data_6QEM # _model_server_result.job_id cFam0RLYvF4IJ7eAFu02EQ _model_server_result.datetime_utc '2025-04-09 21:33:45' _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":"CA","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 . . . CA 6 169.284 118.509 85.171 1 72.57 ? PB ADP 301 L 1 HETATM 2 O O1B ADP . . . CA 6 169.91 117.859 83.966 1 72.57 ? O1B ADP 301 L 1 HETATM 3 O O2B ADP . . . CA 6 167.963 119.197 84.923 1 72.57 ? O2B ADP 301 L 1 HETATM 4 O O3B ADP . . . CA 6 170.266 119.301 85.998 1 72.57 ? O3B ADP 301 L 1 HETATM 5 P PA ADP . . . CA 6 170.107 116.254 86.536 1 72.57 ? PA ADP 301 L 1 HETATM 6 O O1A ADP . . . CA 6 171.382 116.877 86.024 1 72.57 ? O1A ADP 301 L 1 HETATM 7 O O2A ADP . . . CA 6 169.94 115.939 88.001 1 72.57 ? O2A ADP 301 L 1 HETATM 8 O O3A ADP . . . CA 6 168.919 117.243 86.092 1 72.57 ? O3A ADP 301 L 1 HETATM 9 O O5' ADP . . . CA 6 169.819 114.887 85.738 1 72.57 ? O5' ADP 301 L 1 HETATM 10 C C5' ADP . . . CA 6 168.494 114.5 85.377 1 72.57 ? C5' ADP 301 L 1 HETATM 11 C C4' ADP . . . CA 6 168.311 113.019 85.686 1 72.57 ? C4' ADP 301 L 1 HETATM 12 O O4' ADP . . . CA 6 169.162 112.239 84.847 1 72.57 ? O4' ADP 301 L 1 HETATM 13 C C3' ADP . . . CA 6 168.651 112.694 87.135 1 72.57 ? C3' ADP 301 L 1 HETATM 14 O O3' ADP . . . CA 6 167.551 112.047 87.782 1 72.57 ? O3' ADP 301 L 1 HETATM 15 C C2' ADP . . . CA 6 169.852 111.773 87.076 1 72.57 ? C2' ADP 301 L 1 HETATM 16 O O2' ADP . . . CA 6 169.665 110.622 87.903 1 72.57 ? O2' ADP 301 L 1 HETATM 17 C C1' ADP . . . CA 6 169.995 111.372 85.619 1 72.57 ? C1' ADP 301 L 1 HETATM 18 N N9 ADP . . . CA 6 171.397 111.523 85.168 1 72.57 ? N9 ADP 301 L 1 HETATM 19 C C8 ADP . . . CA 6 171.828 112.385 84.226 1 72.57 ? C8 ADP 301 L 1 HETATM 20 N N7 ADP . . . CA 6 173.166 112.263 84.043 1 72.57 ? N7 ADP 301 L 1 HETATM 21 C C5 ADP . . . CA 6 173.605 111.307 84.877 1 72.57 ? C5 ADP 301 L 1 HETATM 22 C C6 ADP . . . CA 6 174.91 110.69 85.186 1 72.57 ? C6 ADP 301 L 1 HETATM 23 N N6 ADP . . . CA 6 176.028 111.097 84.536 1 72.57 ? N6 ADP 301 L 1 HETATM 24 N N1 ADP . . . CA 6 174.935 109.719 86.126 1 72.57 ? N1 ADP 301 L 1 HETATM 25 C C2 ADP . . . CA 6 173.82 109.317 86.769 1 72.57 ? C2 ADP 301 L 1 HETATM 26 N N3 ADP . . . CA 6 172.603 109.838 86.533 1 72.57 ? N3 ADP 301 L 1 HETATM 27 C C4 ADP . . . CA 6 172.434 110.816 85.614 1 72.57 ? C4 ADP 301 L 1 HETATM 28 H "H5'1" ADP . . . CA 6 167.76 115.08 85.938 1 72.57 ? "H5'1" ADP 301 L 1 HETATM 29 H "H5'2" ADP . . . CA 6 168.337 114.68 84.312 1 72.57 ? "H5'2" ADP 301 L 1 HETATM 30 H H4' ADP . . . CA 6 167.262 112.75 85.504 1 72.57 ? H4' ADP 301 L 1 HETATM 31 H H3' ADP . . . CA 6 168.919 113.611 87.675 1 72.57 ? H3' ADP 301 L 1 HETATM 32 H HO3' ADP . . . CA 6 167.707 112.022 88.736 1 72.57 ? HO3' ADP 301 L 1 HETATM 33 H H2' ADP . . . CA 6 170.747 112.327 87.388 1 72.57 ? H2' ADP 301 L 1 HETATM 34 H HO2' ADP . . . CA 6 169.707 110.885 88.832 1 72.57 ? HO2' ADP 301 L 1 HETATM 35 H H1' ADP . . . CA 6 169.676 110.328 85.508 1 72.57 ? H1' ADP 301 L 1 HETATM 36 H H8 ADP . . . CA 6 171.198 113.081 83.688 1 72.57 ? H8 ADP 301 L 1 HETATM 37 H HN61 ADP . . . CA 6 176.92 110.674 84.744 1 72.57 ? HN61 ADP 301 L 1 HETATM 38 H HN62 ADP . . . CA 6 175.967 111.826 83.841 1 72.57 ? HN62 ADP 301 L 1 HETATM 39 H H2 ADP . . . CA 6 173.909 108.534 87.511 1 72.57 ? H2 ADP 301 L 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 68 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 39 #