data_8TKD # _model_server_result.job_id '_QunzMSoYTsJoccnxLXcsQ' _model_server_result.datetime_utc '2024-11-21 14:12:53' _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 8tkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":3002}' # _entry.id 8TKD # _exptl.entry_id 8TKD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 420.096 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE _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 8TKD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H,I,J,K,L,M,N,O,P _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 ? _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 F N N ? 3 I N N ? 3 L N N ? 3 O 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 disulf ? disulf1 A SG CYS 2455 A CYS 2455 1_555 A SG CYS 2461 A CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 2455 B CYS 2455 1_555 B SG CYS 2461 B CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 C SG CYS 2455 C CYS 2455 1_555 C SG CYS 2461 C CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 D SG CYS 2455 D CYS 2455 1_555 D SG CYS 2461 D CYS 2461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A SG CYS 2538 A CYS 2538 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc2 A SG CYS 2541 A CYS 2541 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc3 A NE2 HIS 2558 A HIS 2558 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc4 A ND1 HIS 2563 A HIS 2563 1_555 E ZN ZN . A ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc5 B SG CYS 2538 B CYS 2538 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc6 B SG CYS 2541 B CYS 2541 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc7 B NE2 HIS 2558 B HIS 2558 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc8 B ND1 HIS 2563 B HIS 2563 1_555 H ZN ZN . B ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc9 C SG CYS 2538 C CYS 2538 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc10 C SG CYS 2541 C CYS 2541 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc11 C NE2 HIS 2558 C HIS 2558 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc12 C ND1 HIS 2563 C HIS 2563 1_555 K ZN ZN . C ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc13 D SG CYS 2538 D CYS 2538 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc14 D SG CYS 2541 D CYS 2541 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc15 D NE2 HIS 2558 D HIS 2558 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc16 D ND1 HIS 2563 D HIS 2563 1_555 N ZN ZN . D ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? # _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 199 n n C1 C6 I3P sing 200 n n C1 O1 I3P sing 201 n n C1 H1 I3P sing 202 n n C2 C3 I3P sing 203 n n C2 O2 I3P sing 204 n n C2 H2 I3P sing 205 n n C3 C4 I3P sing 206 n n C3 O3 I3P sing 207 n n C3 H3 I3P sing 208 n n C4 C5 I3P sing 209 n n C4 O4 I3P sing 210 n n C4 H4 I3P sing 211 n n C5 C6 I3P sing 212 n n C5 O5 I3P sing 213 n n C5 H5 I3P sing 214 n n C6 O6 I3P sing 215 n n C6 H6 I3P sing 216 n n O1 P1 I3P sing 217 n n O2 HO2 I3P sing 218 n n O3 HO3 I3P sing 219 n n O4 P4 I3P sing 220 n n O5 P5 I3P sing 221 n n O6 HO6 I3P sing 222 n n P1 O11 I3P doub 223 n n P1 O12 I3P sing 224 n n P1 O13 I3P sing 225 n n O12 HO12 I3P sing 226 n n O13 HO13 I3P sing 227 n n P4 O41 I3P doub 228 n n P4 O42 I3P sing 229 n n P4 O43 I3P sing 230 n n O42 HO42 I3P sing 231 n n O43 HO43 I3P sing 232 n n P5 O51 I3P doub 233 n n P5 O52 I3P sing 234 n n P5 O53 I3P sing 235 n n O52 HO52 I3P sing 236 n n O53 HO53 I3P sing 237 n n # _atom_sites.entry_id 8TKD _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 ZN A 1 3001 3001 ZN ZN . F 3 I3P A 1 3002 3002 I3P I3P . G 4 ATP A 1 3003 3005 ATP ATP . H 2 ZN B 1 3001 3001 ZN ZN . I 3 I3P B 1 3002 3002 I3P I3P . J 4 ATP B 1 3003 3005 ATP ATP . K 2 ZN C 1 3001 3001 ZN ZN . L 3 I3P C 1 3002 3002 I3P I3P . M 4 ATP C 1 3003 3005 ATP ATP . N 2 ZN D 1 3001 3001 ZN ZN . O 3 I3P D 1 3002 3002 I3P I3P . P 4 ATP D 1 3003 3005 ATP ATP . # 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 . . . I 3 163.598 252.627 170.231 1 103.1 ? C1 I3P 3002 B 1 HETATM 2 C C2 I3P . . . I 3 164.717 252.999 169.278 1 103.1 ? C2 I3P 3002 B 1 HETATM 3 C C3 I3P . . . I 3 164.433 252.494 167.866 1 103.1 ? C3 I3P 3002 B 1 HETATM 4 C C4 I3P . . . I 3 164.417 250.968 167.789 1 103.1 ? C4 I3P 3002 B 1 HETATM 5 C C5 I3P . . . I 3 163.902 250.378 169.113 1 103.1 ? C5 I3P 3002 B 1 HETATM 6 C C6 I3P . . . I 3 162.92 251.313 169.832 1 103.1 ? C6 I3P 3002 B 1 HETATM 7 O O1 I3P . . . I 3 162.678 253.692 170.277 1 103.1 ? O1 I3P 3002 B 1 HETATM 8 O O2 I3P . . . I 3 164.897 254.4 169.285 1 103.1 ? O2 I3P 3002 B 1 HETATM 9 O O3 I3P . . . I 3 163.181 252.987 167.429 1 103.1 ? O3 I3P 3002 B 1 HETATM 10 O O4 I3P . . . I 3 165.701 250.487 167.54 1 103.1 ? O4 I3P 3002 B 1 HETATM 11 O O5 I3P . . . I 3 163.282 249.159 168.847 1 103.1 ? O5 I3P 3002 B 1 HETATM 12 O O6 I3P . . . I 3 162.388 250.643 170.942 1 103.1 ? O6 I3P 3002 B 1 HETATM 13 P P1 I3P . . . I 3 161.626 253.809 171.595 1 103.1 ? P1 I3P 3002 B 1 HETATM 14 O O11 I3P . . . I 3 160.747 252.587 171.4 1 103.1 ? O11 I3P 3002 B 1 HETATM 15 O O12 I3P . . . I 3 160.931 255.156 171.469 1 103.1 ? O12 I3P 3002 B 1 HETATM 16 O O13 I3P . . . I 3 162.568 253.724 172.816 1 103.1 ? O13 I3P 3002 B 1 HETATM 17 P P4 I3P . . . I 3 166.333 250.25 165.982 1 103.1 ? P4 I3P 3002 B 1 HETATM 18 O O41 I3P . . . I 3 165.08 250.064 165.134 1 103.1 ? O41 I3P 3002 B 1 HETATM 19 O O42 I3P . . . I 3 167.173 248.978 166.079 1 103.1 ? O42 I3P 3002 B 1 HETATM 20 O O43 I3P . . . I 3 167.148 251.5 165.654 1 103.1 ? O43 I3P 3002 B 1 HETATM 21 P P5 I3P . . . I 3 164.115 247.687 168.767 1 103.1 ? P5 I3P 3002 B 1 HETATM 22 O O51 I3P . . . I 3 163.495 246.926 167.595 1 103.1 ? O51 I3P 3002 B 1 HETATM 23 O O52 I3P . . . I 3 165.589 248.03 168.558 1 103.1 ? O52 I3P 3002 B 1 HETATM 24 O O53 I3P . . . I 3 163.781 247.057 170.115 1 103.1 ? O53 I3P 3002 B 1 HETATM 25 H H1 I3P . . . I 3 164.015 252.494 171.097 1 103.1 ? H1 I3P 3002 B 1 HETATM 26 H H2 I3P . . . I 3 165.524 252.563 169.595 1 103.1 ? H2 I3P 3002 B 1 HETATM 27 H H3 I3P . . . I 3 165.144 252.817 167.291 1 103.1 ? H3 I3P 3002 B 1 HETATM 28 H H4 I3P . . . I 3 163.81 250.703 167.081 1 103.1 ? H4 I3P 3002 B 1 HETATM 29 H H5 I3P . . . I 3 164.666 250.248 169.696 1 103.1 ? H5 I3P 3002 B 1 HETATM 30 H H6 I3P . . . I 3 162.213 251.533 169.205 1 103.1 ? H6 I3P 3002 B 1 HETATM 31 H HO2 I3P . . . I 3 164.131 254.742 169.149 1 103.1 ? HO2 I3P 3002 B 1 HETATM 32 H HO3 I3P . . . I 3 163.094 253.778 167.727 1 103.1 ? HO3 I3P 3002 B 1 HETATM 33 H HO6 I3P . . . I 3 161.794 251.119 171.318 1 103.1 ? HO6 I3P 3002 B 1 # _model_server_stats.io_time_ms 192 _model_server_stats.parse_time_ms 45 _model_server_stats.create_model_time_ms 154 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #