data_5J68 # _model_server_result.job_id B4SNihV4fOSnzutoSeoosw _model_server_result.datetime_utc '2024-11-26 05:56:21' _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 5j68 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1311}' # _entry.id 5J68 # _exptl.entry_id 5J68 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 420.096 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE _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 5J68 _cell.length_a 103.9 _cell.length_b 103.9 _cell.length_c 304.29 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J68 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 5 MAN MAN C1 O1 . O2 HO2 . sing 6 ? 2 7 4 MAN MAN C1 O1 . O6 HO6 . sing 7 ? 2 8 7 MAN MAN C1 O1 . O2 HO2 . sing 8 ? 2 9 3 MAN BMA C1 O1 . O3 HO3 . sing 9 ? 2 10 9 MAN MAN C1 O1 . O2 HO2 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 1300 NAG 2 n B NAG 2 B 2 NAG A 1301 NAG 2 n B BMA 3 B 3 BMA A 1302 BMA 2 n B MAN 4 B 4 MAN A 1303 MAN 2 n B MAN 5 B 5 MAN A 1304 MAN 2 n B MAN 6 B 6 MAN A 1305 MAN 2 n B MAN 7 B 7 MAN A 1306 MAN 2 n B MAN 8 B 8 MAN A 1307 MAN 2 n B MAN 9 B 9 MAN A 1308 MAN 2 n B MAN 10 B 10 MAN A 1309 MAN # 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 58 A CYS 774 1_555 A SG CYS 220 A CYS 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 149 A CYS 865 1_555 A SG CYS 210 A CYS 926 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 216 A CYS 932 1_555 A SG CYS 223 A CYS 939 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 A SG CYS 269 A CYS 985 1_555 A SG CYS 280 A CYS 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 282 A CYS 998 1_555 A SG CYS 295 A CYS 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 A SG CYS 369 A CYS 1085 1_555 A SG CYS 391 A CYS 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 423 A CYS 1139 1_555 A SG CYS 510 A CYS 1226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 A SG CYS 531 A CYS 1247 1_555 A SG CYS 554 A CYS 1270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 3 A ASN 719 1_555 C C1 NAG . A NAG 1310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 16 A ASN 732 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B O3 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 B O6 MAN . B MAN 4 1_555 B C1 MAN . B MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 B O2 MAN . B MAN 5 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale10 B O2 MAN . B MAN 7 1_555 B C1 MAN . B MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 B O2 MAN . B MAN 9 1_555 B C1 MAN . B MAN 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _chem_comp.formula 'C6 H15 O15 P3' _chem_comp.formula_weight 420.096 _chem_comp.id I3P _chem_comp.mon_nstd_flag . _chem_comp.name D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE _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 C2 I3P sing 174 n n C1 C6 I3P sing 175 n n C1 O1 I3P sing 176 n n C1 H1 I3P sing 177 n n C2 C3 I3P sing 178 n n C2 O2 I3P sing 179 n n C2 H2 I3P sing 180 n n C3 C4 I3P sing 181 n n C3 O3 I3P sing 182 n n C3 