data_6QEM # _model_server_result.job_id mN6IYlLIP2v8z_aYkQy56g _model_server_result.datetime_utc '2025-04-15 11:17:42' _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 6qem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":301}' # _entry.id 6QEM # _exptl.entry_id 6QEM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 6QEM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tridecameric _pdbx_struct_assembly.oligomeric_count 13 _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,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 X N N ? 6 Y N N ? 6 Z N N ? 6 AA N N ? 6 BA N N ? 6 CA 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 OG1 THR 238 A THR 238 1_555 O MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc2 A OE1 GLU 262 A GLU 262 1_555 O MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc3 N O2B 08T . A 08T 1001 1_555 O MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc4 B OG1 THR 238 B THR 238 1_555 Q MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc5 B OE1 GLU 262 B GLU 262 1_555 Q MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc6 P O2B 08T . B 08T 1001 1_555 Q MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc7 C OG1 THR 238 C THR 238 1_555 S MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc8 R O2B 08T . C 08T 1001 1_555 S MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc9 D OG1 THR 238 D THR 238 1_555 U MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc10 T O2B 08T . D 08T 1001 1_555 U MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc11 E OG1 THR 238 E THR 238 1_555 W MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc12 E OE1 GLU 262 E GLU 262 1_555 W MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc13 V O2B 08T . E 08T 1001 1_555 W MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? # _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 48 n n PB O2B ADP sing 49 n n PB O3B ADP sing 50 n n PB O3A ADP sing 51 n n O2B HOB2 ADP sing 52 n n O3B HOB3 ADP sing 53 n n PA O1A ADP doub 54 n n PA O2A ADP sing 55 n n PA O3A ADP sing 56 n n PA O5' ADP sing 57 n n O2A HOA2 ADP sing 58 n n O5' C5' ADP sing 59 n n C5' C4' ADP sing 60 n n C5' "H5'1" ADP sing 61 n n C5' "H5'2" ADP sing 62 n n C4' O4' ADP sing 63 n n C4' C3' ADP sing 64 n n C4' H4' ADP sing 65 n n O4' C1' ADP sing 66 n n C3' O3' ADP sing 67 n n C3' C2' ADP sing 68 n n C3' H3' ADP sing 69 n n O3' HO3' ADP sing 70 n n C2' O2' ADP sing 71 n n C2' C1' ADP sing 72 n n C2' H2' ADP sing 73 n n O2' HO2' ADP sing 74 n n C1' N9 ADP sing 75 n n C1' H1' ADP sing 76 n n N9 C8 ADP sing 77 n y N9 C4 ADP sing 78 n y C8 N7 ADP doub 79 n y C8 H8 ADP sing 80 n n N7 C5 ADP sing 81 n y C5 C6 ADP sing 82 n y C5 C4 ADP doub 83 n y C6 N6 ADP sing 84 n n C6 N1 ADP doub 85 n y N6 HN61 ADP sing 86 n n N6 HN62 ADP sing 87 n n N1 C2 ADP sing 88 n y C2 N3 ADP doub 89 n y C2 H2 ADP sing 90 n n N3 C4 ADP sing 91 n y # _atom_sites.entry_id 6QEM _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 N 4 08T A 1 1001 1001 08T 08T . O 5 MG A 1 1002 1002 MG MG . P 4 08T B 1 1001 1001 08T 08T . Q 5 MG B 1 1002 1002 MG MG . R 4 08T C 1 1001 1001 08T 08T . S 5 MG C 1 1002 1002 MG MG . T 4 08T D 1 1001 1001 08T 08T . U 5 MG D 1 1002 1002 MG MG . V 4 08T E 1 1001 1001 08T 08T . W 5 MG E 1 1002 1002 MG MG . X 6 ADP G 1 301 301 ADP ADP . Y 6 ADP H 1 301 301 ADP ADP . Z 6 ADP I 1 301 301 ADP ADP . AA 6 ADP J 1 301 301 ADP ADP . BA 6 ADP K 1 301 301 ADP ADP . CA 6 ADP L 1 301 301 ADP ADP . # 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 . . . BA 6 125.669 125.674 112.709 1 75.47 ? PB ADP 301 K 1 HETATM 2 O O1B ADP . . . BA 6 124.834 125.124 111.58 1 75.47 ? O1B ADP 301 K 1 HETATM 3 O O2B ADP . . . BA 6 126.181 127.077 112.493 1 75.47 ? O2B ADP 301 K 1 HETATM 4 O O3B ADP . . . BA 6 126.7 124.698 113.213 1 75.47 ? O3B ADP 301 K 1 HETATM 5 P PA ADP . . . BA 6 123.737 124.555 114.363 1 75.47 ? PA ADP 301 K 1 HETATM 6 O O1A ADP . . . BA 6 124.639 123.358 114.212 1 75.47 ? O1A ADP 301 K 1 HETATM 7 O O2A ADP . . . BA 6 123.066 124.849 115.681 1 75.47 ? O2A ADP 301 K 1 HETATM 8 O O3A ADP . . . BA 6 124.62 125.822 113.92 1 75.47 ? O3A ADP 301 K 1 HETATM 9 O O5' ADP . . . BA 6 122.559 124.526 113.267 1 75.47 ? O5' ADP 301 K 1 HETATM 10 C C5' ADP . . . BA 6 122.066 125.748 112.72 1 75.47 ? C5' ADP 301 K 1 HETATM 11 C C4' ADP . . . BA 6 120.548 125.706 112.67 1 75.47 ? C4' ADP 301 K 1 HETATM 12 O O4' ADP . . . BA 6 120.119 124.699 111.756 1 75.47 ? O4' ADP 301 K 1 HETATM 13 C C3' ADP . . . BA 6 119.972 125.377 114.036 1 75.47 ? C3' ADP 301 K 1 HETATM 14 O O3' ADP . . . BA 6 118.948 126.324 114.349 1 75.47 ? O3' ADP 301 K 1 HETATM 15 C C2' ADP . . . BA 6 119.464 123.948 113.92 1 75.47 ? C2' ADP 301 K 1 HETATM 16 O O2' ADP . . . BA 6 118.214 123.706 114.582 1 75.47 ? O2' ADP 301 K 1 HETATM 17 C C1' ADP . . . BA 6 119.307 123.734 112.424 1 75.47 ? C1' ADP 301 K 1 HETATM 18 N N9 ADP . . . BA 6 119.742 122.384 112 1 75.47 ? N9 ADP 301 K 1 HETATM 19 C C8 ADP . . . BA 6 120.992 122.032 111.643 1 75.47 ? C8 ADP 301 K 1 HETATM 20 N N7 ADP . . . BA 6 121.04 120.722 111.299 1 75.47 ? N7 ADP 301 K 1 HETATM 21 C C5 ADP . . . BA 6 119.799 120.226 111.433 1 75.47 ? C5 ADP 301 K 1 HETATM 22 C C6 ADP . . . BA 6 119.149 118.916 111.237 1 75.47 ? C6 ADP 301 K 1 HETATM 23 N N6 ADP . . . BA 6 119.866 117.856 110.814 1 75.47 ? N6 ADP 301 K 1 HETATM 24 N N1 ADP . . . BA 6 117.827 118.818 111.489 1 75.47 ? N1 ADP 301 K 1 HETATM 25 C C2 ADP . . . BA 6 117.102 119.871 111.908 1 75.47 ? C2 ADP 301 K 1 HETATM 26 N N3 ADP . . . BA 6 117.633 121.09 112.106 1 75.47 ? N3 ADP 301 K 1 HETATM 27 C C4 ADP . . . BA 6 118.947 121.325 111.891 1 75.47 ? C4 ADP 301 K 1 HETATM 28 H "H5'1" ADP . . . BA 6 122.371 126.591 113.339 1 75.47 ? "H5'1" ADP 301 K 1 HETATM 29 H "H5'2" ADP . . . BA 6 122.464 125.891 111.716 1 75.47 ? "H5'2" ADP 301 K 1 HETATM 30 H H4' ADP . . . BA 6 120.171 126.687 112.352 1 75.47 ? H4' ADP 301 K 1 HETATM 31 H H3' ADP . . . BA 6 120.769 125.421 114.79 1 75.47 ? H3' ADP 301 K 1 HETATM 32 H HO3' ADP . . . BA 6 118.635 126.168 115.248 1 75.47 ? HO3' ADP 301 K 1 HETATM 33 H H2' ADP . . . BA 6 120.235 123.261 114.295 1 75.47 ? H2' ADP 301 K 1 HETATM 34 H HO2' ADP . . . BA 6 117.55 124.363 114.337 1 75.47 ? HO2' ADP 301 K 1 HETATM 35 H H1' ADP . . . BA 6 118.251 123.885 112.176 1 75.47 ? H1' ADP 301 K 1 HETATM 36 H H8 ADP . . . BA 6 121.843 122.699 111.634 1 75.47 ? H8 ADP 301 K 1 HETATM 37 H HN61 ADP . . . BA 6 119.415 116.963 110.683 1 75.47 ? HN61 ADP 301 K 1 HETATM 38 H HN62 ADP . . . BA 6 120.855 117.96 110.635 1 75.47 ? HN62 ADP 301 K 1 HETATM 39 H H2 ADP . . . BA 6 116.045 119.732 112.094 1 75.47 ? H2 ADP 301 K 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 62 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 39 #