data_6S7B # _model_server_result.job_id wrbu8_mUlSp7GYI4ElO0rg _model_server_result.datetime_utc '2024-11-07 14:35:54' _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 6s7b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 6S7B # _exptl.entry_id 6S7B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 436.512 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azanylpropyl)amino]butyl]guanidine _entity.pdbx_number_of_molecules 4 _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 6S7B _cell.length_a 75.455 _cell.length_b 99.367 _cell.length_c 208.463 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S7B _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # 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 dimeric 2 author_and_software_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,E,G,I,K 1 1 B,D,F,H,J,L 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C18 H32 N10 O3' _chem_comp.formula_weight 436.512 _chem_comp.id KYH _chem_comp.mon_nstd_flag . _chem_comp.name 1-[4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azanylpropyl)amino]butyl]guanidine _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 N31 C29 KYH doub 173 n n N30 C29 KYH sing 174 n n C29 N28 KYH sing 175 n n N28 C27 KYH sing 176 n n C27 C26 KYH sing 177 n n C26 C25 KYH sing 178 n n C25 C24 KYH sing 179 n n C24 N19 KYH sing 180 n n N19 C18 KYH sing 181 n n N19 C20 KYH sing 182 n n C18 C17 KYH sing 183 n n C20 C21 KYH sing 184 n n C21 C22 KYH sing 185 n n N23 C22 KYH sing 186 n n C15 N14 KYH doub 187 n y C15 N06 KYH sing 188 n y C17 O16 KYH sing 189 n n C17 C02 KYH sing 190 n n N14 C13 KYH sing 191 n y O16 C05 KYH sing 192 n n C02 C03 KYH sing 193 n n C02 O01 KYH sing 194 n n C03 C05 KYH sing 195 n n C03 O04 KYH sing 196 n n N06 C05 KYH sing 197 n n N06 C07 KYH sing 198 n y C13 C07 KYH doub 199 n y C13 C11 KYH sing 200 n y N12 C11 KYH sing 201 n n C07 N08 KYH sing 202 n y C11 N10 KYH doub 203 n y N08 C09 KYH doub 204 n y N10 C09 KYH sing 205 n y C17 H1 KYH sing 206 n n C15 H2 KYH sing 207 n n C22 H3 KYH sing 208 n n C22 H4 KYH sing 209 n n C20 H5 KYH sing 210 n n C20 H6 KYH sing 211 n n C21 H7 KYH sing 212 n n C21 H8 KYH sing 213 n n C24 H9 KYH sing 214 n n C24 H10 KYH sing 215 n n C25 H11 KYH sing 216 n n C25 H12 KYH sing 217 n n C27 H13 KYH sing 218 n n C27 H14 KYH sing 219 n n N28 H15 KYH sing 220 n n C02 H16 KYH sing 221 n n C03 H17 KYH sing 222 n n C05 H18 KYH sing 223 n n C09 H19 KYH sing 224 n n C18 H20 KYH sing 225 n n C18 H21 KYH sing 226 n n C26 H22 KYH sing 227 n n C26 H23 KYH sing 228 n n N12 H24 KYH sing 229 n n N12 H25 KYH sing 230 n n N23 H27 KYH sing 231 n n N23 H28 KYH sing 232 n n N30 H30 KYH sing 233 n n N30 H31 KYH sing 234 n n N31 H32 KYH sing 235 n n O01 H33 KYH sing 236 n n O04 H34 KYH sing 237 n n # _atom_sites.entry_id 6S7B _atom_sites.fract_transf_matrix[1][1] 0.013253 _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] 0.010064 _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] 0.004797 _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 E 2 KYH A 1 501 2 KYH 249 . F 2 KYH B 1 501 3 KYH 249 . G 2 KYH C 1 501 1 KYH 249 . H 2 KYH D 1 501 4 KYH 249 . I 3 HOH A 1 601 30 HOH HOH . I 3 HOH A 2 602 74 HOH HOH . I 3 HOH A 3 603 32 HOH HOH . I 3 HOH A 4 604 53 HOH HOH . I 3 HOH A 5 605 7 HOH HOH . I 3 HOH A 6 606 25 HOH HOH . I 3 HOH A 7 607 24 HOH HOH . I 3 HOH A 8 608 16 HOH HOH . I 3 HOH A 9 609 4 HOH HOH . I 3 HOH A 10 610 9 HOH HOH . I 3 HOH A 11 611 84 HOH HOH . I 3 HOH A 12 612 98 HOH HOH . I 3 HOH A 13 613 83 HOH HOH . I 3 HOH A 14 614 2 HOH HOH . I 3 HOH A 15 615 82 HOH HOH . I 3 HOH A 16 616 79 HOH HOH . I 3 HOH A 17 617 31 HOH HOH . I 3 HOH A 18 618 55 HOH HOH . I 3 HOH A 19 619 26 HOH HOH . I 3 HOH A 20 620 49 HOH HOH . I 3 HOH A 21 621 96 HOH HOH . I 3 HOH A 22 622 50 HOH HOH . I 3 HOH A 23 623 43 HOH HOH . I 3 HOH A 24 624 48 HOH HOH . I 3 HOH A 25 625 76 HOH HOH . I 3 HOH A 26 626 34 HOH HOH . I 3 HOH A 27 627 81 HOH HOH . I 3 HOH A 28 628 94 HOH HOH . I 3 HOH A 29 629 87 HOH HOH . I 3 HOH A 30 630 45 HOH HOH . I 3 HOH A 31 631 57 HOH HOH . I 3 HOH A 32 632 86 HOH HOH . I 3 HOH A 33 633 107 HOH HOH . I 3 HOH A 34 634 93 HOH HOH . J 3 HOH B 1 601 27 HOH HOH . J 3 HOH B 2 602 5 HOH HOH . J 3 HOH B 3 603 88 HOH HOH . J 3 HOH B 4 604 36 HOH HOH . J 3 HOH B 5 605 18 HOH HOH . J 3 HOH B 6 606 61 HOH HOH . J 3 HOH B 7 607 105 HOH HOH . J 3 HOH B 8 608 11 HOH HOH . J 3 HOH B 9 609 51 HOH HOH . J 3 HOH B 10 610 68 HOH HOH . J 3 HOH B 11 611 67 HOH HOH . J 3 HOH B 12 612 17 HOH HOH . J 3 HOH B 13 613 89 HOH HOH . J 3 HOH B 14 614 29 HOH HOH . J 3 HOH B 15 615 33 HOH HOH . J 3 HOH B 16 616 14 HOH HOH . J 3 HOH B 17 617 59 HOH HOH . J 3 HOH B 18 618 3 HOH HOH . J 3 HOH B 19 619 46 HOH HOH . J 3 HOH B 20 620 101 HOH HOH . J 3 HOH B 21 621 41 HOH HOH . J 3 HOH B 22 622 58 HOH HOH . J 3 HOH B 23 623 40 HOH HOH . J 3 HOH B 24 624 73 HOH HOH . J 3 HOH B 25 625 100 HOH HOH . J 3 HOH B 26 626 19 HOH HOH . J 3 HOH B 27 627 91 HOH HOH . J 3 HOH B 28 628 56 HOH HOH . J 3 HOH B 29 629 80 HOH HOH . J 3 HOH B 30 630 65 HOH HOH . J 3 HOH B 31 631 60 HOH HOH . J 3 HOH B 32 632 106 HOH HOH . J 3 HOH B 33 633 47 HOH HOH . J 3 HOH B 34 634 95 HOH HOH . K 3 HOH C 1 601 37 HOH HOH . K 3 HOH C 2 602 62 HOH HOH . K 3 HOH C 3 603 1 HOH HOH . K 3 HOH C 4 604 97 HOH HOH . K 3 HOH C 5 605 8 HOH HOH . K 3 HOH C 6 606 69 HOH HOH . K 3 HOH C 7 607 110 HOH HOH . K 3 HOH C 8 608 10 HOH HOH . K 3 HOH C 9 609 112 HOH HOH . K 3 HOH C 10 610 22 HOH HOH . K 3 HOH C 11 611 42 HOH HOH . K 3 HOH C 12 612 21 HOH HOH . K 3 HOH C 13 613 85 HOH HOH . K 3 HOH C 14 614 111 HOH HOH . K 3 HOH C 15 615 102 HOH HOH . K 3 HOH C 16 616 70 HOH HOH . K 3 HOH C 17 617 92 HOH HOH . K 3 HOH C 18 618 23 HOH HOH . K 3 HOH C 19 619 78 HOH HOH . K 3 HOH C 20 620 66 HOH HOH . K 3 HOH C 21 621 104 HOH HOH . K 3 HOH C 22 622 109 HOH HOH . K 3 HOH C 23 623 108 HOH HOH . L 3 HOH D 1 601 64 HOH HOH . L 3 HOH D 2 602 15 HOH HOH . L 3 HOH D 3 603 90 HOH HOH . L 3 HOH D 4 604 28 HOH HOH . L 3 HOH D 5 605 13 HOH HOH . L 3 HOH D 6 606 99 HOH HOH . L 3 HOH D 7 607 44 HOH HOH . L 3 HOH D 8 608 38 HOH HOH . L 3 HOH D 9 609 75 HOH HOH . L 3 HOH D 10 610 12 HOH HOH . L 3 HOH D 11 611 35 HOH HOH . L 3 HOH D 12 612 71 HOH HOH . L 3 HOH D 13 613 77 HOH HOH . L 3 HOH D 14 614 20 HOH HOH . L 3 HOH D 15 615 6 HOH HOH . L 3 HOH D 16 616 52 HOH HOH . L 3 HOH D 17 617 39 HOH HOH . L 3 HOH D 18 618 72 HOH HOH . L 3 HOH D 19 619 103 HOH HOH . L 3 HOH D 20 620 63 HOH HOH . L 3 HOH D 21 621 54 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 C13 KYH . . . E 2 -24.745 9.572 -23.746 1 46.51 ? C13 KYH 501 A 1 HETATM 2 C C17 KYH . . . E 2 -24.821 13.149 -27.988 1 54.6 ? C17 KYH 501 A 1 HETATM 3 C C15 KYH . . . E 2 -24.974 11.63 -24.386 1 46.61 ? C15 KYH 501 A 1 HETATM 4 C C11 KYH . . . E 2 -24.585 8.321 -23.091 1 45.01 ? C11 KYH 501 A 1 HETATM 5 C C22 KYH . . . E 2 -22.15 14.729 -32.015 1 77.56 ? C22 KYH 501 A 1 HETATM 6 C C20 KYH . . . E 2 -23.014 14.226 -29.644 1 69.4 ? C20 KYH 501 A 1 HETATM 7 C C21 KYH . . . E 2 -23.4 14.346 -31.158 1 70.3 ? C21 KYH 501 A 1 HETATM 8 C C24 KYH . . . E 2 -22.79 16.199 -28.361 1 65.21 ? C24 KYH 501 A 1 HETATM 9 C C25 KYH . . . E 2 -23.468 17.398 -27.603 1 68.94 ? C25 KYH 501 A 1 HETATM 10 C C27 KYH . . . E 2 -23.079 19.462 -26.143 1 78.87 ? C27 KYH 501 A 1 HETATM 11 N N28 KYH . . . E 2 -23.132 20.962 -26.246 1 75.6 ? N28 KYH 501 A 1 HETATM 12 C C02 KYH . . . E 2 -26.37 12.911 -27.966 1 52.45 ? C02 KYH 501 A 1 HETATM 13 C C03 KYH . . . E 2 -26.576 12.296 -26.894 1 49.81 ? C03 KYH 501 A 1 HETATM 14 C C05 KYH . . . E 2 -25.236 11.371 -26.763 1 52.26 ? C05 KYH 501 A 1 HETATM 15 C C07 KYH . . . E 2 -24.943 9.575 -25.089 1 48.98 ? C07 KYH 501 A 1 HETATM 16 C C09 KYH . . . E 2 -24.799 7.242 -25.152 1 47.74 ? C09 KYH 501 A 1 HETATM 17 C C18 KYH . . . E 2 -24.45 14.475 -27.649 1 58.05 ? C18 KYH 501 A 1 HETATM 18 C C26 KYH . . . E 2 -22.521 18.613 -27.351 1 74.51 ? C26 KYH 501 A 1 HETATM 19 C C29 KYH . . . E 2 -23.974 21.643 -27.078 1 79.82 ? C29 KYH 501 A 1 HETATM 20 N N06 KYH . . . E 2 -25.086 10.87 -25.446 1 49.34 ? N06 KYH 501 A 1 HETATM 21 N N08 KYH . . . E 2 -24.972 8.393 -25.797 1 46.5 ? N08 KYH 501 A 1 HETATM 22 N N10 KYH . . . E 2 -24.607 7.201 -23.826 1 47.36 ? N10 KYH 501 A 1 HETATM 23 N N12 KYH . . . E 2 -24.394 8.266 -21.64 1 42.63 ? N12 KYH 501 A 1 HETATM 24 N N14 KYH . . . E 2 -24.763 10.839 -23.327 1 45.09 ? N14 KYH 501 A 1 HETATM 25 N N19 KYH . . . E 2 -23.766 15.177 -28.805 1 64.94 ? N19 KYH 501 A 1 HETATM 26 N N23 KYH . . . E 2 -21.076 13.679 -31.994 1 78.71 ? N23 KYH 501 A 1 HETATM 27 N N30 KYH . . . E 2 -23.929 22.99 -27.045 1 80.89 ? N30 KYH 501 A 1 HETATM 28 N N31 KYH . . . E 2 -24.802 21.03 -27.913 1 81.44 ? N31 KYH 501 A 1 HETATM 29 O O01 KYH . . . E 2 -26.732 12.134 -29.234 1 46.7 ? O01 KYH 501 A 1 HETATM 30 O O04 KYH . . . E 2 -27.71 11.368 -26.88 1 43.36 ? O04 KYH 501 A 1 HETATM 31 O O16 KYH . . . E 2 -24.259 12.177 -26.979 1 53.84 ? O16 KYH 501 A 1 # _model_server_stats.io_time_ms 89 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #