH HOH . H 5 HOH L 45 549 73 HOH HOH . H 5 HOH L 46 550 75 HOH HOH . H 5 HOH L 47 551 78 HOH HOH . H 5 HOH L 48 552 81 HOH HOH . H 5 HOH L 49 553 82 HOH HOH . H 5 HOH L 50 554 84 HOH HOH . H 5 HOH L 51 555 85 HOH HOH . H 5 HOH L 52 556 86 HOH HOH . H 5 HOH L 53 557 87 HOH HOH . H 5 HOH L 54 558 89 HOH HOH . H 5 HOH L 55 559 90 HOH HOH . H 5 HOH L 56 560 93 HOH HOH . H 5 HOH L 57 561 94 HOH HOH . H 5 HOH L 58 562 95 HOH HOH . H 5 HOH L 59 563 97 HOH HOH . H 5 HOH L 60 564 98 HOH HOH . H 5 HOH L 61 565 100 HOH HOH . H 5 HOH L 62 566 101 HOH HOH . H 5 HOH L 63 567 104 HOH HOH . H 5 HOH L 64 568 107 HOH HOH . H 5 HOH L 65 569 110 HOH HOH . H 5 HOH L 66 570 111 HOH HOH . H 5 HOH L 67 571 112 HOH HOH . H 5 HOH L 68 572 114 HOH HOH . H 5 HOH L 69 573 118 HOH HOH . H 5 HOH L 70 574 120 HOH HOH . H 5 HOH L 71 575 121 HOH HOH . H 5 HOH L 72 576 125 HOH HOH . H 5 HOH L 73 577 127 HOH HOH . H 5 HOH L 74 578 130 HOH HOH . H 5 HOH L 75 579 131 HOH HOH . H 5 HOH L 76 580 132 HOH HOH . H 5 HOH L 77 581 134 HOH HOH . H 5 HOH L 78 582 136 HOH HOH . H 5 HOH L 79 583 138 HOH HOH . H 5 HOH L 80 584 139 HOH HOH . H 5 HOH L 81 585 141 HOH HOH . H 5 HOH L 82 586 142 HOH HOH . I 5 HOH H 1 402 5 HOH HOH . I 5 HOH H 2 403 6 HOH HOH . I 5 HOH H 3 404 8 HOH HOH . I 5 HOH H 4 405 10 HOH HOH . I 5 HOH H 5 406 12 HOH HOH . I 5 HOH H 6 407 18 HOH HOH . I 5 HOH H 7 408 20 HOH HOH . I 5 HOH H 8 409 23 HOH HOH . I 5 HOH H 9 410 26 HOH HOH . I 5 HOH H 10 411 28 HOH HOH . I 5 HOH H 11 412 29 HOH HOH . I 5 HOH H 12 413 30 HOH HOH . I 5 HOH H 13 414 33 HOH HOH . I 5 HOH H 14 415 42 HOH HOH . I 5 HOH H 15 416 44 HOH HOH . I 5 HOH H 16 417 47 HOH HOH . I 5 HOH H 17 418 51 HOH HOH . I 5 HOH H 18 419 53 HOH HOH . I 5 HOH H 19 420 56 HOH HOH . I 5 HOH H 20 421 59 HOH HOH . I 5 HOH H 21 422 62 HOH HOH . I 5 HOH H 22 423 63 HOH HOH . I 5 HOH H 23 424 67 HOH HOH . I 5 HOH H 24 425 68 HOH HOH . I 5 HOH H 25 426 70 HOH HOH . I 5 HOH H 26 427 72 HOH HOH . I 5 HOH H 27 428 74 HOH HOH . I 5 HOH H 28 429 76 HOH HOH . I 5 HOH H 29 430 77 HOH HOH . I 5 HOH H 30 431 79 HOH HOH . I 5 HOH H 31 432 80 HOH HOH . I 5 HOH H 32 433 83 HOH HOH . I 5 HOH H 33 434 88 HOH HOH . I 5 HOH H 34 435 91 HOH HOH . I 5 HOH H 35 436 92 HOH HOH . I 5 HOH H 36 437 96 HOH HOH . I 5 HOH H 37 438 99 HOH HOH . I 5 HOH H 38 439 102 HOH HOH . I 5 HOH H 39 440 103 HOH HOH . I 5 HOH H 40 441 105 HOH HOH . I 5 HOH H 41 442 106 HOH HOH . I 5 HOH H 42 443 108 HOH HOH . I 5 HOH H 43 444 109 HOH HOH . I 5 HOH H 44 445 113 HOH HOH . I 5 HOH H 45 446 115 HOH HOH . I 5 HOH H 46 447 116 HOH HOH . I 5 HOH H 47 448 117 HOH HOH . I 5 HOH H 48 449 119 HOH HOH . I 5 HOH H 49 450 122 HOH HOH . I 5 HOH H 50 451 123 HOH HOH . I 5 HOH H 51 452 124 HOH HOH . I 5 HOH H 52 453 126 HOH HOH . I 5 HOH H 53 454 129 HOH HOH . I 5 HOH H 54 455 133 HOH HOH . I 5 HOH H 55 456 135 HOH HOH . I 5 HOH H 56 457 137 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 HOP . . . G 4 11.294 8.147 0.644 1 67.96 ? C1 HOP 401 H 1 HETATM 2 C C2 HOP . . . G 4 10.258 7.514 -0.112 1 68.27 ? C2 HOP 401 H 1 HETATM 3 C C6 HOP . . . G 4 11.812 9.403 0.235 1 68.32 ? C6 HOP 401 H 1 HETATM 4 C C5 HOP . . . G 4 11.305 10.042 -0.93 1 69.74 ? C5 HOP 401 H 1 HETATM 5 C C4 HOP . . . G 4 10.26 9.419 -1.704 1 69.33 ? C4 HOP 401 H 1 HETATM 6 C C3 HOP . . . G 4 9.749 8.145 -1.279 1 69.51 ? C3 HOP 401 H 1 HETATM 7 C C7 HOP . . . G 4 9.71 10.084 -2.986 1 69 ? C7 HOP 401 H 1 HETATM 8 C C12 HOP . . . G 4 10.798 10.891 -3.786 1 68.94 ? C12 HOP 401 H 1 HETATM 9 C C11 HOP . . . G 4 10.249 11.562 -5.069 1 68.66 ? C11 HOP 401 H 1 HETATM 10 C C10 HOP . . . G 4 9.057 12.518 -4.71 1 68.75 ? C10 HOP 401 H 1 HETATM 11 C C9 HOP . . . G 4 7.925 11.692 -3.955 1 69.1 ? C9 HOP 401 H 1 HETATM 12 C C8 HOP . . . G 4 8.476 11.008 -2.663 1 68.78 ? C8 HOP 401 H 1 HETATM 13 C C13 HOP . . . G 4 8.491 13.216 -6.01 1 69.32 ? C13 HOP 401 H 1 HETATM 14 C C14 HOP . . . G 4 9.106 14.438 -6.47 1 70.56 ? C14 HOP 401 H 1 HETATM 15 C C15 HOP . . . G 4 8.63 15.092 -7.612 1 70.15 ? C15 HOP 401 H 1 HETATM 16 C C16 HOP . . . G 4 7.515 14.56 -8.347 1 70.72 ? C16 HOP 401 H 1 HETATM 17 C C17 HOP . . . G 4 6.92 13.342 -7.894 1 69.4 ? C17 HOP 401 H 1 HETATM 18 C C18 HOP . . . G 4 7.39 12.667 -6.742 1 69.54 ? C18 HOP 401 H 1 HETATM 19 O O19 HOP . . . G 4 11.323 12.268 -5.734 1 68.4 ? O19 HOP 401 H 1 HETATM 20 C C20 HOP . . . G 4 7.03 15.263 -9.577 1 71.62 ? C20 HOP 401 H 1 HETATM 21 O O21 HOP . . . G 4 5.933 14.956 -10.062 1 70.55 ? O21 HOP 401 H 1 HETATM 22 N N22 HOP . . . G 4 7.827 16.24 -10.12 1 74.33 ? N22 HOP 401 H 1 HETATM 23 C C23 HOP . . . G 4 7.563 17.107 -11.309 1 73.31 ? C23 HOP 401 H 1 HETATM 24 C C24 HOP . . . G 4 8.63 18.245 -11.371 1 74.88 ? C24 HOP 401 H 1 HETATM 25 C C25 HOP . . . G 4 9.494 18.325 -10.086 1 77.03 ? C25 HOP 401 H 1 HETATM 26 C C26 HOP . . . G 4 10.459 19.489 -10.028 1 79.27 ? C26 HOP 401 H 1 HETATM 27 O O27 HOP . . . G 4 11.412 19.624 -10.812 1 79.39 ? O27 HOP 401 H 1 HETATM 28 O O28 HOP . . . G 4 10.159 20.366 -8.988 1 78.39 ? O28 HOP 401 H 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #