data_6K7K # _model_server_result.job_id L34cMVwLZujvLOsN8ZQAww _model_server_result.datetime_utc '2024-10-18 16:32:18' _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 6k7k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1201}' # _entry.id 6K7K # _exptl.entry_id 6K7K _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.entry_id 6K7K _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6K7K _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,H,I,J _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 ? _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 # _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 # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 B 1 NAG C 401 NAG 3 n C NAG 2 B 2 NAG C 402 NAG 3 n C MAN 3 B 3 MAN C 403 MAN # 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 disulf ? disulf1 B SG CYS 91 C CYS 91 1_555 B SG CYS 104 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 B SG CYS 94 C CYS 94 1_555 B SG CYS 102 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 157 C CYS 157 1_555 B SG CYS 171 C CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 B ND2 ASN 107 C ASN 107 1_555 I C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 180 C ASN 180 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale3 B ND2 ASN 294 C ASN 294 1_555 H C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 C O4 NAG . B NAG 2 1_555 C C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A OD1 ASP 414 A ASP 409 1_555 G MG MG . A MG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? metalc ? metalc2 A O THR 416 A THR 411 1_555 G MG MG . A MG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc3 A OD1 ASP 791 A ASP 786 1_555 G MG MG . A MG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc4 A OE2 GLU 812 A GLU 807 1_555 F MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc5 A OE1 GLU 812 A GLU 807 1_555 G MG MG . A MG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? metalc ? metalc6 D O2B ADP . A ADP 1201 1_555 F MG MG . A MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? # _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 ? # _atom_sites.entry_id 6K7K _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 ADP A 1 1201 1101 ADP ADP . E 5 ALF A 1 1202 1201 ALF ALF . F 6 MG A 1 1203 1 MG MG . G 6 MG A 1 1204 2 MG MG . H 7 NAG C 1 401 404 NAG NAG . I 7 NAG C 1 402 405 NAG NAG . J 8 Y01 C 1 403 501 Y01 Y01 . # 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 4 113.008 116.864 155.873 1 108.76 ? PB ADP 1201 A 1 HETATM 2 O O1B ADP . . . D 4 112.765 116.167 154.568 1 108.76 ? O1B ADP 1201 A 1 HETATM 3 O O2B ADP . . . D 4 112.581 118.306 155.864 1 108.76 ? O2B ADP 1201 A 1 HETATM 4 O O3B ADP . . . D 4 114.411 116.67 156.38 1 108.76 ? O3B ADP 1201 A 1 HETATM 5 P PA ADP . . . D 4 111.636 116.401 158.414 1 108.76 ? PA ADP 1201 A 1 HETATM 6 O O1A ADP . . . D 4 111.387 117.859 158.604 1 108.76 ? O1A ADP 1201 A 1 HETATM 7 O O2A ADP . . . D 4 110.545 115.457 158.782 1 108.76 ? O2A ADP 1201 A 1 HETATM 8 O O3A ADP . . . D 4 112.011 116.133 156.886 1 108.76 ? O3A ADP 1201 A 1 HETATM 9 O O5' ADP . . . D 4 112.982 115.986 159.178 1 108.76 ? O5' ADP 1201 A 1 HETATM 10 C C5' ADP . . . D 4 113.918 117.02 159.567 1 108.76 ? C5' ADP 1201 A 1 HETATM 11 C C4' ADP . . . D 4 114.008 117.075 161.071 1 108.76 ? C4' ADP 1201 A 1 HETATM 12 O O4' ADP . . . D 4 114.568 118.353 161.462 1 108.76 ? O4' ADP 1201 A 1 HETATM 13 C C3' ADP . . . D 4 112.689 116.96 161.844 1 108.76 ? C3' ADP 1201 A 1 HETATM 14 O O3' ADP . . . D 4 112.305 115.613 162.093 1 108.76 ? O3' ADP 1201 A 1 HETATM 15 C C2' ADP . . . D 4 112.995 117.746 163.119 1 108.76 ? C2' ADP 1201 A 1 HETATM 16 O O2' ADP . . . D 4 113.735 116.948 164.012 1 108.76 ? O2' ADP 1201 A 1 HETATM 17 C C1' ADP . . . D 4 113.873 118.869 162.575 1 108.76 ? C1' ADP 1201 A 1 HETATM 18 N N9 ADP . . . D 4 113.162 120.082 162.186 1 108.76 ? N9 ADP 1201 A 1 HETATM 19 C C8 ADP . . . D 4 112.449 120.309 161.036 1 108.76 ? C8 ADP 1201 A 1 HETATM 20 N N7 ADP . . . D 4 111.931 121.508 160.97 1 108.76 ? N7 ADP 1201 A 1 HETATM 21 C C5 ADP . . . D 4 112.336 122.118 162.146 1 108.76 ? C5 ADP 1201 A 1 HETATM 22 C C6 ADP . . . D 4 112.116 123.404 162.672 1 108.76 ? C6 ADP 1201 A 1 HETATM 23 N N6 ADP . . . D 4 111.413 124.346 162.053 1 108.76 ? N6 ADP 1201 A 1 HETATM 24 N N1 ADP . . . D 4 112.665 123.69 163.874 1 108.76 ? N1 ADP 1201 A 1 HETATM 25 C C2 ADP . . . D 4 113.38 122.747 164.494 1 108.76 ? C2 ADP 1201 A 1 HETATM 26 N N3 ADP . . . D 4 113.653 121.509 164.096 1 108.76 ? N3 ADP 1201 A 1 HETATM 27 C C4 ADP . . . D 4 113.097 121.252 162.902 1 108.76 ? C4 ADP 1201 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #