data_2F89 # _model_server_result.job_id 2XumIjtZK6tcUpWzX_7Jwg _model_server_result.datetime_utc '2024-11-05 23:32:06' _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 2f89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":9001}' # _entry.id 2F89 # _exptl.entry_id 2F89 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 235.069 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description PAMIDRONATE _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 2F89 _cell.length_a 111.569 _cell.length_b 111.569 _cell.length_c 66.482 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F89 _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,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 111.569 111.569 33.241 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _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 A OD1 ASP 100 F ASP 103 1_555 C MN MN . F MN 5001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc2 A OD2 ASP 100 F ASP 103 1_555 E MN MN . F MN 5003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc3 A OD2 ASP 104 F ASP 107 1_555 C MN MN . F MN 5001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc4 A OD2 ASP 104 F ASP 107 1_555 E MN MN . F MN 5003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc5 A OD2 ASP 240 F ASP 243 1_555 D MN MN . F MN 5002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc6 C MN MN . F MN 5001 1_555 F O2 210 . F 210 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc7 C MN MN . F MN 5001 1_555 F O9 210 . F 210 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc8 C MN MN . F MN 5001 1_555 G O HOH . F HOH 9005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc9 C MN MN . F MN 5001 1_555 G O HOH . F HOH 9028 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc10 D MN MN . F MN 5002 1_555 F O3 210 . F 210 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc11 D MN MN . F MN 5002 1_555 F O10 210 . F 210 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc12 D MN MN . F MN 5002 1_555 G O HOH . F HOH 9003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc13 D MN MN . F MN 5002 1_555 G O HOH . F HOH 9004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc14 D MN MN . F MN 5002 1_555 G O HOH . F HOH 9034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc15 E MN MN . F MN 5003 1_555 F O9 210 . F 210 9001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc16 E MN MN . F MN 5003 1_555 G O HOH . F HOH 9009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? metalc ? metalc17 E MN MN . F MN 5003 1_555 G O HOH . F HOH 9012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc18 E MN MN . F MN 5003 1_555 G O HOH . F HOH 9033 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? # _chem_comp.formula 'C3 H11 N O7 P2' _chem_comp.formula_weight 235.069 _chem_comp.id 210 _chem_comp.mon_nstd_flag . _chem_comp.name PAMIDRONATE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID' # 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 P1 O2 210 sing 1 n n P1 O3 210 sing 2 n n P1 O5 210 doub 3 n n P1 C7 210 sing 4 n n O2 HO2 210 sing 5 n n O3 HO3 210 sing 6 n n C7 P8 210 sing 7 n n C7 O14 210 sing 8 n n C7 C16 210 sing 9 n n P8 O9 210 doub 10 n n P8 O10 210 sing 11 n n P8 O12 210 sing 12 n n O10 HO10 210 sing 13 n n O12 HO12 210 sing 14 n n O14 HO14 210 sing 15 n n C16 C19 210 sing 16 n n C16 H161 