data_7PMB # _model_server_result.job_id H0Olz43GUhvCKHGmmBNkHA _model_server_result.datetime_utc '2024-11-24 18:02:15' _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 7pmb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1902}' # _entry.id 7PMB # _exptl.entry_id 7PMB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 7PMB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PMB _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H _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 ? 6 F N N ? 6 G 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 A C TRP 1 H TRP 1 1_555 A N EEP 2 H EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale2 A CD1 TRP 1 H TRP 1 1_555 A SG CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.732 ? covale ? covale3 A N TRP 1 H TRP 1 1_555 A C ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale4 A C EEP 2 H EEP 2 1_555 A N ALA 3 H ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale5 A C ALA 3 H ALA 3 1_555 A N DTH 4 H DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 A C DTH 4 H DTH 4 1_555 A N CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale7 A C CYS 5 H CYS 5 1_555 A N HYP 6 H HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale8 A C HYP 6 H HYP 6 1_555 A N ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.369 ? covale ? covale9 D C GLU 74 C GLU 72 1_555 D N HIC 75 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 D C HIC 75 C HIC 73 1_555 D N GLY 76 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 C OG1 THR 170 A THR 170 1_555 E MG MG . A MG 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc2 E MG MG . A MG 1901 1_555 F O1B ADP . A ADP 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc3 G O2B ADP . C ADP 401 1_555 H MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7PMB _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 5 MG A 1 1901 793 MG MG . F 6 ADP A 1 1902 794 ADP ADP . G 6 ADP C 1 401 376 ADP ADP . H 5 MG C 1 402 377 MG MG . # 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 P PB ADP . . . F 6 176.956 167.433 169.53 1 54.07 ? PB ADP 1902 A 1 HETATM 2 O O1B ADP . . . F 6 177.21 167.302 168.052 1 54.07 ? O1B ADP 1902 A 1 HETATM 3 O O2B ADP . . . F 6 176.696 166.139 170.254 1 54.07 ? O2B ADP 1902 A 1 HETATM 4 O O3B ADP . . . F 6 175.999 168.539 169.881 1 54.07 ? O3B ADP 1902 A 1 HETATM 5 P PA ADP . . . F 6 179.645 166.935 170.063 1 54.07 ? PA ADP 1902 A 1 HETATM 6 O O1A ADP . . . F 6 179.249 165.674 169.342 1 54.07 ? O1A ADP 1902 A 1 HETATM 7 O O2A ADP . . . F 6 180.834 167.727 169.596 1 54.07 ? O2A ADP 1902 A 1 HETATM 8 O O3A ADP . . . F 6 178.377 167.919 170.096 1 54.07 ? O3A ADP 1902 A 1 HETATM 9 O O5' ADP . . . F 6 179.827 166.594 171.624 1 54.07 ? O5' ADP 1902 A 1 HETATM 10 C C5' ADP . . . F 6 180.319 167.586 172.525 1 54.07 ? C5' ADP 1902 A 1 HETATM 11 C C4' ADP . . . F 6 181.767 167.354 172.96 1 54.07 ? C4' ADP 1902 A 1 HETATM 12 O O4' ADP . . . F 6 181.882 166.37 173.994 1 54.07 ? O4' ADP 1902 A 1 HETATM 13 C C3' ADP . . . F 6 182.708 166.881 171.88 1 54.07 ? C3' ADP 1902 A 1 HETATM 14 O O3' ADP . . . F 6 183.14 167.99 171.095 1 54.07 ? O3' ADP 1902 A 1 HETATM 15 C C2' ADP . . . F 6 183.845 166.379 172.726 1 54.07 ? C2' ADP 1902 A 1 HETATM 16 O O2' ADP . . . F 6 184.574 167.491 173.243 1 54.07 ? O2' ADP 1902 A 1 HETATM 17 C C1' ADP . . . F 6 183.13 165.679 173.863 1 54.07 ? C1' ADP 1902 A 1 HETATM 18 N N9 ADP . . . F 6 182.831 164.263 173.564 1 54.07 ? N9 ADP 1902 A 1 HETATM 19 C C8 ADP . . . F 6 181.628 163.787 173.214 1 54.07 ? C8 ADP 1902 A 1 HETATM 20 N N7 ADP . . . F 6 181.669 162.446 173.032 1 54.07 ? N7 ADP 1902 A 1 HETATM 21 C C5 ADP . . . F 6 182.922 162.046 173.285 1 54.07 ? C5 ADP 1902 A 1 HETATM 22 C C6 ADP . . . F 6 183.642 160.76 173.28 1 54.07 ? C6 ADP 1902 A 1 HETATM 23 N N6 ADP . . . F 6 183.008 159.61 172.957 1 54.07 ? N6 ADP 1902 A 1 HETATM 24 N N1 ADP . . . F 6 184.948 160.774 173.606 1 54.07 ? N1 ADP 1902 A 1 HETATM 25 C C2 ADP . . . F 6 185.581 161.915 173.924 1 54.07 ? C2 ADP 1902 A 1 HETATM 26 N N3 ADP . . . F 6 184.989 163.118 173.948 1 54.07 ? N3 ADP 1902 A 1 HETATM 27 C C4 ADP . . . F 6 183.68 163.245 173.65 1 54.07 ? C4 ADP 1902 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #