data_8B2J # _model_server_result.job_id z9kdi0IxAI4eUTffS2lXtA _model_server_result.datetime_utc '2024-10-10 13:21:43' _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 8b2j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8B2J # _exptl.entry_id 8B2J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.543 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1~{R},3~{S},6~{R},8~{R},9~{R},10~{S},12~{S},15~{R},17~{R},18~{R})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecane-9,18-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 8B2J _cell.length_a 67.357 _cell.length_b 67.368 _cell.length_c 136.317 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B2J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,N 1 1 B,I,J,K,L,M,O 2 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 2 _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 metalc ? metalc1 A O ILE 34 A ILE 171 1_555 F NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc2 A OD1 ASN 50 A ASN 187 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc3 A O ASN 51 A ASN 188 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc4 A O ARG 54 A ARG 191 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc5 A O SER 58 A SER 195 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc6 A O ARG 60 A ARG 197 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc7 A OE1 GLN 91 A GLN 228 1_555 F NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc8 A O ARG 95 A ARG 232 1_555 E NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc9 A OG SER 104 A SER 241 1_555 H NA NA . A NA 406 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc10 A OG SER 106 A SER 243 1_555 H NA NA . A NA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc11 H NA NA . A NA 406 1_555 B O LYS 99 B LYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc12 B O ILE 34 B ILE 171 1_555 M NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc13 B OD1 ASN 50 B ASN 187 1_555 I CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc14 B O ASN 51 B ASN 188 1_555 I CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.889 ? metalc ? metalc15 B OD1 ASN 51 B ASN 188 1_555 K NA NA . B NA 403 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc16 B O ARG 54 B ARG 191 1_555 I CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? metalc ? metalc17 B O SER 58 B SER 195 1_555 L NA NA . B NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc18 B O ARG 60 B ARG 197 1_555 L NA NA . B NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc19 B O GLY 70 B GLY 207 1_555 K NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc20 B OE1 GLN 91 B GLN 228 1_555 M NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc21 B O ARG 95 B ARG 232 1_555 J NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc22 B O GLN 129 B GLN 266 1_555 K NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? # _chem_comp.formula 'C20 H24 N10 O10 P2 S2' _chem_comp.formula_weight 690.543 _chem_comp.id GJF _chem_comp.mon_nstd_flag . _chem_comp.name (1~{R},3~{S},6~{R},8~{R},9~{R},10~{S},12~{S},15~{R},17~{R},18~{R})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanylidene)-3,12-bis(sulfanyl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecane-9,18-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 O5 P2 GJF doub 83 n n O10 C18 GJF sing 84 n n C20 N2 GJF doub 85 n y C20 N1 GJF sing 86 n y P2 S2 GJF sing 87 n n P2 O9 GJF sing 88 n n P2 O6 GJF sing 89 n n N2 C1 GJF sing 90 n y N1 C3 GJF doub 91 n y C18 C17 GJF sing 92 n n C18 C19 GJF sing 93 n n O9 C17 GJF sing 94 n n O6 C9 GJF sing 95 n n C1 C2 GJF doub 96 n y C1 N10 GJF sing 97 n y C9 C7 GJF sing 98 n n C17 C16 GJF sing 99 n n C3 C2 GJF sing 100 n y C3 N8 GJF sing 101 n n C19 N10 GJF sing 102 n n C19 O8 GJF sing 103 n n C2 N9 GJF sing 104 n y N10 C4 GJF sing 105 n y C16 O8 GJF sing 106 n n C16 C15 GJF sing 107 n n O1 C7 GJF sing 108 n n O1 C6 GJF sing 109 n n C7 C8 GJF sing 110 n n N9 C4 GJF doub 111 n y C12 N4 GJF doub 112 n y C12 N3 GJF sing 113 n y N4 C11 GJF sing 114 n y C15 O7 GJF sing 115 n n C8 C5 GJF sing 116 n n C8 O2 GJF sing 117 n n N3 C6 GJF sing 118 n n N3 C10 GJF sing 119 n y C6 C5 GJF sing 120 n n C5 O3 GJF sing 121 n n O7 P1 GJF sing 122 n n C11 C10 GJF doub 123 n y C11 C14 GJF sing 124 n y N7 C14 GJF sing 125 n n C10 N5 GJF sing 126 n y C14 N6 GJF doub 127 n y O3 P1 GJF sing 128 n n N5 C13 GJF doub 129 n y P1 O4 GJF doub 130 n n P1 S1 GJF sing 131 n n N6 C13 GJF sing 132 n y C4 H1 GJF sing 133 n n C5 H2 GJF sing 134 n n C6 H3 GJF sing 135 n n C7 H4 GJF sing 136 n n C8 H5 GJF sing 137 n n O2 H6 GJF sing 138 n n S1 H7 GJF sing 139 n n C9 H8 GJF sing 140 n n C9 H9 GJF sing 141 n n C12 H10 GJF sing 142 n n C13 H11 GJF sing 143 n n N7 H12 GJF sing 144 n n N7 H13 GJF sing 145 n n S2 H14 GJF sing 146 n n C15 H15 GJF sing 147 n n C15 H16 GJF sing 148 n n C16 H17 GJF sing 149 n n C17 H18 GJF sing 150 n n C18 H19 GJF sing 151 n n O10 H20 GJF sing 152 n n C19 H21 GJF sing 153 n n C20 H22 GJF sing 154 n n N8 H23 GJF sing 155 n n N8 H24 GJF sing 156 n n # _atom_sites.entry_id 8B2J _atom_sites.fract_transf_matrix[1][1] 0.014846 _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] 0.014844 _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] 0.007336 _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 2 GJF A 1 401 1 GJF LIG . D 3 CA A 1 402 2 CA CA . E 4 NA A 1 403 2 NA NA . F 4 NA A 1 404 3 NA NA . G 4 NA A 1 405 4 NA NA . H 4 NA A 1 406 8 NA NA . I 3 CA B 1 401 1 CA CA . J 4 NA B 1 402 1 NA NA . K 4 NA B 1 403 5 NA NA . L 4 NA B 1 404 6 NA NA . M 4 NA B 1 405 7 NA NA . N 5 HOH A 1 501 30 HOH HOH . N 5 HOH A 2 502 66 HOH HOH . N 5 HOH A 3 503 33 HOH HOH . N 5 HOH A 4 504 10 HOH HOH . N 5 HOH A 5 505 29 HOH HOH . N 5 HOH A 6 506 26 HOH HOH . N 5 HOH A 7 507 51 HOH HOH . N 5 HOH A 8 508 2 HOH HOH . N 5 HOH A 9 509 48 HOH HOH . N 5 HOH A 10 510 69 HOH HOH . N 5 HOH A 11 511 20 HOH HOH . N 5 HOH A 12 512 16 HOH HOH . N 5 HOH A 13 513 25 HOH HOH . N 5 HOH A 14 514 19 HOH HOH . N 5 HOH A 15 515 45 HOH HOH . N 5 HOH A 16 516 5 HOH HOH . N 5 HOH A 17 517 54 HOH HOH . N 5 HOH A 18 518 12 HOH HOH . N 5 HOH A 19 519 36 HOH HOH . N 5 HOH A 20 520 23 HOH HOH . N 5 HOH A 21 521 11 HOH HOH . N 5 HOH A 22 522 44 HOH HOH . N 5 HOH A 23 523 60 HOH HOH . N 5 HOH A 24 524 70 HOH HOH . N 5 HOH A 25 525 50 HOH HOH . N 5 HOH A 26 526 55 HOH HOH . O 5 HOH B 1 501 42 HOH HOH . O 5 HOH B 2 502 67 HOH HOH . O 5 HOH B 3 503 27 HOH HOH . O 5 HOH B 4 504 28 HOH HOH . O 5 HOH B 5 505 40 HOH HOH . O 5 HOH B 6 506 37 HOH HOH . O 5 HOH B 7 507 56 HOH HOH . O 5 HOH B 8 508 49 HOH HOH . O 5 HOH B 9 509 58 HOH HOH . O 5 HOH B 10 510 62 HOH HOH . O 5 HOH B 11 511 3 HOH HOH . O 5 HOH B 12 512 53 HOH HOH . O 5 HOH B 13 513 8 HOH HOH . O 5 HOH B 14 514 38 HOH HOH . O 5 HOH B 15 515 6 HOH HOH . O 5 HOH B 16 516 9 HOH HOH . O 5 HOH B 17 517 43 HOH HOH . O 5 HOH B 18 518 17 HOH HOH . O 5 HOH B 19 519 34 HOH HOH . O 5 HOH B 20 520 52 HOH HOH . O 5 HOH B 21 521 65 HOH HOH . O 5 HOH B 22 522 64 HOH HOH . O 5 HOH B 23 523 41 HOH HOH . O 5 HOH B 24 524 63 HOH HOH . O 5 HOH B 25 525 21 HOH HOH . O 5 HOH B 26 526 59 HOH HOH . O 5 HOH B 27 527 61 HOH HOH . O 5 HOH B 28 528 24 HOH HOH . O 5 HOH B 29 529 35 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 GJF . . . C 2 4.55 9.656 14.022 1 41.07 ? C1 GJF 401 A 1 HETATM 2 C C2 GJF . . . C 2 3.786 10.283 14.993 1 41.06 ? C2 GJF 401 A 1 HETATM 3 C C3 GJF . . . C 2 3.01 11.383 14.58 1 40.96 ? C3 GJF 401 A 1 HETATM 4 C C4 GJF . . . C 2 4.676 8.602 15.934 1 41.13 ? C4 GJF 401 A 1 HETATM 5 N N1 GJF . . . C 2 3.043 11.717 13.273 1 40.63 ? N1 GJF 401 A 1 HETATM 6 N N2 GJF . . . C 2 4.633 9.993 12.726 1 40.93 ? N2 GJF 401 A 1 HETATM 7 C C5 GJF . . . C 2 8.954 8.828 18.946 1 42.54 ? C5 GJF 401 A 1 HETATM 8 C C6 GJF . . . C 2 9.165 10.082 19.793 1 42.31 ? C6 GJF 401 A 1 HETATM 9 C C7 GJF . . . C 2 11.189 9.585 18.679 1 42.58 ? C7 GJF 401 A 1 HETATM 10 C C8 GJF . . . C 2 10.364 8.31 18.683 1 43.2 ? C8 GJF 401 A 1 HETATM 11 O O1 GJF . . . C 2 10.478 10.523 19.513 1 42.3 ? O1 GJF 401 A 1 HETATM 12 O O2 GJF . . . C 2 10.864 7.398 19.657 1 44.01 ? O2 GJF 401 A 1 HETATM 13 O O3 GJF . . . C 2 8.248 7.802 19.667 1 42.02 ? O3 GJF 401 A 1 HETATM 14 O O4 GJF . . . C 2 5.847 7.951 19.541 1 42.49 ? O4 GJF 401 A 1 HETATM 15 S S1 GJF . . . C 2 7.067 5.332 20.112 1 42.35 ? S1 GJF 401 A 1 HETATM 16 C C9 GJF . . . C 2 11.406 10.185 17.32 1 42.8 ? C9 GJF 401 A 1 HETATM 17 C C10 GJF . . . C 2 7.383 11.844 20.248 1 42.51 ? C10 GJF 401 A 1 HETATM 18 C C11 GJF . . . C 2 6.725 12.747 19.427 1 42.08 ? C11 GJF 401 A 1 HETATM 19 C C12 GJF . . . C 2 8.133 11.744 18.196 1 42.38 ? C12 GJF 401 A 1 HETATM 20 C C13 GJF . . . C 2 6.259 12.505 22.024 1 42.04 ? C13 GJF 401 A 1 HETATM 21 C C14 GJF . . . C 2 5.735 13.549 20.027 1 41.81 ? C14 GJF 401 A 1 HETATM 22 N N3 GJF . . . C 2 8.273 11.181 19.437 1 42.45 ? N3 GJF 401 A 1 HETATM 23 N N4 GJF . . . C 2 7.218 12.681 18.132 1 42.16 ? N4 GJF 401 A 1 HETATM 24 N N5 GJF . . . C 2 7.199 11.675 21.566 1 42.53 ? N5 GJF 401 A 1 HETATM 25 N N6 GJF . . . C 2 5.532 13.404 21.354 1 41.72 ? N6 GJF 401 A 1 HETATM 26 N N7 GJF . . . C 2 4.982 14.429 19.356 1 41.57 ? N7 GJF 401 A 1 HETATM 27 O O5 GJF . . . C 2 8.892 10.817 14.42 1 41.01 ? O5 GJF 401 A 1 HETATM 28 O O6 GJF . . . C 2 10.194 10.046 16.551 1 42.19 ? O6 GJF 401 A 1 HETATM 29 S S2 GJF . . . C 2 11.552 9.916 13.726 1 41.52 ? S2 GJF 401 A 1 HETATM 30 P P1 GJF . . . C 2 6.974 7.075 19.167 1 42.12 ? P1 GJF 401 A 1 HETATM 31 P P2 GJF . . . C 2 9.903 9.837 14.966 1 41.25 ? P2 GJF 401 A 1 HETATM 32 C C15 GJF . . . C 2 7.684 5.932 16.723 1 41.43 ? C15 GJF 401 A 1 HETATM 33 O O7 GJF . . . C 2 7.038 6.91 17.579 1 41.99 ? O7 GJF 401 A 1 HETATM 34 C C16 GJF . . . C 2 7.605 6.431 15.3 1 40.86 ? C16 GJF 401 A 1 HETATM 35 O O8 GJF . . . C 2 6.221 6.502 14.889 1 40.46 ? O8 GJF 401 A 1 HETATM 36 C C17 GJF . . . C 2 8.053 7.87 15.096 1 41.03 ? C17 GJF 401 A 1 HETATM 37 O O9 GJF . . . C 2 9.439 8.129 14.817 1 41.02 ? O9 GJF 401 A 1 HETATM 38 C C18 GJF . . . C 2 7.387 8.223 13.776 1 41.27 ? C18 GJF 401 A 1 HETATM 39 O O10 GJF . . . C 2 8.01 7.683 12.615 1 42.11 ? O10 GJF 401 A 1 HETATM 40 C C19 GJF . . . C 2 6.023 7.611 14.018 1 40.77 ? C19 GJF 401 A 1 HETATM 41 C C20 GJF . . . C 2 3.837 11.027 12.45 1 40.63 ? C20 GJF 401 A 1 HETATM 42 N N8 GJF . . . C 2 2.285 12.137 15.415 1 41.18 ? N8 GJF 401 A 1 HETATM 43 N N9 GJF . . . C 2 3.883 9.611 16.202 1 41.19 ? N9 GJF 401 A 1 HETATM 44 N N10 GJF . . . C 2 5.115 8.566 14.637 1 40.92 ? N10 GJF 401 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 44 #