210 sing 17 n n C16 H162 210 sing 18 n n C19 N22 210 sing 19 n n C19 H191 210 sing 20 n n C19 H192 210 sing 21 n n N22 H221 210 sing 22 n n N22 H222 210 sing 23 n n # _atom_sites.entry_id 2F89 _atom_sites.fract_transf_matrix[1][1] 0.008963 _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] 0.008963 _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] 0.015042 _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 B 2 PO4 F 1 1001 1001 PO4 PO4 . C 3 MN F 1 5001 5001 MN MN . D 3 MN F 1 5002 5002 MN MN . E 3 MN F 1 5003 5003 MN MN . F 4 210 F 1 9001 9001 210 210 . G 5 HOH F 1 9002 1 HOH HOH . G 5 HOH F 2 9003 2 HOH HOH . G 5 HOH F 3 9004 3 HOH HOH . G 5 HOH F 4 9005 4 HOH HOH . G 5 HOH F 5 9006 5 HOH HOH . G 5 HOH F 6 9007 6 HOH HOH . G 5 HOH F 7 9008 7 HOH HOH . G 5 HOH F 8 9009 8 HOH HOH . G 5 HOH F 9 9010 9 HOH HOH . G 5 HOH F 10 9011 10 HOH HOH . G 5 HOH F 11 9012 11 HOH HOH . G 5 HOH F 12 9013 12 HOH HOH . G 5 HOH F 13 9014 13 HOH HOH . G 5 HOH F 14 9015 14 HOH HOH . G 5 HOH F 15 9016 15 HOH HOH . G 5 HOH F 16 9017 16 HOH HOH . G 5 HOH F 17 9018 17 HOH HOH . G 5 HOH F 18 9019 18 HOH HOH . G 5 HOH F 19 9020 19 HOH HOH . G 5 HOH F 20 9021 20 HOH HOH . G 5 HOH F 21 9022 21 HOH HOH . G 5 HOH F 22 9023 22 HOH HOH . G 5 HOH F 23 9024 23 HOH HOH . G 5 HOH F 24 9025 24 HOH HOH . G 5 HOH F 25 9026 25 HOH HOH . G 5 HOH F 26 9027 26 HOH HOH . G 5 HOH F 27 9028 27 HOH HOH . G 5 HOH F 28 9029 28 HOH HOH . G 5 HOH F 29 9030 29 HOH HOH . G 5 HOH F 30 9031 30 HOH HOH . G 5 HOH F 31 9032 31 HOH HOH . G 5 HOH F 32 9033 32 HOH HOH . G 5 HOH F 33 9034 33 HOH HOH . G 5 HOH F 34 9035 34 HOH HOH . G 5 HOH F 35 9036 35 HOH HOH . G 5 HOH F 36 9037 36 HOH HOH . G 5 HOH F 37 9038 37 HOH HOH . G 5 HOH F 38 9039 38 HOH HOH . G 5 HOH F 39 9040 39 HOH HOH . G 5 HOH F 40 9041 40 HOH HOH . G 5 HOH F 41 9042 41 HOH HOH . G 5 HOH F 42 9043 42 HOH HOH . G 5 HOH F 43 9044 43 HOH HOH . G 5 HOH F 44 9045 44 HOH HOH . G 5 HOH F 45 9046 45 HOH HOH . G 5 HOH F 46 9047 46 HOH HOH . G 5 HOH F 47 9048 47 HOH HOH . G 5 HOH F 48 9049 48 HOH HOH . G 5 HOH F 49 9050 49 HOH HOH . G 5 HOH F 50 9051 50 HOH HOH . G 5 HOH F 51 9052 51 HOH HOH . G 5 HOH F 52 9053 52 HOH HOH . G 5 HOH F 53 9054 53 HOH HOH . G 5 HOH F 54 9055 54 HOH HOH . G 5 HOH F 55 9056 55 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 P1 210 . . . F 4 15.496 75.787 24.112 1 59.7 ? P1 210 9001 F 1 HETATM 2 O O2 210 . . . F 4 16.81 75.932 23.464 1 61.09 ? O2 210 9001 F 1 HETATM 3 O O3 210 . . . F 4 15.289 74.362 24.771 1 60.78 ? O3 210 9001 F 1 HETATM 4 O O5 210 . . . F 4 14.126 75.803 23.273 1 64.24 ? O5 210 9001 F 1 HETATM 5 C C7 210 . . . F 4 15.148 77.225 25.251 1 61.24 ? C7 210 9001 F 1 HETATM 6 P P8 210 . . . F 4 16.511 77.47 26.518 1 63.69 ? P8 210 9001 F 1 HETATM 7 O O9 210 . . . F 4 17.871 77.919 26.054 1 60.11 ? O9 210 9001 F 1 HETATM 8 O O10 210 . . . F 4 16.502 76.019 27.221 1 51.56 ? O10 210 9001 F 1 HETATM 9 O O12 210 . . . F 4 15.868 78.601 27.425 1 59.52 ? O12 210 9001 F 1 HETATM 10 O O14 210 . . . F 4 13.948 76.85 25.913 1 63.97 ? O14 210 9001 F 1 HETATM 11 C C16 210 . . . F 4 14.88 78.559 24.424 1 62.38 ? C16 210 9001 F 1 HETATM 12 C C19 210 . . . F 4 14.28 79.743 25.279 1 64.28 ? C19 210 9001 F 1 HETATM 13 N N22 210 . . . F 4 12.847 80.057 24.916 1 67.81 ? N22 210 9001 F 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 13 #