data_4O3M # _model_server_result.job_id ucx5gE8aHy3R65HKxCz2kQ _model_server_result.datetime_utc '2024-12-26 10:59:20' _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 4o3m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1303}' # _entry.id 4O3M # _exptl.entry_id 4O3M _exptl.method 'X-RAY DIFFRACTION' # _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.14 _cell.angle_gamma 90 _cell.entry_id 4O3M _cell.length_a 100.93 _cell.length_b 164.68 _cell.length_c 50.98 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O3M _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 397 A CYS 1036 1_555 E ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc2 A SG CYS 416 A CYS 1055 1_555 E ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc3 A SG CYS 424 A CYS 1063 1_555 E ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc4 A SG CYS 427 A CYS 1066 1_555 E ZN ZN . A ZN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc5 D CA CA . A CA 1301 1_555 F O1B ADP . A ADP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc6 D CA CA . A CA 1301 1_555 O O HOH . A HOH 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc7 D CA CA . A CA 1301 1_555 O O HOH . A HOH 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc8 D CA CA . A CA 1301 1_555 O O HOH . A HOH 1443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? hydrog WATSON-CRICK hydrog1 B N3 DC 3 P DC 3 1_555 C N1 DG 14 T DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 3 P DC 3 1_555 C O6 DG 14 T DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 3 P DC 3 1_555 C N2 DG 14 T DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 4 P DG 4 1_555 C N3 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 4 P DG 4 1_555 C O2 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 4 P DG 4 1_555 C N4 DC 13 T DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DT 5 P DT 5 1_555 C N1 DA 12 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O4 DT 5 P DT 5 1_555 C N6 DA 12 T DA 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 6 P DC 6 1_555 C N1 DG 11 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 6 P DC 6 1_555 C O6 DG 11 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 6 P DC 6 1_555 C N2 DG 11 T DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 7 P DG 7 1_555 C N3 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 7 P DG 7 1_555 C O2 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 7 P DG 7 1_555 C N4 DC 10 T DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DA 8 P DA 8 1_555 C N3 DT 9 T DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N6 DA 8 P DA 8 1_555 C O4 DT 9 T DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 DG 9 P DG 9 1_555 C N3 DC 8 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 DG 9 P DG 9 1_555 C O2 DC 8 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 DG 9 P DG 9 1_555 C N4 DC 8 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DA 10 P DA 10 1_555 C N3 DT 7 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N6 DA 10 P DA 10 1_555 C O4 DT 7 T DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N3 DT 11 P DT 11 1_555 C N1 DA 6 T DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O4 DT 11 P DT 11 1_555 C N6 DA 6 T DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog24 B N4 DC 12 P DC 12 1_555 C O6 DG 5 T DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog25 B N4 DC 13 P DC 13 1_555 C O6 DG 4 T DG 4 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 4O3M _atom_sites.fract_transf_matrix[1][1] 0.009908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000024 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006072 _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] 0.019616 _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 CA A 1 1301 3000 CA CA . E 5 ZN A 1 1302 3500 ZN ZN . F 6 ADP A 1 1303 4000 ADP ADP . G 7 EDO A 1 1304 1 EDO EDO . H 7 EDO A 1 1305 2 EDO EDO . I 7 EDO A 1 1306 3 EDO EDO . J 7 EDO A 1 1307 4 EDO EDO . K 7 EDO A 1 1308 5 EDO EDO . L 7 EDO A 1 1309 6 EDO EDO . M 7 EDO A 1 1310 7 EDO EDO . N 7 EDO A 1 1311 8 EDO EDO . O 8 HOH A 1 1401 1 HOH HOH . O 8 HOH A 2 1402 2 HOH HOH . O 8 HOH A 3 1403 3 HOH HOH . O 8 HOH A 4 1404 6 HOH HOH . O 8 HOH A 5 1405 7 HOH HOH . O 8 HOH A 6 1406 8 HOH HOH . O 8 HOH A 7 1407 9 HOH HOH . O 8 HOH A 8 1408 10 HOH HOH . O 8 HOH A 9 1409 11 HOH HOH . O 8 HOH A 10 1410 12 HOH HOH . O 8 HOH A 11 1411 13 HOH HOH . O 8 HOH A 12 1412 14 HOH HOH . O 8 HOH A 13 1413 15 HOH HOH . O 8 HOH A 14 1414 16 HOH HOH . O 8 HOH A 15 1415 17 HOH HOH . O 8 HOH A 16 1416 18 HOH HOH . O 8 HOH A 17 1417 19 HOH HOH . O 8 HOH A 18 1418 20 HOH HOH . O 8 HOH A 19 1419 21 HOH HOH . O 8 HOH A 20 1420 24 HOH HOH . O 8 HOH A 21 1421 29 HOH HOH . O 8 HOH A 22 1422 30 HOH HOH . O 8 HOH A 23 1423 31 HOH HOH . O 8 HOH A 24 1424 32 HOH HOH . O 8 HOH A 25 1425 33 HOH HOH . O 8 HOH A 26 1426 36 HOH HOH . O 8 HOH A 27 1427 37 HOH HOH . O 8 HOH A 28 1428 40 HOH HOH . O 8 HOH A 29 1429 42 HOH HOH . O 8 HOH A 30 1430 44 HOH HOH . O 8 HOH A 31 1431 45 HOH HOH . O 8 HOH A 32 1432 46 HOH HOH . O 8 HOH A 33 1433 47 HOH HOH . O 8 HOH A 34 1434 50 HOH HOH . O 8 HOH A 35 1435 51 HOH HOH . O 8 HOH A 36 1436 52 HOH HOH . O 8 HOH A 37 1437 53 HOH HOH . O 8 HOH A 38 1438 55 HOH HOH . O 8 HOH A 39 1439 56 HOH HOH . O 8 HOH A 40 1440 57 HOH HOH . O 8 HOH A 41 1441 59 HOH HOH . O 8 HOH A 42 1442 61 HOH HOH . O 8 HOH A 43 1443 64 HOH HOH . O 8 HOH A 44 1444 65 HOH HOH . O 8 HOH A 45 1445 66 HOH HOH . O 8 HOH A 46 1446 67 HOH HOH . O 8 HOH A 47 1447 68 HOH HOH . O 8 HOH A 48 1448 69 HOH HOH . O 8 HOH A 49 1449 73 HOH HOH . O 8 HOH A 50 1450 74 HOH HOH . O 8 HOH A 51 1451 81 HOH HOH . O 8 HOH A 52 1452 82 HOH HOH . O 8 HOH A 53 1453 88 HOH HOH . O 8 HOH A 54 1454 89 HOH HOH . O 8 HOH A 55 1455 91 HOH HOH . O 8 HOH A 56 1456 92 HOH HOH . O 8 HOH A 57 1457 93 HOH HOH . O 8 HOH A 58 1458 94 HOH HOH . P 8 HOH P 1 101 83 HOH HOH . Q 8 HOH T 1 101 27 HOH HOH . # 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 . . . F 6 125.423 12.335 61.801 1 63.99 ? PB ADP 1303 A 1 HETATM 2 O O1B ADP . . . F 6 124.171 13.231 61.644 1 65.51 ? O1B ADP 1303 A 1 HETATM 3 O O2B ADP . . . F 6 126.456 12.463 60.659 1 63.35 ? O2B ADP 1303 A 1 HETATM 4 O O3B ADP . . . F 6 124.948 10.812 61.902 1 59.96 ? O3B ADP 1303 A 1 HETATM 5 P PA ADP . . . F 6 126.213 13.695 64.315 1 62.87 ? PA ADP 1303 A 1 HETATM 6 O O1A ADP . . . F 6 125.993 15.117 63.964 1 62.19 ? O1A ADP 1303 A 1 HETATM 7 O O2A ADP . . . F 6 125.049 13.218 65.175 1 66.81 ? O2A ADP 1303 A 1 HETATM 8 O O3A ADP . . . F 6 126.341 12.744 63.042 1 61.07 ? O3A ADP 1303 A 1 HETATM 9 O O5' ADP . . . F 6 127.637 13.492 64.983 1 64.92 ? O5' ADP 1303 A 1 HETATM 10 C C5' ADP . . . F 6 128.124 12.3 65.641 1 65.03 ? C5' ADP 1303 A 1 HETATM 11 C C4' ADP . . . F 6 128.806 12.704 66.93 1 65.42 ? C4' ADP 1303 A 1 HETATM 12 O O4' ADP . . . F 6 130.032 13.425 66.659 1 62.7 ? O4' ADP 1303 A 1 HETATM 13 C C3' ADP . . . F 6 127.994 13.581 67.883 1 67.87 ? C3' ADP 1303 A 1 HETATM 14 O O3' ADP . . . F 6 128.195 13.115 69.211 1 75.35 ? O3' ADP 1303 A 1 HETATM 15 C C2' ADP . . . F 6 128.598 14.971 67.67 1 65.87 ? C2' ADP 1303 A 1 HETATM 16 O O2' ADP . . . F 6 128.365 15.833 68.778 1 68.19 ? O2' ADP 1303 A 1 HETATM 17 C C1' ADP . . . F 6 130.065 14.62 67.414 1 62.83 ? C1' ADP 1303 A 1 HETATM 18 N N9 ADP . . . F 6 130.834 15.609 66.656 1 64.08 ? N9 ADP 1303 A 1 HETATM 19 C C8 ADP . . . F 6 130.492 16.174 65.454 1 61.48 ? C8 ADP 1303 A 1 HETATM 20 N N7 ADP . . . F 6 131.398 16.989 64.968 1 62.6 ? N7 ADP 1303 A 1 HETATM 21 C C5 ADP . . . F 6 132.412 16.956 65.915 1 62.47 ? C5 ADP 1303 A 1 HETATM 22 C C6 ADP . . . F 6 133.69 17.559 65.965 1 60.41 ? C6 ADP 1303 A 1 HETATM 23 N N6 ADP . . . F 6 134.183 18.342 65 1 56.57 ? N6 ADP 1303 A 1 HETATM 24 N N1 ADP . . . F 6 134.478 17.279 67.034 1 62.75 ? N1 ADP 1303 A 1 HETATM 25 C C2 ADP . . . F 6 134.019 16.446 67.975 1 57.87 ? C2 ADP 1303 A 1 HETATM 26 N N3 ADP . . . F 6 132.838 15.823 68.033 1 59.59 ? N3 ADP 1303 A 1 HETATM 27 C C4 ADP . . . F 6 132.077 16.114 66.966 1 62.54 ? C4 ADP 1303 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 27 #