data_3LTD # _model_server_result.job_id 5dPk2smUgJJcH1IdW_jgBw _model_server_result.datetime_utc '2024-11-23 21:46:53' _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 3ltd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":82}' # _entry.id 3LTD # _exptl.entry_id 3LTD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 120 _cell.entry_id 3LTD _cell.length_a 73.145 _cell.length_b 73.145 _cell.length_c 54.804 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LTD _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _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' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 18.268 # _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 # 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 SG CYS 25 A CYS 23 1_555 C ZN ZN . A ZN 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 A SG CYS 28 A CYS 26 1_555 C ZN ZN . A ZN 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc3 A SG CYS 48 A CYS 46 1_555 C ZN ZN . A ZN 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc4 A SG CYS 51 A CYS 49 1_555 C ZN ZN . A ZN 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? # _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 3LTD _atom_sites.fract_transf_matrix[1][1] 0.013671 _atom_sites.fract_transf_matrix[1][2] 0.007893 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015786 _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] 0.018247 _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 PEG A 1 80 80 PEG PEG . C 3 ZN A 1 81 81 ZN ZN . D 4 ADP A 1 82 82 ADP ADP . E 2 PEG A 1 83 83 PEG PEG . F 5 CL A 1 84 84 CL CL . G 6 HOH A 1 85 85 HOH HOH . G 6 HOH A 2 86 86 HOH HOH . G 6 HOH A 3 87 87 HOH HOH . G 6 HOH A 4 88 88 HOH HOH . G 6 HOH A 5 89 89 HOH HOH . G 6 HOH A 6 90 90 HOH HOH . G 6 HOH A 7 91 91 HOH HOH . G 6 HOH A 8 92 92 HOH HOH . G 6 HOH A 9 93 93 HOH HOH . G 6 HOH A 10 94 94 HOH HOH . G 6 HOH A 11 95 95 HOH HOH . G 6 HOH A 12 96 96 HOH HOH . G 6 HOH A 13 97 97 HOH HOH . G 6 HOH A 14 98 98 HOH HOH . G 6 HOH A 15 99 99 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 . . . D 4 -22.069 13.978 17.306 1 49.59 ? PB ADP 82 A 1 HETATM 2 O O1B ADP . . . D 4 -21.485 12.559 17.41 1 47.22 ? O1B ADP 82 A 1 HETATM 3 O O2B ADP . . . D 4 -21.612 14.946 18.421 1 48.3 ? O2B ADP 82 A 1 HETATM 4 O O3B ADP . . . D 4 -21.995 14.553 15.876 1 46.21 ? O3B ADP 82 A 1 HETATM 5 P PA ADP . . . D 4 -24.865 14.727 17.284 1 34.34 ? PA ADP 82 A 1 HETATM 6 O O1A ADP . . . D 4 -25.708 13.972 16.267 1 33.17 ? O1A ADP 82 A 1 HETATM 7 O O2A ADP . . . D 4 -24.343 16.152 17.02 1 32.84 ? O2A ADP 82 A 1 HETATM 8 O O3A ADP . . . D 4 -23.645 13.747 17.699 1 40.75 ? O3A ADP 82 A 1 HETATM 9 O O5' ADP . . . D 4 -25.778 14.731 18.618 1 33.53 ? O5' ADP 82 A 1 HETATM 10 C C5' ADP . . . D 4 -25.268 14.853 19.946 1 31.7 ? C5' ADP 82 A 1 HETATM 11 C C4' ADP . . . D 4 -26.379 14.471 20.914 1 29.7 ? C4' ADP 82 A 1 HETATM 12 O O4' ADP . . . D 4 -27.467 15.365 20.688 1 27.97 ? O4' ADP 82 A 1 HETATM 13 C C3' ADP . . . D 4 -26.942 13.07 20.678 1 29.28 ? C3' ADP 82 A 1 HETATM 14 O O3' ADP . . . D 4 -27.329 12.522 21.946 1 30.97 ? O3' ADP 82 A 1 HETATM 15 C C2' ADP . . . D 4 -28.197 13.321 19.886 1 27.29 ? C2' ADP 82 A 1 HETATM 16 O O2' ADP . . . D 4 -29.207 12.328 20.063 1 26.92 ? O2' ADP 82 A 1 HETATM 17 C C1' ADP . . . D 4 -28.658 14.604 20.53 1 26.25 ? C1' ADP 82 A 1 HETATM 18 N N9 ADP . . . D 4 -29.603 15.309 19.65 1 25.11 ? N9 ADP 82 A 1 HETATM 19 C C8 ADP . . . D 4 -29.266 16.23 18.721 1 23.79 ? C8 ADP 82 A 1 HETATM 20 N N7 ADP . . . D 4 -30.375 16.68 18.08 1 23.33 ? N7 ADP 82 A 1 HETATM 21 C C5 ADP . . . D 4 -31.431 16.027 18.599 1 21.34 ? C5 ADP 82 A 1 HETATM 22 C C6 ADP . . . D 4 -32.868 16.05 18.369 1 19.31 ? C6 ADP 82 A 1 HETATM 23 N N6 ADP . . . D 4 -33.379 16.873 17.432 1 18.6 ? N6 ADP 82 A 1 HETATM 24 N N1 ADP . . . D 4 -33.626 15.235 19.129 1 20.92 ? N1 ADP 82 A 1 HETATM 25 C C2 ADP . . . D 4 -33.104 14.423 20.076 1 21.11 ? C2 ADP 82 A 1 HETATM 26 N N3 ADP . . . D 4 -31.792 14.344 20.327 1 20.89 ? N3 ADP 82 A 1 HETATM 27 C C4 ADP . . . D 4 -30.927 15.117 19.633 1 22.74 ? C4 ADP 82 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #