data_5DN2 # _model_server_result.job_id YLLZ00FlCcih92IvuyHWYw _model_server_result.datetime_utc '2024-10-28 02:42:43' _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 5dn2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 5DN2 # _exptl.entry_id 5DN2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.105 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4-DIETHYLENE DIOXIDE' _entity.pdbx_number_of_molecules 2 _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 5DN2 _cell.length_a 110.25 _cell.length_b 139.52 _cell.length_c 106.04 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DN2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,F,K,P 1 1 B,H,I,L 2 1 C,G,M,Q 3 1 D,E,J,N,O 4 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 J N 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 4 A CYS 277 1_555 A SG CYS 154 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 B SG CYS 4 B CYS 277 1_555 B SG CYS 154 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 C SG CYS 4 C CYS 277 1_555 C SG CYS 154 C CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf4 D SG CYS 4 D CYS 277 1_555 D SG CYS 154 D CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? # _chem_comp.formula 'C4 H8 O2' _chem_comp.formula_weight 88.105 _chem_comp.id DIO _chem_comp.mon_nstd_flag . _chem_comp.name '1,4-DIETHYLENE DIOXIDE' _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 C1' DIO sing 83 n n C1 O1 DIO sing 84 n n C1 H11 DIO sing 85 n n C1 H12 DIO sing 86 n n C2 C2' DIO sing 87 n n C2 O1 DIO sing 88 n n C2 H21 DIO sing 89 n n C2 H22 DIO sing 90 n n C1' O1' DIO sing 91 n n C1' "H1'1" DIO sing 92 n n C1' "H1'2" DIO sing 93 n n C2' O1' DIO sing 94 n n C2' "H2'1" DIO sing 95 n n C2' "H2'2" DIO sing 96 n n # _atom_sites.entry_id 5DN2 _atom_sites.fract_transf_matrix[1][1] 0.00907 _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] 0.007167 _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] 0.00943 _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 H 3 DIO B 1 501 2 DIO DIO . I 4 GOL B 1 502 1 GOL GOL . J 3 DIO D 1 501 3 DIO DIO . K 5 HOH A 1 501 231 HOH HOH . K 5 HOH A 2 502 259 HOH HOH . K 5 HOH A 3 503 224 HOH HOH . K 5 HOH A 4 504 24 HOH HOH . K 5 HOH A 5 505 158 HOH HOH . K 5 HOH A 6 506 150 HOH HOH . K 5 HOH A 7 507 61 HOH HOH . K 5 HOH A 8 508 31 HOH HOH . K 5 HOH A 9 509 101 HOH HOH . K 5 HOH A 10 510 135 HOH HOH . K 5 HOH A 11 511 8 HOH HOH . K 5 HOH A 12 512 179 HOH HOH . K 5 HOH A 13 513 199 HOH HOH . K 5 HOH A 14 514 100 HOH HOH . K 5 HOH A 15 515 72 HOH HOH . K 5 HOH A 16 516 230 HOH HOH . K 5 HOH A 17 517 10 HOH HOH . K 5 HOH A 18 518 36 HOH HOH . K 5 HOH A 19 519 153 HOH HOH . K 5 HOH A 20 520 16 HOH HOH . K 5 HOH A 21 521 120 HOH HOH . K 5 HOH A 22 522 65 HOH HOH . K 5 HOH A 23 523 159 HOH HOH . K 5 HOH A 24 524 73 HOH HOH . K 5 HOH A 25 525 6 HOH HOH . K 5 HOH A 26 526 15 HOH HOH . K 5 HOH A 27 527 68 HOH HOH . K 5 HOH A 28 528 85 HOH HOH . K 5 HOH A 29 529 107 HOH HOH . K 5 HOH A 30 530 92 HOH HOH . K 5 HOH A 31 531 227 HOH HOH . K 5 HOH A 32 532 114 HOH HOH . K 5 HOH A 33 533 258 HOH HOH . K 5 HOH A 34 534 46 HOH HOH . K 5 HOH A 35 535 244 HOH HOH . K 5 HOH A 36 536 182 HOH HOH . K 5 HOH A 37 537 67 HOH HOH . K 5 HOH A 38 538 59 HOH HOH . K 5 HOH A 39 539 242 HOH HOH . K 5 HOH A 40 540 22 HOH HOH . K 5 HOH A 41 541 2 HOH HOH . K 5 HOH A 42 542 220 HOH HOH . K 5 HOH A 43 543 74 HOH HOH . K 5 HOH A 44 544 143 HOH HOH . K 5 HOH A 45 545 60 HOH HOH . K 5 HOH A 46 546 213 HOH HOH . K 5 HOH A 47 547 5 HOH HOH . K 5 HOH A 48 548 63 HOH HOH . K 5 HOH A 49 549 216 HOH HOH . K 5 HOH A 50 550 111 HOH HOH . K 5 HOH A 51 551 253 HOH HOH . K 5 HOH A 52 552 203 HOH HOH . K 5 HOH A 53 553 4 HOH HOH . K 5 HOH A 54 554 174 HOH HOH . K 5 HOH A 55 555 144 HOH HOH . K 5 HOH A 56 556 130 HOH HOH . K 5 HOH A 57 557 161 HOH HOH . K 5 HOH A 58 558 12 HOH HOH . K 5 HOH A 59 559 160 HOH HOH . K 5 HOH A 60 560 51 HOH HOH . K 5 HOH A 61 561 76 HOH HOH . K 5 HOH A 62 562 208 HOH HOH . K 5 HOH A 63 563 172 HOH HOH . K 5 HOH A 64 564 147 HOH HOH . K 5 HOH A 65 565 265 HOH HOH . K 5 HOH A 66 566 136 HOH HOH . K 5 HOH A 67 567 193 HOH HOH . K 5 HOH A 68 568 80 HOH HOH . K 5 HOH A 69 569 126 HOH HOH . K 5 HOH A 70 570 246 HOH HOH . L 5 HOH B 1 601 207 HOH HOH . L 5 HOH B 2 602 192 HOH HOH . L 5 HOH B 3 603 177 HOH HOH . L 5 HOH B 4 604 225 HOH HOH . L 5 HOH B 5 605 94 HOH HOH . L 5 HOH B 6 606 99 HOH HOH . L 5 HOH B 7 607 121 HOH HOH . L 5 HOH B 8 608 95 HOH HOH . L 5 HOH B 9 609 267 HOH HOH . L 5 HOH B 10 610 47 HOH HOH . L 5 HOH B 11 611 89 HOH HOH . L 5 HOH B 12 612 180 HOH HOH . L 5 HOH B 13 613 212 HOH HOH . L 5 HOH B 14 614 149 HOH HOH . L 5 HOH B 15 615 45 HOH HOH . L 5 HOH B 16 616 71 HOH HOH . L 5 HOH B 17 617 98 HOH HOH . L 5 HOH B 18 618 118 HOH HOH . L 5 HOH B 19 619 53 HOH HOH . L 5 HOH B 20 620 255 HOH HOH . L 5 HOH B 21 621 66 HOH HOH . L 5 HOH B 22 622 146 HOH HOH . L 5 HOH B 23 623 210 HOH HOH . L 5 HOH B 24 624 166 HOH HOH . L 5 HOH B 25 625 90 HOH HOH . L 5 HOH B 26 626 56 HOH HOH . L 5 HOH B 27 627 23 HOH HOH . L 5 HOH B 28 628 127 HOH HOH . L 5 HOH B 29 629 196 HOH HOH . L 5 HOH B 30 630 164 HOH HOH . L 5 HOH B 31 631 33 HOH HOH . L 5 HOH B 32 632 11 HOH HOH . L 5 HOH B 33 633 19 HOH HOH . L 5 HOH B 34 634 233 HOH HOH . L 5 HOH B 35 635 30 HOH HOH . L 5 HOH B 36 636 178 HOH HOH . L 5 HOH B 37 637 132 HOH HOH . L 5 HOH B 38 638 77 HOH HOH . L 5 HOH B 39 639 140 HOH HOH . L 5 HOH B 40 640 155 HOH HOH . L 5 HOH B 41 641 165 HOH HOH . L 5 HOH B 42 642 26 HOH HOH . L 5 HOH B 43 643 91 HOH HOH . L 5 HOH B 44 644 28 HOH HOH . L 5 HOH B 45 645 137 HOH HOH . L 5 HOH B 46 646 9 HOH HOH . L 5 HOH B 47 647 44 HOH HOH . L 5 HOH B 48 648 119 HOH HOH . L 5 HOH B 49 649 254 HOH HOH . L 5 HOH B 50 650 240 HOH HOH . L 5 HOH B 51 651 129 HOH HOH . L 5 HOH B 52 652 82 HOH HOH . L 5 HOH B 53 653 1 HOH HOH . L 5 HOH B 54 654 217 HOH HOH . L 5 HOH B 55 655 32 HOH HOH . L 5 HOH B 56 656 251 HOH HOH . L 5 HOH B 57 657 261 HOH HOH . L 5 HOH B 58 658 103 HOH HOH . L 5 HOH B 59 659 131 HOH HOH . L 5 HOH B 60 660 104 HOH HOH . L 5 HOH B 61 661 209 HOH HOH . L 5 HOH B 62 662 260 HOH HOH . L 5 HOH B 63 663 64 HOH HOH . L 5 HOH B 64 664 7 HOH HOH . L 5 HOH B 65 665 145 HOH HOH . L 5 HOH B 66 666 79 HOH HOH . L 5 HOH B 67 667 128 HOH HOH . L 5 HOH B 68 668 169 HOH HOH . L 5 HOH B 69 669 215 HOH HOH . L 5 HOH B 70 670 186 HOH HOH . L 5 HOH B 71 671 238 HOH HOH . L 5 HOH B 72 672 248 HOH HOH . L 5 HOH B 73 673 116 HOH HOH . L 5 HOH B 74 674 236 HOH HOH . L 5 HOH B 75 675 170 HOH HOH . M 5 HOH C 1 501 223 HOH HOH . M 5 HOH C 2 502 105 HOH HOH . M 5 HOH C 3 503 41 HOH HOH . M 5 HOH C 4 504 229 HOH HOH . M 5 HOH C 5 505 194 HOH HOH . M 5 HOH C 6 506 58 HOH HOH . M 5 HOH C 7 507 25 HOH HOH . M 5 HOH C 8 508 204 HOH HOH . M 5 HOH C 9 509 123 HOH HOH . M 5 HOH C 10 510 27 HOH HOH . M 5 HOH C 11 511 141 HOH HOH . M 5 HOH C 12 512 62 HOH HOH . M 5 HOH C 13 513 20 HOH HOH . M 5 HOH C 14 514 110 HOH HOH . M 5 HOH C 15 515 43 HOH HOH . M 5 HOH C 16 516 3 HOH HOH . M 5 HOH C 17 517 201 HOH HOH . M 5 HOH C 18 518 154 HOH HOH . M 5 HOH C 19 519 122 HOH HOH . M 5 HOH C 20 520 87 HOH HOH . M 5 HOH C 21 521 78 HOH HOH . M 5 HOH C 22 522 34 HOH HOH . M 5 HOH C 23 523 96 HOH HOH . M 5 HOH C 24 524 205 HOH HOH . M 5 HOH C 25 525 117 HOH HOH . M 5 HOH C 26 526 168 HOH HOH . M 5 HOH C 27 527 241 HOH HOH . M 5 HOH C 28 528 134 HOH HOH . M 5 HOH C 29 529 157 HOH HOH . M 5 HOH C 30 530 247 HOH HOH . M 5 HOH C 31 531 269 HOH HOH . M 5 HOH C 32 532 83 HOH HOH . M 5 HOH C 33 533 42 HOH HOH . M 5 HOH C 34 534 55 HOH HOH . M 5 HOH C 35 535 142 HOH HOH . M 5 HOH C 36 536 115 HOH HOH . M 5 HOH C 37 537 226 HOH HOH . M 5 HOH C 38 538 38 HOH HOH . M 5 HOH C 39 539 124 HOH HOH . M 5 HOH C 40 540 257 HOH HOH . M 5 HOH C 41 541 86 HOH HOH . M 5 HOH C 42 542 112 HOH HOH . M 5 HOH C 43 543 184 HOH HOH . M 5 HOH C 44 544 17 HOH HOH . M 5 HOH C 45 545 245 HOH HOH . M 5 HOH C 46 546 113 HOH HOH . M 5 HOH C 47 547 109 HOH HOH . M 5 HOH C 48 548 190 HOH HOH . M 5 HOH C 49 549 54 HOH HOH . M 5 HOH C 50 550 93 HOH HOH . M 5 HOH C 51 551 106 HOH HOH . M 5 HOH C 52 552 40 HOH HOH . M 5 HOH C 53 553 156 HOH HOH . M 5 HOH C 54 554 48 HOH HOH . M 5 HOH C 55 555 29 HOH HOH . M 5 HOH C 56 556 239 HOH HOH . M 5 HOH C 57 557 195 HOH HOH . M 5 HOH C 58 558 138 HOH HOH . N 5 HOH D 1 601 264 HOH HOH . N 5 HOH D 2 602 266 HOH HOH . N 5 HOH D 3 603 206 HOH HOH . N 5 HOH D 4 604 243 HOH HOH . N 5 HOH D 5 605 232 HOH HOH . N 5 HOH D 6 606 263 HOH HOH . N 5 HOH D 7 607 125 HOH HOH . N 5 HOH D 8 608 218 HOH HOH . N 5 HOH D 9 609 39 HOH HOH . N 5 HOH D 10 610 139 HOH HOH . N 5 HOH D 11 611 52 HOH HOH . N 5 HOH D 12 612 214 HOH HOH . N 5 HOH D 13 613 237 HOH HOH . N 5 HOH D 14 614 57 HOH HOH . N 5 HOH D 15 615 202 HOH HOH . N 5 HOH D 16 616 163 HOH HOH . N 5 HOH D 17 617 211 HOH HOH . N 5 HOH D 18 618 21 HOH HOH . N 5 HOH D 19 619 102 HOH HOH . N 5 HOH D 20 620 84 HOH HOH . N 5 HOH D 21 621 176 HOH HOH . N 5 HOH D 22 622 197 HOH HOH . N 5 HOH D 23 623 81 HOH HOH . N 5 HOH D 24 624 75 HOH HOH . N 5 HOH D 25 625 200 HOH HOH . N 5 HOH D 26 626 13 HOH HOH . N 5 HOH D 27 627 69 HOH HOH . N 5 HOH D 28 628 108 HOH HOH . N 5 HOH D 29 629 187 HOH HOH . N 5 HOH D 30 630 18 HOH HOH . N 5 HOH D 31 631 181 HOH HOH . N 5 HOH D 32 632 49 HOH HOH . N 5 HOH D 33 633 183 HOH HOH . N 5 HOH D 34 634 175 HOH HOH . N 5 HOH D 35 635 167 HOH HOH . N 5 HOH D 36 636 70 HOH HOH . N 5 HOH D 37 637 228 HOH HOH . N 5 HOH D 38 638 14 HOH HOH . N 5 HOH D 39 639 152 HOH HOH . N 5 HOH D 40 640 162 HOH HOH . N 5 HOH D 41 641 235 HOH HOH . N 5 HOH D 42 642 256 HOH HOH . N 5 HOH D 43 643 133 HOH HOH . N 5 HOH D 44 644 262 HOH HOH . N 5 HOH D 45 645 37 HOH HOH . N 5 HOH D 46 646 97 HOH HOH . N 5 HOH D 47 647 151 HOH HOH . N 5 HOH D 48 648 268 HOH HOH . N 5 HOH D 49 649 185 HOH HOH . N 5 HOH D 50 650 148 HOH HOH . N 5 HOH D 51 651 88 HOH HOH . N 5 HOH D 52 652 234 HOH HOH . N 5 HOH D 53 653 249 HOH HOH . N 5 HOH D 54 654 50 HOH HOH . N 5 HOH D 55 655 35 HOH HOH . N 5 HOH D 56 656 198 HOH HOH . N 5 HOH D 57 657 219 HOH HOH . N 5 HOH D 58 658 188 HOH HOH . N 5 HOH D 59 659 250 HOH HOH . N 5 HOH D 60 660 252 HOH HOH . N 5 HOH D 61 661 191 HOH HOH . N 5 HOH D 62 662 171 HOH HOH . O 5 HOH F 1 301 189 HOH HOH . P 5 HOH G 1 301 173 HOH HOH . P 5 HOH G 2 302 221 HOH HOH . Q 5 HOH E 1 301 222 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 DIO . . . J 3 23.077 62.541 38.893 1 29.99 ? C1 DIO 501 D 1 HETATM 2 C C2 DIO . . . J 3 22.164 60.55 39.799 1 29.41 ? C2 DIO 501 D 1 HETATM 3 C C1' DIO . . . J 3 24.49 62.048 39.191 1 29.35 ? C1' DIO 501 D 1 HETATM 4 C C2' DIO . . . J 3 23.579 60.006 40.015 1 29.04 ? C2' DIO 501 D 1 HETATM 5 O O1 DIO . . . J 3 22.18 61.975 39.857 1 30.26 ? O1 DIO 501 D 1 HETATM 6 O O1' DIO . . . J 3 24.505 60.62 39.111 1 27.94 ? O1' DIO 501 D 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #