data_1GLD # _model_server_result.job_id 5g57AGOe0cGRuojVJ2Q3_g _model_server_result.datetime_utc '2024-10-10 20:24:55' _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 1gld # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 1GLD # _exptl.entry_id 1GLD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 1GLD _cell.length_a 122.98 _cell.length_b 125.87 _cell.length_c 134.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GLD _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 125.87 0 3 'crystal symmetry operation' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 125.87 0 4 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 C MN MN . G MN 502 1_555 D O4P G3H . G G3H 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc2 C MN MN . G MN 502 1_555 E O2B ADP . G ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc3 C MN MN . G MN 502 1_555 G O HOH . G HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? # _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 ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1GLD _atom_sites.fract_transf_matrix[1][1] 0.008131 _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] 0.007945 _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] 0.007437 _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 MN G 1 502 3 MN MN . D 4 G3H G 1 503 1 G3H G3P . E 5 ADP G 1 504 2 ADP ADP . F 6 HOH F 1 169 21 HOH HOH . F 6 HOH F 2 170 22 HOH HOH . G 6 HOH G 1 505 52 HOH HOH . G 6 HOH G 2 506 54 HOH HOH . G 6 HOH G 3 507 55 HOH HOH . G 6 HOH G 4 508 4 HOH HOH . G 6 HOH G 5 509 5 HOH HOH . G 6 HOH G 6 510 2 HOH HOH . G 6 HOH G 7 511 56 HOH HOH . G 6 HOH G 8 512 13 HOH HOH . G 6 HOH G 9 513 14 HOH HOH . G 6 HOH G 10 514 16 HOH HOH . G 6 HOH G 11 515 17 HOH HOH . G 6 HOH G 12 516 23 HOH HOH . G 6 HOH G 13 517 40 HOH HOH . G 6 HOH G 14 518 48 HOH HOH . G 6 HOH G 15 519 50 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 P PB ADP . . . E 5 20.815 51.5 11.517 1 37.1 ? PB ADP 504 G 1 HETATM 2 O O1B ADP . . . E 5 20.291 50.275 10.803 1 28.46 ? O1B ADP 504 G 1 HETATM 3 O O2B ADP . . . E 5 21.801 51.021 12.549 1 23.86 ? O2B ADP 504 G 1 HETATM 4 O O3B ADP . . . E 5 21.485 52.41 10.515 1 28.58 ? O3B ADP 504 G 1 HETATM 5 P PA ADP . . . E 5 19.278 52.432 13.754 1 44.16 ? PA ADP 504 G 1 HETATM 6 O O1A ADP . . . E 5 19.537 53.911 13.594 1 9.05 ? O1A ADP 504 G 1 HETATM 7 O O2A ADP . . . E 5 19.606 51.741 15.054 1 62.5 ? O2A ADP 504 G 1 HETATM 8 O O3A ADP . . . E 5 19.605 52.44 12.146 1 25.79 ? O3A ADP 504 G 1 HETATM 9 O O5' ADP . . . E 5 17.724 52.299 13.406 1 75 ? O5' ADP 504 G 1 HETATM 10 C C5' ADP . . . E 5 16.988 53.437 12.783 1 13.07 ? C5' ADP 504 G 1 HETATM 11 C C4' ADP . . . E 5 15.642 52.916 12.342 1 30.76 ? C4' ADP 504 G 1 HETATM 12 O O4' ADP . . . E 5 14.564 53.405 13.174 1 72.74 ? O4' ADP 504 G 1 HETATM 13 C C3' ADP . . . E 5 15.302 53.228 10.94 1 5 ? C3' ADP 504 G 1 HETATM 14 O O3' ADP . . . E 5 15.078 52.022 10.255 1 29.36 ? O3' ADP 504 G 1 HETATM 15 C C2' ADP . . . E 5 14.097 54.178 11.045 1 5 ? C2' ADP 504 G 1 HETATM 16 O O2' ADP . . . E 5 13.445 54.118 9.799 1 13.04 ? O2' ADP 504 G 1 HETATM 17 C C1' ADP . . . E 5 13.516 53.89 12.388 1 5 ? C1' ADP 504 G 1 HETATM 18 N N9 ADP . . . E 5 12.969 55.003 13.115 1 5 ? N9 ADP 504 G 1 HETATM 19 C C8 ADP . . . E 5 13.241 56.181 13.73 1 11.24 ? C8 ADP 504 G 1 HETATM 20 N N7 ADP . . . E 5 12.277 56.61 14.52 1 55.35 ? N7 ADP 504 G 1 HETATM 21 C C5 ADP . . . E 5 11.311 55.622 14.432 1 5 ? C5 ADP 504 G 1 HETATM 22 C C6 ADP . . . E 5 10.035 55.507 14.986 1 5 ? C6 ADP 504 G 1 HETATM 23 N N6 ADP . . . E 5 9.465 56.461 15.771 1 40.12 ? N6 ADP 504 G 1 HETATM 24 N N1 ADP . . . E 5 9.294 54.431 14.603 1 34.85 ? N1 ADP 504 G 1 HETATM 25 C C2 ADP . . . E 5 9.808 53.546 13.75 1 5 ? C2 ADP 504 G 1 HETATM 26 N N3 ADP . . . E 5 11.008 53.525 13.238 1 7.71 ? N3 ADP 504 G 1 HETATM 27 C C4 ADP . . . E 5 11.73 54.601 13.603 1 19.55 ? C4 ADP 504 G 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #