data_7PBO # _model_server_result.job_id rqDSYkq0AUmhPxGbzoZuyQ _model_server_result.datetime_utc '2024-10-20 07:34:09' _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 7pbo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":600}' # _entry.id 7PBO # _exptl.entry_id 7PBO _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 _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 _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 K N N ? 6 P N N ? 6 Q N N ? 6 R 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 B OG1 THR 48 B THR 66 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc2 L O2G AGS . B AGS 401 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? metalc ? metalc3 L O2B AGS . B AGS 401 1_555 M MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc4 C OG1 THR 48 C THR 66 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc5 N O2G AGS . C AGS 401 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc6 N O2B AGS . C AGS 401 1_555 O MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? hydrog WATSON-CRICK hydrog1 I N1 DG 1 U DG 1 1_555 J N3 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 I N2 DG 1 U DG 1 1_555 J O2 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 I O6 DG 1 U DG 1 1_555 J N4 DC 15 V DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 I N1 DA 2 U DA 2 1_555 J N3 DT 14 V DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 I N6 DA 2 U DA 2 1_555 J O4 DT 14 V DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 I N1 DA 3 U DA 3 1_555 J N3 DT 13 V DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 I N6 DA 3 U DA 3 1_555 J O4 DT 13 V DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 I N3 DC 4 U DC 4 1_555 J N1 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 I N4 DC 4 U DC 4 1_555 J O6 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 I O2 DC 4 U DC 4 1_555 J N2 DG 12 V DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 I N3 DC 5 U DC 5 1_555 J N1 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 I N4 DC 5 U DC 5 1_555 J O6 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 I O2 DC 5 U DC 5 1_555 J N2 DG 11 V DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 I N3 DT 6 U DT 6 1_555 J N1 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 I O4 DT 6 U DT 6 1_555 J N6 DA 10 V DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 I N3 DT 7 U DT 7 1_555 J N1 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 I O4 DT 7 U DT 7 1_555 J N6 DA 9 V DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 I N3 DC 8 U DC 8 1_555 J N1 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 I N4 DC 8 U DC 8 1_555 J O6 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 I O2 DC 8 U DC 8 1_555 J N2 DG 8 V DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 I N1 DG 9 U DG 9 1_555 J N3 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 I N2 DG 9 U DG 9 1_555 J O2 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 I O6 DG 9 U DG 9 1_555 J N4 DC 7 V DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 I N1 DA 10 U DA 10 1_555 J N3 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 I N6 DA 10 U DA 10 1_555 J O4 DT 6 V DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 I N1 DG 11 U DG 11 1_555 J N3 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 I N2 DG 11 U DG 11 1_555 J O2 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 I O6 DG 11 U DG 11 1_555 J N4 DC 5 V DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 I N1 DG 12 U DG 12 1_555 J N3 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 I N2 DG 12 U DG 12 1_555 J O2 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 I O6 DG 12 U DG 12 1_555 J N4 DC 4 V DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 I N1 DA 13 U DA 13 1_555 J N3 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 I N6 DA 13 U DA 13 1_555 J O4 DT 3 V DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 I N1 DA 14 U DA 14 1_555 J N3 DT 2 V DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 I N6 DA 14 U DA 14 1_555 J O4 DT 2 V DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 I N1 DG 15 U DG 15 1_555 J N3 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 I N2 DG 15 U DG 15 1_555 J O2 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 I O6 DG 15 U DG 15 1_555 J N4 DC 1 V DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 7PBO _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 K 6 ADP A 1 600 600 ADP ADP . L 7 AGS B 1 401 600 AGS AGS . M 8 MG B 1 402 2 MG MG . N 7 AGS C 1 401 600 AGS AGS . O 8 MG C 1 402 1 MG MG . P 6 ADP D 1 600 600 ADP ADP . Q 6 ADP E 1 600 600 ADP ADP . R 6 ADP F 1 600 600 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 . . . Q 6 209.447 226.467 186.514 1 67.92 ? PB ADP 600 E 1 HETATM 2 O O1B ADP . . . Q 6 210.281 226.397 185.262 1 67.92 -1 O1B ADP 600 E 1 HETATM 3 O O2B ADP . . . Q 6 210.224 226.539 187.803 1 67.92 ? O2B ADP 600 E 1 HETATM 4 O O3B ADP . . . Q 6 208.277 225.52 186.546 1 67.92 ? O3B ADP 600 E 1 HETATM 5 P PA ADP . . . Q 6 209.049 228.881 185.182 1 67.92 ? PA ADP 600 E 1 HETATM 6 O O1A ADP . . . Q 6 208.667 228.198 183.894 1 67.92 ? O1A ADP 600 E 1 HETATM 7 O O2A ADP . . . Q 6 210.427 229.479 185.324 1 67.92 -1 O2A ADP 600 E 1 HETATM 8 O O3A ADP . . . Q 6 208.766 227.912 186.428 1 67.92 ? O3A ADP 600 E 1 HETATM 9 O O5' ADP . . . Q 6 207.976 230.028 185.498 1 67.92 ? O5' ADP 600 E 1 HETATM 10 C C5' ADP . . . Q 6 208.113 230.802 186.683 1 67.92 ? C5' ADP 600 E 1 HETATM 11 C C4' ADP . . . Q 6 207.094 231.923 186.641 1 67.92 ? C4' ADP 600 E 1 HETATM 12 O O4' ADP . . . Q 6 207.313 232.797 187.746 1 67.92 ? O4' ADP 600 E 1 HETATM 13 C C3' ADP . . . Q 6 207.271 232.815 185.436 1 67.92 ? C3' ADP 600 E 1 HETATM 14 O O3' ADP . . . Q 6 206.072 233.561 185.207 1 67.92 ? O3' ADP 600 E 1 HETATM 15 C C2' ADP . . . Q 6 208.445 233.677 185.853 1 67.92 ? C2' ADP 600 E 1 HETATM 16 O O2' ADP . . . Q 6 208.473 234.939 185.179 1 67.92 ? O2' ADP 600 E 1 HETATM 17 C C1' ADP . . . Q 6 208.221 233.834 187.355 1 67.92 ? C1' ADP 600 E 1 HETATM 18 N N9 ADP . . . Q 6 209.479 233.75 188.139 1 67.92 ? N9 ADP 600 E 1 HETATM 19 C C8 ADP . . . Q 6 209.912 232.695 188.85 1 67.92 ? C8 ADP 600 E 1 HETATM 20 N N7 ADP . . . Q 6 211.105 232.968 189.435 1 67.92 ? N7 ADP 600 E 1 HETATM 21 C C5 ADP . . . Q 6 211.45 234.217 189.096 1 67.92 ? C5 ADP 600 E 1 HETATM 22 C C6 ADP . . . Q 6 212.581 235.127 189.374 1 67.92 ? C6 ADP 600 E 1 HETATM 23 N N6 ADP . . . Q 6 213.619 234.748 190.15 1 67.92 ? N6 ADP 600 E 1 HETATM 24 N N1 ADP . . . Q 6 212.551 236.354 188.821 1 67.92 ? N1 ADP 600 E 1 HETATM 25 C C2 ADP . . . Q 6 211.534 236.757 188.044 1 67.92 ? C2 ADP 600 E 1 HETATM 26 N N3 ADP . . . Q 6 210.476 235.982 187.755 1 67.92 ? N3 ADP 600 E 1 HETATM 27 C C4 ADP . . . Q 6 210.379 234.724 188.236 1 67.92 ? C4 ADP 600 E 1 HETATM 28 H "H5'1" ADP . . . Q 6 209.125 231.204 186.741 1 67.92 ? "H5'1" ADP 600 E 1 HETATM 29 H "H5'2" ADP . . . Q 6 207.941 230.174 187.56 1 67.92 ? "H5'2" ADP 600 E 1 HETATM 30 H H4' ADP . . . Q 6 206.076 231.51 186.659 1 67.92 ? H4' ADP 600 E 1 HETATM 31 H H3' ADP . . . Q 6 207.54 232.214 184.556 1 67.92 ? H3' ADP 600 E 1 HETATM 32 H HO3' ADP . . . Q 6 206.277 234.466 184.94 1 67.92 ? HO3' ADP 600 E 1 HETATM 33 H H2' ADP . . . Q 6 209.382 233.13 185.678 1 67.92 ? H2' ADP 600 E 1 HETATM 34 H HO2' ADP . . . Q 6 209.192 235.479 185.534 1 67.92 ? HO2' ADP 600 E 1 HETATM 35 H H1' ADP . . . Q 6 207.751 234.811 187.53 1 67.92 ? H1' ADP 600 E 1 HETATM 36 H H8 ADP . . . Q 6 209.383 231.755 188.944 1 67.92 ? H8 ADP 600 E 1 HETATM 37 H HN61 ADP . . . Q 6 213.637 233.827 190.558 1 67.92 ? HN61 ADP 600 E 1 HETATM 38 H HN62 ADP . . . Q 6 214.378 235.391 190.318 1 67.92 ? HN62 ADP 600 E 1 HETATM 39 H H2 ADP . . . Q 6 211.57 237.755 187.634 1 67.92 ? H2 ADP 600 E 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 39 #