data_5L22 # _model_server_result.job_id jdZNI5QzXAfsA18U1-d9ag _model_server_result.datetime_utc '2024-11-21 14:15:30' _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 5l22 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5L22 # _exptl.entry_id 5L22 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 100.47 _cell.angle_gamma 90 _cell.entry_id 5L22 _cell.length_a 118.672 _cell.length_b 97.938 _cell.length_c 179.823 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L22 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 _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 x,y,z _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 ? 2 C N N ? 2 E 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 metalc ? metalc1 A OG SER 373 B SER 373 1_555 D MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 A OE1 GLN 414 B GLN 414 1_555 D MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc3 C O2B ADP . B ADP 601 1_555 D MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc4 C O3B ADP . B ADP 601 1_555 D MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc5 B OG SER 373 A SER 373 1_555 F MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc6 B OE1 GLN 414 A GLN 414 1_555 F MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc7 B OE1 GLU 494 A GLU 494 1_555 F MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc8 E O2B ADP . A ADP 701 1_555 F MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? # _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 5L22 _atom_sites.fract_transf_matrix[1][1] 0.008427 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001556 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010211 _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] 0.005655 _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 2 ADP B 1 601 700 ADP ADP . D 3 MG B 1 602 1 MG MG . E 2 ADP A 1 701 701 ADP ADP . F 3 MG A 1 702 2 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 . . . C 2 45.625 0.206 16.461 1 78.66 ? PB ADP 601 B 1 HETATM 2 O O1B ADP . . . C 2 46.571 -0.383 15.442 1 69.07 ? O1B ADP 601 B 1 HETATM 3 O O2B ADP . . . C 2 45.865 1.665 16.765 1 121.07 ? O2B ADP 601 B 1 HETATM 4 O O3B ADP . . . C 2 44.174 -0.155 16.246 1 63.41 ? O3B ADP 601 B 1 HETATM 5 P PA ADP . . . C 2 45.191 -0.253 19.185 1 67.94 ? PA ADP 601 B 1 HETATM 6 O O1A ADP . . . C 2 43.73 -0.117 18.83 1 76.01 ? O1A ADP 601 B 1 HETATM 7 O O2A ADP . . . C 2 45.892 0.856 19.932 1 96.84 ? O2A ADP 601 B 1 HETATM 8 O O3A ADP . . . C 2 46.013 -0.545 17.831 1 73.89 ? O3A ADP 601 B 1 HETATM 9 O O5' ADP . . . C 2 45.383 -1.62 20.014 1 157.57 ? O5' ADP 601 B 1 HETATM 10 C C5' ADP . . . C 2 44.498 -2.719 19.813 1 158.76 ? C5' ADP 601 B 1 HETATM 11 C C4' ADP . . . C 2 44.705 -3.747 20.918 1 149.01 ? C4' ADP 601 B 1 HETATM 12 O O4' ADP . . . C 2 44.615 -3.109 22.194 1 171.13 ? O4' ADP 601 B 1 HETATM 13 C C3' ADP . . . C 2 43.644 -4.835 20.865 1 161.82 ? C3' ADP 601 B 1 HETATM 14 O O3' ADP . . . C 2 44.26 -6.113 20.682 1 169.64 ? O3' ADP 601 B 1 HETATM 15 C C2' ADP . . . C 2 42.925 -4.791 22.198 1 201.33 ? C2' ADP 601 B 1 HETATM 16 O O2' ADP . . . C 2 43.075 -6.041 22.877 1 260.25 ? O2' ADP 601 B 1 HETATM 17 C C1' ADP . . . C 2 43.581 -3.679 23.001 1 179.32 ? C1' ADP 601 B 1 HETATM 18 N N9 ADP . . . C 2 42.574 -2.64 23.333 1 175.92 ? N9 ADP 601 B 1 HETATM 19 C C8 ADP . . . C 2 42.192 -1.63 22.529 1 176.35 ? C8 ADP 601 B 1 HETATM 20 N N7 ADP . . . C 2 41.254 -0.854 23.13 1 189.42 ? N7 ADP 601 B 1 HETATM 21 C C5 ADP . . . C 2 41.022 -1.372 24.35 1 188.81 ? C5 ADP 601 B 1 HETATM 22 C C6 ADP . . . C 2 40.15 -1.043 25.502 1 201.76 ? C6 ADP 601 B 1 HETATM 23 N N6 ADP . . . C 2 39.315 0.023 25.467 1 209.81 ? N6 ADP 601 B 1 HETATM 24 N N1 ADP . . . C 2 40.215 -1.845 26.589 1 194.56 ? N1 ADP 601 B 1 HETATM 25 C C2 ADP . . . C 2 41.039 -2.907 26.636 1 191.05 ? C2 ADP 601 B 1 HETATM 26 N N3 ADP . . . C 2 41.857 -3.263 25.629 1 190.48 ? N3 ADP 601 B 1 HETATM 27 C C4 ADP . . . C 2 41.895 -2.549 24.479 1 189.38 ? C4 ADP 601 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #