data_3IWD # _model_server_result.job_id gIV77lzpU-vDDIswTVSpDg _model_server_result.datetime_utc '2024-11-13 12:17:07' _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 3iwd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":368}' # _entry.id 3IWD # _exptl.entry_id 3IWD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 313.376 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine" _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 120 _cell.entry_id 3IWD _cell.length_a 105.465 _cell.length_b 105.465 _cell.length_c 70.111 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IWD _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # 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 tetrameric 4 software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,E,G,H 2 1 C,D,F,I,J 3 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 E N N ? 3 F 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 covale ? covale1 B C PYR 1 A PYR 63 1_555 B N HIS 2 A HIS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 D C PYR 1 C PYR 63 1_555 D N HIS 2 C HIS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? # _chem_comp.formula 'C12 H19 N5 O3 S' _chem_comp.formula_weight 313.376 _chem_comp.id M2T _chem_comp.mon_nstd_flag . _chem_comp.name "5'-deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine" _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 SD CG M2T sing 218 n n CG HG M2T sing 219 n n CG HGA M2T sing 220 n n CG HGB M2T sing 221 n n CE SD M2T sing 222 n n SD C5' M2T sing 223 n n CE HE M2T sing 224 n n CE HEA M2T sing 225 n n CE HEB M2T sing 226 n n C4' C5' M2T sing 227 n n C5' H5' M2T sing 228 n n C5' "H5'A" M2T sing 229 n n O4' C4' M2T sing 230 n n C4' C3' M2T sing 231 n n C4' H4' M2T sing 232 n n C1' O4' M2T sing 233 n n N9 C1' M2T sing 234 n n C1' C2' M2T sing 235 n n C1' H1' M2T sing 236 n n C8 N9 M2T sing 237 n y N9 C4 M2T sing 238 n y C5 C4 M2T sing 239 n y C4 N3 M2T doub 240 n y N3 C2 M2T sing 241 n y N1 C2 M2T doub 242 n y C2 H2 M2T sing 243 n n C6 N1 M2T sing 244 n y C5 C6 M2T doub 245 n y N6 C6 M2T sing 246 n n N6 HN6 M2T sing 247 n n N6 HN6A M2T sing 248 n n N7 C5 M2T sing 249 n y N7 C8 M2T doub 250 n y C8 H8 M2T sing 251 n n O2' C2' M2T sing 252 n n C2' C3' M2T sing 253 n n C2' H2' M2T sing 254 n n O2' HO2' M2T sing 255 n n O3' C3' M2T sing 256 n n C3' H3' M2T sing 257 n n O3' HO3' M2T sing 258 n n SD HSD M2T sing 259 n n # _atom_sites.entry_id 3IWD _atom_sites.fract_transf_matrix[1][1] 0.009482 _atom_sites.fract_transf_matrix[1][2] 0.005474 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010949 _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] 0.014263 _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 3 M2T A 1 368 368 M2T M2T . F 3 M2T D 1 368 368 M2T M2T . G 4 HOH B 1 63 63 HOH HOH . G 4 HOH B 2 64 9 HOH HOH . G 4 HOH B 3 65 13 HOH HOH . G 4 HOH B 4 66 14 HOH HOH . G 4 HOH B 5 67 20 HOH HOH . G 4 HOH B 6 68 22 HOH HOH . G 4 HOH B 7 69 25 HOH HOH . G 4 HOH B 8 70 37 HOH HOH . G 4 HOH B 9 72 39 HOH HOH . G 4 HOH B 10 73 40 HOH HOH . G 4 HOH B 11 74 41 HOH HOH . G 4 HOH B 12 75 42 HOH HOH . G 4 HOH B 13 76 43 HOH HOH . G 4 HOH B 14 77 44 HOH HOH . G 4 HOH B 15 78 45 HOH HOH . G 4 HOH B 16 79 46 HOH HOH . G 4 HOH B 17 80 47 HOH HOH . G 4 HOH B 18 81 48 HOH HOH . G 4 HOH B 19 82 49 HOH HOH . H 4 HOH A 1 1 1 HOH HOH . H 4 HOH A 2 5 5 HOH HOH . H 4 HOH A 3 6 6 HOH HOH . H 4 HOH A 4 8 8 HOH HOH . H 4 HOH A 5 10 10 HOH HOH . H 4 HOH A 6 11 11 HOH HOH . H 4 HOH A 7 12 12 HOH HOH . H 4 HOH A 8 16 16 HOH HOH . H 4 HOH A 9 21 21 HOH HOH . H 4 HOH A 10 23 23 HOH HOH . H 4 HOH A 11 24 24 HOH HOH . H 4 HOH A 12 33 33 HOH HOH . H 4 HOH A 13 34 34 HOH HOH . H 4 HOH A 14 50 50 HOH HOH . H 4 HOH A 15 52 52 HOH HOH . H 4 HOH A 16 54 54 HOH HOH . H 4 HOH A 17 55 55 HOH HOH . H 4 HOH A 18 131 38 HOH HOH . I 4 HOH D 1 63 3 HOH HOH . I 4 HOH D 2 64 64 HOH HOH . I 4 HOH D 3 65 17 HOH HOH . I 4 HOH D 4 66 30 HOH HOH . I 4 HOH D 5 67 32 HOH HOH . I 4 HOH D 6 68 35 HOH HOH . I 4 HOH D 7 69 57 HOH HOH . I 4 HOH D 8 70 58 HOH HOH . J 4 HOH C 1 4 4 HOH HOH . J 4 HOH C 2 7 7 HOH HOH . J 4 HOH C 3 15 15 HOH HOH . J 4 HOH C 4 26 26 HOH HOH . J 4 HOH C 5 27 27 HOH HOH . J 4 HOH C 6 28 28 HOH HOH . J 4 HOH C 7 29 29 HOH HOH . J 4 HOH C 8 31 31 HOH HOH . J 4 HOH C 9 36 36 HOH HOH . J 4 HOH C 10 51 51 HOH HOH . J 4 HOH C 11 53 53 HOH HOH . J 4 HOH C 12 56 56 HOH HOH . J 4 HOH C 13 59 59 HOH HOH . J 4 HOH C 14 60 60 HOH HOH . J 4 HOH C 15 61 61 HOH HOH . J 4 HOH C 16 62 62 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 CG M2T . . . F 3 39.618 -19.381 24.864 1 38.19 ? CG M2T 368 D 1 HETATM 2 S SD M2T . . . F 3 39.954 -20.282 23.495 1 37.43 ? SD M2T 368 D 1 HETATM 3 C CE M2T . . . F 3 41.355 -19.984 23.055 1 38.84 ? CE M2T 368 D 1 HETATM 4 C C5' M2T . . . F 3 38.857 -19.884 22.276 1 41.15 ? C5' M2T 368 D 1 HETATM 5 C C4' M2T . . . F 3 39.109 -20.672 21.008 1 42.39 ? C4' M2T 368 D 1 HETATM 6 O O4' M2T . . . F 3 39.194 -22.083 21.343 1 45.76 ? O4' M2T 368 D 1 HETATM 7 C C1' M2T . . . F 3 38.226 -22.806 20.605 1 46.26 ? C1' M2T 368 D 1 HETATM 8 N N9 M2T . . . F 3 37.769 -23.904 21.444 1 48.53 ? N9 M2T 368 D 1 HETATM 9 C C4 M2T . . . F 3 37.119 -23.776 22.647 1 49.26 ? C4 M2T 368 D 1 HETATM 10 N N3 M2T . . . F 3 36.776 -22.627 23.283 1 50.81 ? N3 M2T 368 D 1 HETATM 11 C C2 M2T . . . F 3 36.154 -22.884 24.436 1 50.79 ? C2 M2T 368 D 1 HETATM 12 N N1 M2T . . . F 3 35.857 -24.076 24.982 1 50.64 ? N1 M2T 368 D 1 HETATM 13 C C6 M2T . . . F 3 36.217 -25.205 24.312 1 51.17 ? C6 M2T 368 D 1 HETATM 14 N N6 M2T . . . F 3 35.924 -26.382 24.848 1 51.53 ? N6 M2T 368 D 1 HETATM 15 C C5 M2T . . . F 3 36.883 -25.066 23.079 1 49.69 ? C5 M2T 368 D 1 HETATM 16 N N7 M2T . . . F 3 37.375 -25.994 22.169 1 48.99 ? N7 M2T 368 D 1 HETATM 17 C C8 M2T . . . F 3 37.889 -25.256 21.219 1 49.14 ? C8 M2T 368 D 1 HETATM 18 C C2' M2T . . . F 3 37.15 -21.788 20.262 1 46.1 ? C2' M2T 368 D 1 HETATM 19 O O2' M2T . . . F 3 36.312 -22.228 19.207 1 46.01 ? O2' M2T 368 D 1 HETATM 20 C C3' M2T . . . F 3 37.995 -20.563 19.961 1 44.47 ? C3' M2T 368 D 1 HETATM 21 O O3' M2T . . . F 3 38.55 -20.675 18.65 1 41.17 ? O3' M2T 368 D 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #