data_8PW9 # _model_server_result.job_id ja4cUAdXYMEw6xfF78YRMA _model_server_result.datetime_utc '2024-11-22 16:36:16' _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 8pw9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8PW9 # _exptl.entry_id 8PW9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.535 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[2-[[9-[(2~{R},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethylamino]methyl]oxolane-3,4-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 120 _cell.entry_id 8PW9 _cell.length_a 63.94 _cell.length_b 63.94 _cell.length_c 225.14 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PW9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall 'P 32 2"' _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 B SG CYS 233 B CYS 338 1_555 B SG CYS 283 B CYS 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc1 B OE2 GLU 115 B GLU 220 1_555 E MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? # _chem_comp.formula 'C22 H29 N11 O7' _chem_comp.formula_weight 559.535 _chem_comp.id H9D _chem_comp.mon_nstd_flag . _chem_comp.name (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[2-[[9-[(2~{R},3~{R},4~{S},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]ethylamino]methyl]oxolane-3,4-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 C11 N6 H9D doub 135 n y C11 N7 H9D sing 136 n y C12 N8 H9D doub 137 n y C12 N11 H9D sing 138 n y C13 C14 H9D sing 139 n n C13 N9 H9D sing 140 n n C14 N10 H9D sing 141 n n C15 N9 H9D sing 142 n n C15 C21 H9D sing 143 n n C16 N6 H9D sing 144 n y C16 N10 H9D sing 145 n n C16 C17 H9D doub 146 n y N7 C18 H9D doub 147 n y N8 C17 H9D sing 148 n y O5 C19 H9D sing 149 n n O6 C20 H9D sing 150 n n O7 C21 H9D sing 151 n n O7 C22 H9D sing 152 n n C17 C18 H9D sing 153 n y C18 N11 H9D sing 154 n y C19 C20 H9D sing 155 n n C19 C21 H9D sing 156 n n C20 C22 H9D sing 157 n n C22 N5 H9D sing 158 n n N11 C5 H9D sing 159 n n C10 O4 H9D sing 160 n n C10 C9 H9D sing 161 n n C9 O3 H9D sing 162 n n C9 C8 H9D sing 163 n n O3 C5 H9D sing 164 n n C8 O2 H9D sing 165 n n C8 C7 H9D sing 166 n n C7 O1 H9D sing 167 n n C7 C5 H9D sing 168 n n N1 C6 H9D doub 169 n y N1 C3 H9D sing 170 n y C6 N2 H9D sing 171 n y N2 C1 H9D doub 172 n y C1 C2 H9D sing 173 n y C1 N5 H9D sing 174 n y C2 C3 H9D doub 175 n y C2 N4 H9D sing 176 n y C3 N3 H9D sing 177 n n N4 C4 H9D doub 178 n y C4 N5 H9D sing 179 n y C4 H1 H9D sing 180 n n C5 H2 H9D sing 181 n n C6 H3 H9D sing 182 n n C7 H4 H9D sing 183 n n C8 H5 H9D sing 184 n n C9 H6 H9D sing 185 n n C10 H7 H9D sing 186 n n C10 H8 H9D sing 187 n n C11 H9 H9D sing 188 n n C12 H10 H9D sing 189 n n C13 H11 H9D sing 190 n n C13 H12 H9D sing 191 n n C14 H13 H9D sing 192 n n C14 H14 H9D sing 193 n n C15 H15 H9D sing 194 n n C15 H16 H9D sing 195 n n C19 H17 H9D sing 196 n n C20 H18 H9D sing 197 n n C21 H19 H9D sing 198 n n C22 H20 H9D sing 199 n n N3 H21 H9D sing 200 n n N3 H22 H9D sing 201 n n N9 H23 H9D sing 202 n n N10 H25 H9D sing 203 n n O1 H26 H9D sing 204 n n O2 H27 H9D sing 205 n n O4 H28 H9D sing 206 n n O5 H29 H9D sing 207 n n O6 H30 H9D sing 208 n n # _atom_sites.entry_id 8PW9 _atom_sites.fract_transf_matrix[1][1] 0.01564 _atom_sites.fract_transf_matrix[1][2] 0.00903 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018059 _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] 0.004442 _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 H9D A 1 601 601 H9D LIG . D 4 ACT B 1 401 401 ACT ACT . E 5 MG B 1 402 1 MG MG . F 6 HOH A 1 701 99 HOH HOH . F 6 HOH A 2 702 82 HOH HOH . F 6 HOH A 3 703 17 HOH HOH . F 6 HOH A 4 704 35 HOH HOH . F 6 HOH A 5 705 107 HOH HOH . F 6 HOH A 6 706 19 HOH HOH . F 6 HOH A 7 707 18 HOH HOH . F 6 HOH A 8 708 16 HOH HOH . F 6 HOH A 9 709 57 HOH HOH . F 6 HOH A 10 710 26 HOH HOH . F 6 HOH A 11 711 9 HOH HOH . F 6 HOH A 12 712 13 HOH HOH . F 6 HOH A 13 713 106 HOH HOH . F 6 HOH A 14 714 38 HOH HOH . F 6 HOH A 15 715 20 HOH HOH . F 6 HOH A 16 716 34 HOH HOH . F 6 HOH A 17 717 50 HOH HOH . F 6 HOH A 18 718 74 HOH HOH . F 6 HOH A 19 719 24 HOH HOH . F 6 HOH A 20 720 47 HOH HOH . F 6 HOH A 21 721 101 HOH HOH . F 6 HOH A 22 722 59 HOH HOH . F 6 HOH A 23 723 15 HOH HOH . F 6 HOH A 24 724 39 HOH HOH . F 6 HOH A 25 725 96 HOH HOH . F 6 HOH A 26 726 85 HOH HOH . F 6 HOH A 27 727 23 HOH HOH . F 6 HOH A 28 728 53 HOH HOH . F 6 HOH A 29 729 41 HOH HOH . F 6 HOH A 30 730 11 HOH HOH . F 6 HOH A 31 731 79 HOH HOH . F 6 HOH A 32 732 36 HOH HOH . F 6 HOH A 33 733 63 HOH HOH . F 6 HOH A 34 734 117 HOH HOH . F 6 HOH A 35 735 98 HOH HOH . F 6 HOH A 36 736 102 HOH HOH . F 6 HOH A 37 737 64 HOH HOH . F 6 HOH A 38 738 87 HOH HOH . F 6 HOH A 39 739 88 HOH HOH . F 6 HOH A 40 740 73 HOH HOH . F 6 HOH A 41 741 58 HOH HOH . F 6 HOH A 42 742 113 HOH HOH . F 6 HOH A 43 743 108 HOH HOH . F 6 HOH A 44 744 130 HOH HOH . F 6 HOH A 45 745 128 HOH HOH . F 6 HOH A 46 746 129 HOH HOH . F 6 HOH A 47 747 81 HOH HOH . F 6 HOH A 48 748 125 HOH HOH . F 6 HOH A 49 749 100 HOH HOH . F 6 HOH A 50 750 116 HOH HOH . F 6 HOH A 51 751 118 HOH HOH . G 6 HOH B 1 501 54 HOH HOH . G 6 HOH B 2 502 61 HOH HOH . G 6 HOH B 3 503 49 HOH HOH . G 6 HOH B 4 504 3 HOH HOH . G 6 HOH B 5 505 28 HOH HOH . G 6 HOH B 6 506 70 HOH HOH . G 6 HOH B 7 507 2 HOH HOH . G 6 HOH B 8 508 33 HOH HOH . G 6 HOH B 9 509 8 HOH HOH . G 6 HOH B 10 510 10 HOH HOH . G 6 HOH B 11 511 55 HOH HOH . G 6 HOH B 12 512 92 HOH HOH . G 6 HOH B 13 513 72 HOH HOH . G 6 HOH B 14 514 1 HOH HOH . G 6 HOH B 15 515 37 HOH HOH . G 6 HOH B 16 516 12 HOH HOH . G 6 HOH B 17 517 5 HOH HOH . G 6 HOH B 18 518 31 HOH HOH . G 6 HOH B 19 519 4 HOH HOH . G 6 HOH B 20 520 29 HOH HOH . G 6 HOH B 21 521 22 HOH HOH . G 6 HOH B 22 522 104 HOH HOH . G 6 HOH B 23 523 83 HOH HOH . G 6 HOH B 24 524 7 HOH HOH . G 6 HOH B 25 525 65 HOH HOH . G 6 HOH B 26 526 40 HOH HOH . G 6 HOH B 27 527 44 HOH HOH . G 6 HOH B 28 528 21 HOH HOH . G 6 HOH B 29 529 114 HOH HOH . G 6 HOH B 30 530 32 HOH HOH . G 6 HOH B 31 531 56 HOH HOH . G 6 HOH B 32 532 68 HOH HOH . G 6 HOH B 33 533 69 HOH HOH . G 6 HOH B 34 534 27 HOH HOH . G 6 HOH B 35 535 48 HOH HOH . G 6 HOH B 36 536 25 HOH HOH . G 6 HOH B 37 537 30 HOH HOH . G 6 HOH B 38 538 110 HOH HOH . G 6 HOH B 39 539 62 HOH HOH . G 6 HOH B 40 540 66 HOH HOH . G 6 HOH B 41 541 93 HOH HOH . G 6 HOH B 42 542 6 HOH HOH . G 6 HOH B 43 543 78 HOH HOH . G 6 HOH B 44 544 42 HOH HOH . G 6 HOH B 45 545 86 HOH HOH . G 6 HOH B 46 546 103 HOH HOH . G 6 HOH B 47 547 121 HOH HOH . G 6 HOH B 48 548 76 HOH HOH . G 6 HOH B 49 549 109 HOH HOH . G 6 HOH B 50 550 14 HOH HOH . G 6 HOH B 51 551 51 HOH HOH . G 6 HOH B 52 552 52 HOH HOH . G 6 HOH B 53 553 67 HOH HOH . G 6 HOH B 54 554 71 HOH HOH . G 6 HOH B 55 555 45 HOH HOH . G 6 HOH B 56 556 91 HOH HOH . G 6 HOH B 57 557 43 HOH HOH . G 6 HOH B 58 558 94 HOH HOH . G 6 HOH B 59 559 77 HOH HOH . G 6 HOH B 60 560 89 HOH HOH . G 6 HOH B 61 561 111 HOH HOH . G 6 HOH B 62 562 95 HOH HOH . G 6 HOH B 63 563 46 HOH HOH . G 6 HOH B 64 564 80 HOH HOH . G 6 HOH B 65 565 112 HOH HOH . G 6 HOH B 66 566 105 HOH HOH . G 6 HOH B 67 567 90 HOH HOH . G 6 HOH B 68 568 124 HOH HOH . G 6 HOH B 69 569 75 HOH HOH . G 6 HOH B 70 570 60 HOH HOH . G 6 HOH B 71 571 119 HOH HOH . G 6 HOH B 72 572 97 HOH HOH . G 6 HOH B 73 573 120 HOH HOH . G 6 HOH B 74 574 84 HOH HOH . G 6 HOH B 75 575 127 HOH HOH . G 6 HOH B 76 576 122 HOH HOH . G 6 HOH B 77 577 123 HOH HOH . G 6 HOH B 78 578 115 HOH HOH . G 6 HOH B 79 579 126 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 N N1 H9D . . . C 3 -39.132 40.335 26.666 1 44.34 ? N1 H9D 601 A 1 HETATM 2 N N2 H9D . . . C 3 -40.48 38.485 27.151 1 43.59 ? N2 H9D 601 A 1 HETATM 3 C C1 H9D . . . C 3 -41.015 38.501 25.907 1 45.88 ? C1 H9D 601 A 1 HETATM 4 C C2 H9D . . . C 3 -40.617 39.471 24.988 1 45.69 ? C2 H9D 601 A 1 HETATM 5 C C3 H9D . . . C 3 -39.623 40.418 25.425 1 47.31 ? C3 H9D 601 A 1 HETATM 6 C C4 H9D . . . C 3 -42.148 38.174 24.045 1 51.25 ? C4 H9D 601 A 1 HETATM 7 C C5 H9D . . . C 3 -51.219 32.44 23.397 1 150.55 ? C5 H9D 601 A 1 HETATM 8 C C6 H9D . . . C 3 -39.556 39.391 27.516 1 47.45 ? C6 H9D 601 A 1 HETATM 9 C C7 H9D . . . C 3 -51.464 32.365 24.909 1 144.35 ? C7 H9D 601 A 1 HETATM 10 C C8 H9D . . . C 3 -51.741 33.816 25.316 1 154.64 ? C8 H9D 601 A 1 HETATM 11 C C9 H9D . . . C 3 -51.235 34.644 24.151 1 174.53 ? C9 H9D 601 A 1 HETATM 12 C C10 H9D . . . C 3 -51.958 35.935 23.858 1 167.73 ? C10 H9D 601 A 1 HETATM 13 C C11 H9D . . . C 3 -47.117 33.278 25.171 1 98.72 ? C11 H9D 601 A 1 HETATM 14 C C12 H9D . . . C 3 -49.571 31.098 22.096 1 125.36 ? C12 H9D 601 A 1 HETATM 15 C C13 H9D . . . C 3 -42.863 31.366 23.495 1 69.83 ? C13 H9D 601 A 1 HETATM 16 C C14 H9D . . . C 3 -44.083 30.468 23.62 1 83.25 ? C14 H9D 601 A 1 HETATM 17 C C15 H9D . . . C 3 -42.418 33.569 24.383 1 61.38 ? C15 H9D 601 A 1 HETATM 18 C C16 H9D . . . C 3 -46.333 31.824 23.53 1 121.21 ? C16 H9D 601 A 1 HETATM 19 C C17 H9D . . . C 3 -47.687 31.635 23.073 1 121.2 ? C17 H9D 601 A 1 HETATM 20 C C18 H9D . . . C 3 -48.718 32.312 23.724 1 130.47 ? C18 H9D 601 A 1 HETATM 21 C C19 H9D . . . C 3 -44.12 35.072 25.609 1 58.04 ? C19 H9D 601 A 1 HETATM 22 C C20 H9D . . . C 3 -43.946 36.24 25.192 1 59.45 ? C20 H9D 601 A 1 HETATM 23 C C21 H9D . . . C 3 -42.629 34.412 25.593 1 54.5 ? C21 H9D 601 A 1 HETATM 24 C C22 H9D . . . C 3 -42.581 36.644 25.887 1 51.63 ? C22 H9D 601 A 1 HETATM 25 N N3 H9D . . . C 3 -39.1 41.496 24.545 1 51.2 ? N3 H9D 601 A 1 HETATM 26 N N4 H9D . . . C 3 -41.337 39.237 23.847 1 46.87 ? N4 H9D 601 A 1 HETATM 27 N N5 H9D . . . C 3 -41.968 37.726 25.291 1 49.1 ? N5 H9D 601 A 1 HETATM 28 N N6 H9D . . . C 3 -46.084 32.638 24.564 1 100.07 ? N6 H9D 601 A 1 HETATM 29 N N7 H9D . . . C 3 -48.384 33.13 24.78 1 113.78 ? N7 H9D 601 A 1 HETATM 30 N N8 H9D . . . C 3 -48.265 30.897 22.066 1 117.18 ? N8 H9D 601 A 1 HETATM 31 N N9 H9D . . . C 3 -42.799 32.224 24.735 1 64.23 ? N9 H9D 601 A 1 HETATM 32 N N10 H9D . . . C 3 -45.196 31.099 22.836 1 109.77 ? N10 H9D 601 A 1 HETATM 33 N N11 H9D . . . C 3 -49.895 31.967 23.096 1 131.72 ? N11 H9D 601 A 1 HETATM 34 O O1 H9D . . . C 3 -52.476 31.415 25.248 1 138.51 ? O1 H9D 601 A 1 HETATM 35 O O2 H9D . . . C 3 -53.14 34.012 25.471 1 158.4 ? O2 H9D 601 A 1 HETATM 36 O O3 H9D . . . C 3 -51.394 33.78 23 1 153.29 ? O3 H9D 601 A 1 HETATM 37 O O4 H9D . . . C 3 -53.052 35.703 22.978 1 160.68 ? O4 H9D 601 A 1 HETATM 38 O O5 H9D . . . C 3 -44.58 35.076 27.046 1 51.84 ? O5 H9D 601 A 1 HETATM 39 O O6 H9D . . . C 3 -44.946 37.259 25.706 1 62.4 ? O6 H9D 601 A 1 HETATM 40 O O7 H9D . . . C 3 -41.777 35.429 25.623 1 55.43 ? O7 H9D 601 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 40 #