H3 I3P sing 183 n n C4 C5 I3P sing 184 n n C4 O4 I3P sing 185 n n C4 H4 I3P sing 186 n n C5 C6 I3P sing 187 n n C5 O5 I3P sing 188 n n C5 H5 I3P sing 189 n n C6 O6 I3P sing 190 n n C6 H6 I3P sing 191 n n O1 P1 I3P sing 192 n n O2 HO2 I3P sing 193 n n O3 HO3 I3P sing 194 n n O4 P4 I3P sing 195 n n O5 P5 I3P sing 196 n n O6 HO6 I3P sing 197 n n P1 O11 I3P doub 198 n n P1 O12 I3P sing 199 n n P1 O13 I3P sing 200 n n O12 HO12 I3P sing 201 n n O13 HO13 I3P sing 202 n n P4 O41 I3P doub 203 n n P4 O42 I3P sing 204 n n P4 O43 I3P sing 205 n n O42 HO42 I3P sing 206 n n O43 HO43 I3P sing 207 n n P5 O51 I3P doub 208 n n P5 O52 I3P sing 209 n n P5 O53 I3P sing 210 n n O52 HO52 I3P sing 211 n n O53 HO53 I3P sing 212 n n # _atom_sites.entry_id 5J68 _atom_sites.fract_transf_matrix[1][1] 0.009625 _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] 0.009625 _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] 0.003286 _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 NAG A 1 1310 1315 NAG NAG . D 4 I3P A 1 1311 1316 I3P I3P . # 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 I3P . . . D 4 -44.789 37.686 -29.123 0 346.47 ? C1 I3P 1311 A 1 HETATM 2 C C2 I3P . . . D 4 -44.95 39.033 -29.83 0 341.76 ? C2 I3P 1311 A 1 HETATM 3 C C3 I3P . . . D 4 -43.857 40.025 -29.421 0 342.42 ? C3 I3P 1311 A 1 HETATM 4 C C4 I3P . . . D 4 -42.454 39.447 -29.658 0 349.83 ? C4 I3P 1311 A 1 HETATM 5 C C5 I3P . . . D 4 -42.302 38.103 -28.941 0 353.11 ? C5 I3P 1311 A 1 HETATM 6 C C6 I3P . . . D 4 -43.386 37.106 -29.358 0 349.8 ? C6 I3P 1311 A 1 HETATM 7 O O1 I3P . . . D 4 -45.769 36.814 -29.635 0 347.68 ? O1 I3P 1311 A 1 HETATM 8 O O2 I3P . . . D 4 -44.856 38.813 -31.216 0 340.72 ? O2 I3P 1311 A 1 HETATM 9 O O3 I3P . . . D 4 -44.038 41.192 -30.184 0 332.21 ? O3 I3P 1311 A 1 HETATM 10 O O4 I3P . . . D 4 -41.475 40.322 -29.149 0 357.89 ? O4 I3P 1311 A 1 HETATM 11 O O5 I3P . . . D 4 -41.035 37.557 -29.216 0 358.53 ? O5 I3P 1311 A 1 HETATM 12 O O6 I3P . . . D 4 -43.199 35.938 -28.597 0 348.79 ? O6 I3P 1311 A 1 HETATM 13 P P1 I3P . . . D 4 -46.161 35.466 -28.777 0 350.3 ? P1 I3P 1311 A 1 HETATM 14 O O11 I3P . . . D 4 -45.607 34.254 -29.484 0 350.57 ? O11 I3P 1311 A 1 HETATM 15 O O12 I3P . . . D 4 -47.661 35.336 -28.656 0 348.86 ? O12 I3P 1311 A 1 HETATM 16 O O13 I3P . . . D 4 -45.553 35.545 -27.398 0 353.44 ? O13 I3P 1311 A 1 HETATM 17 P P4 I3P . . . D 4 -41.028 41.644 -30.021 0 360.68 ? P4 I3P 1311 A 1 HETATM 18 O O41 I3P . . . D 4 -41.985 41.873 -31.162 0 356.26 ? O41 I3P 1311 A 1 HETATM 19 O O42 I3P . . . D 4 -41.058 42.845 -29.109 0 359.47 ? O42 I3P 1311 A 1 HETATM 20 O O43 I3P . . . D 4 -39.643 41.456 -30.592 0 361.62 ? O43 I3P 1311 A 1 HETATM 21 P P5 I3P . . . D 4 -39.989 37.426 -27.955 0 362.34 ? P5 I3P 1311 A 1 HETATM 22 O O51 I3P . . . D 4 -39.014 36.306 -28.223 0 360.86 ? O51 I3P 1311 A 1 HETATM 23 O O52 I3P . . . D 4 -39.234 38.722 -27.782 0 355.14 ? O52 I3P 1311 A 1 HETATM 24 O O53 I3P . . . D 4 -40.761 37.13 -26.692 0 361.88 ? O53 I3P 1311 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #