data_5L22 # _model_server_result.job_id zaK1p_4D28h1rizUpofeXw _model_server_result.datetime_utc '2024-11-23 10:08:53' _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 5l22 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _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 . . . E 2 28.536 10.439 1.939 1 74.94 ? PB ADP 701 A 1 HETATM 2 O O1B ADP . . . E 2 29.011 10.215 0.523 1 48.9 ? O1B ADP 701 A 1 HETATM 3 O O2B ADP . . . E 2 28.433 9.182 2.768 1 87.49 ? O2B ADP 701 A 1 HETATM 4 O O3B ADP . . . E 2 29.201 11.598 2.643 1 116.02 ? O3B ADP 701 A 1 HETATM 5 P PA ADP . . . E 2 26.068 11.132 3.053 1 79.92 ? PA ADP 701 A 1 HETATM 6 O O1A ADP . . . E 2 24.99 10.075 3.034 1 92.61 ? O1A ADP 701 A 1 HETATM 7 O O2A ADP . . . E 2 26.955 11.283 4.266 1 107.09 ? O2A ADP 701 A 1 HETATM 8 O O3A ADP . . . E 2 27.008 10.916 1.765 1 74.61 ? O3A ADP 701 A 1 HETATM 9 O O5' ADP . . . E 2 25.381 12.557 2.752 1 186.62 ? O5' ADP 701 A 1 HETATM 10 C C5' ADP . . . E 2 26.059 13.77 3.074 1 174.14 ? C5' ADP 701 A 1 HETATM 11 C C4' ADP . . . E 2 25.051 14.911 3.146 1 143.85 ? C4' ADP 701 A 1 HETATM 12 O O4' ADP . . . E 2 23.791 14.413 3.604 1 152.25 ? O4' ADP 701 A 1 HETATM 13 C C3' ADP . . . E 2 25.507 15.988 4.117 1 151.99 ? C3' ADP 701 A 1 HETATM 14 O O3' ADP . . . E 2 25.643 17.238 3.434 1 153.46 ? O3' ADP 701 A 1 HETATM 15 C C2' ADP . . . E 2 24.429 16.089 5.176 1 180.3 ? C2' ADP 701 A 1 HETATM 16 O O2' ADP . . . E 2 23.867 17.405 5.179 1 229.74 ? O2' ADP 701 A 1 HETATM 17 C C1' ADP . . . E 2 23.366 15.069 4.802 1 158 ? C1' ADP 701 A 1 HETATM 18 N N9 ADP . . . E 2 23.221 14.073 5.894 1 151.63 ? N9 ADP 701 A 1 HETATM 19 C C8 ADP . . . E 2 23.998 12.989 6.078 1 149.62 ? C8 ADP 701 A 1 HETATM 20 N N7 ADP . . . E 2 23.602 12.282 7.167 1 143.94 ? N7 ADP 701 A 1 HETATM 21 C C5 ADP . . . E 2 22.546 12.922 7.702 1 140.78 ? C5 ADP 701 A 1 HETATM 22 C C6 ADP . . . E 2 21.648 12.716 8.862 1 129.78 ? C6 ADP 701 A 1 HETATM 23 N N6 ADP . . . E 2 21.805 11.655 9.69 1 119.9 ? N6 ADP 701 A 1 HETATM 24 N N1 ADP . . . E 2 20.666 13.622 9.066 1 143.35 ? N1 ADP 701 A 1 HETATM 25 C C2 ADP . . . E 2 20.499 14.68 8.251 1 144.41 ? C2 ADP 701 A 1 HETATM 26 N N3 ADP . . . E 2 21.276 14.929 7.182 1 137.35 ? N3 ADP 701 A 1 HETATM 27 C C4 ADP . . . E 2 22.299 14.102 6.859 1 141.94 ? C4 ADP 701 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #