data_1Y8O # _model_server_result.job_id Nn00OLLS2KK4htuiOGsglA _model_server_result.datetime_utc '2024-11-05 16:27:41' _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 1y8o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":504}' # _entry.id 1Y8O # _exptl.entry_id 1Y8O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 120 _cell.entry_id 1Y8O _cell.length_a 120.752 _cell.length_b 120.752 _cell.length_c 239.153 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y8O _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_455 -x+y-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -120.752 0 119.5765 # _struct_asym.details ? _struct_asym.entity_id 5 _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 O SER 33 A SER 20 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc2 A O PHE 35 A PHE 22 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc3 A OD1 ASN 72 A ASN 59 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc4 A OD1 ASN 264 A ASN 251 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc5 A O LEU 313 A LEU 300 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc6 A O ASN 315 A ASN 302 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.325 ? metalc ? metalc7 A O SER 319 A SER 306 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.323 ? metalc ? metalc8 A O GLY 338 A GLY 325 1_555 D K K . A K 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc9 A O PHE 385 A PHE 372 1_555 E K K . A K 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc10 C MG MG . A MG 501 1_555 F O2A ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc11 C MG MG . A MG 501 1_555 F O3B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc12 C MG MG . A MG 501 1_555 H O HOH . A HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc13 D K K . A K 502 1_555 F O1A ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? # _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 1Y8O _atom_sites.fract_transf_matrix[1][1] 0.008281 _atom_sites.fract_transf_matrix[1][2] 0.004781 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009563 _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] 0.004181 _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 C 3 MG A 1 501 1 MG MG . D 4 K A 1 502 2 K K . E 4 K A 1 503 3 K K . F 5 ADP A 1 504 1 ADP ADP . G 6 RED B 1 373 173 RED LPA . H 7 HOH A 1 505 1 HOH WAT . H 7 HOH A 2 506 2 HOH WAT . H 7 HOH A 3 507 3 HOH WAT . H 7 HOH A 4 508 4 HOH WAT . H 7 HOH A 5 509 5 HOH WAT . H 7 HOH A 6 510 6 HOH WAT . H 7 HOH A 7 511 7 HOH WAT . H 7 HOH A 8 512 8 HOH WAT . H 7 HOH A 9 513 9 HOH WAT . H 7 HOH A 10 514 10 HOH WAT . H 7 HOH A 11 515 11 HOH WAT . H 7 HOH A 12 516 12 HOH WAT . H 7 HOH A 13 517 13 HOH WAT . H 7 HOH A 14 518 14 HOH WAT . H 7 HOH A 15 519 15 HOH WAT . H 7 HOH A 16 520 16 HOH WAT . H 7 HOH A 17 521 17 HOH WAT . H 7 HOH A 18 522 18 HOH WAT . H 7 HOH A 19 523 19 HOH WAT . H 7 HOH A 20 524 20 HOH WAT . H 7 HOH A 21 525 21 HOH WAT . H 7 HOH A 22 526 22 HOH WAT . H 7 HOH A 23 527 23 HOH WAT . H 7 HOH A 24 528 24 HOH WAT . H 7 HOH A 25 529 25 HOH WAT . H 7 HOH A 26 530 26 HOH WAT . H 7 HOH A 27 531 27 HOH WAT . H 7 HOH A 28 532 28 HOH WAT . H 7 HOH A 29 533 29 HOH WAT . H 7 HOH A 30 534 30 HOH WAT . H 7 HOH A 31 535 31 HOH WAT . H 7 HOH A 32 536 32 HOH WAT . H 7 HOH A 33 537 33 HOH WAT . H 7 HOH A 34 538 34 HOH WAT . H 7 HOH A 35 539 35 HOH WAT . H 7 HOH A 36 540 36 HOH WAT . H 7 HOH A 37 541 37 HOH WAT . H 7 HOH A 38 542 38 HOH WAT . H 7 HOH A 39 543 39 HOH WAT . H 7 HOH A 40 544 40 HOH WAT . H 7 HOH A 41 545 41 HOH WAT . H 7 HOH A 42 546 42 HOH WAT . H 7 HOH A 43 547 43 HOH WAT . H 7 HOH A 44 548 44 HOH WAT . H 7 HOH A 45 549 45 HOH WAT . H 7 HOH A 46 550 46 HOH WAT . H 7 HOH A 47 551 47 HOH WAT . H 7 HOH A 48 552 48 HOH WAT . H 7 HOH A 49 553 49 HOH WAT . H 7 HOH A 50 554 50 HOH WAT . H 7 HOH A 51 555 51 HOH WAT . H 7 HOH A 52 556 52 HOH WAT . H 7 HOH A 53 557 53 HOH WAT . H 7 HOH A 54 558 54 HOH WAT . H 7 HOH A 55 559 55 HOH WAT . H 7 HOH A 56 560 56 HOH WAT . H 7 HOH A 57 561 58 HOH WAT . H 7 HOH A 58 562 59 HOH WAT . H 7 HOH A 59 563 62 HOH WAT . H 7 HOH A 60 564 63 HOH WAT . H 7 HOH A 61 565 64 HOH WAT . H 7 HOH A 62 566 65 HOH WAT . H 7 HOH A 63 567 68 HOH WAT . I 7 HOH B 1 57 57 HOH WAT . I 7 HOH B 2 60 60 HOH WAT . I 7 HOH B 3 61 61 HOH WAT . I 7 HOH B 4 67 67 HOH WAT . # 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 5 -46.255 16.565 73.318 1 84.62 ? PB ADP 504 A 1 HETATM 2 O O1B ADP . . . F 5 -45.279 16.363 72.175 1 80.24 ? O1B ADP 504 A 1 HETATM 3 O O2B ADP . . . F 5 -45.842 16.078 74.709 1 84.02 ? O2B ADP 504 A 1 HETATM 4 O O3B ADP . . . F 5 -46.946 17.921 73.363 1 81.63 ? O3B ADP 504 A 1 HETATM 5 P PA ADP . . . F 5 -48.814 15.741 72.222 1 83.65 ? PA ADP 504 A 1 HETATM 6 O O1A ADP . . . F 5 -49.433 14.36 72.041 1 83 ? O1A ADP 504 A 1 HETATM 7 O O2A ADP . . . F 5 -49.512 16.836 73.021 1 82.68 ? O2A ADP 504 A 1 HETATM 8 O O3A ADP . . . F 5 -47.4 15.448 72.973 1 85.69 ? O3A ADP 504 A 1 HETATM 9 O O5' ADP . . . F 5 -48.387 16.396 70.793 1 80.17 ? O5' ADP 504 A 1 HETATM 10 C C5' ADP . . . F 5 -47.719 15.634 69.79 1 79.24 ? C5' ADP 504 A 1 HETATM 11 C C4' ADP . . . F 5 -46.991 16.48 68.739 1 79.87 ? C4' ADP 504 A 1 HETATM 12 O O4' ADP . . . F 5 -47.85 17.023 67.703 1 79.04 ? O4' ADP 504 A 1 HETATM 13 C C3' ADP . . . F 5 -46.179 17.662 69.283 1 78.51 ? C3' ADP 504 A 1 HETATM 14 O O3' ADP . . . F 5 -44.898 17.178 69.701 1 78.8 ? O3' ADP 504 A 1 HETATM 15 C C2' ADP . . . F 5 -46.078 18.6 68.087 1 76.47 ? C2' ADP 504 A 1 HETATM 16 O O2' ADP . . . F 5 -44.956 18.221 67.276 1 75.7 ? O2' ADP 504 A 1 HETATM 17 C C1' ADP . . . F 5 -47.325 18.308 67.259 1 74.64 ? C1' ADP 504 A 1 HETATM 18 N N9 ADP . . . F 5 -48.382 19.347 67.428 1 69.36 ? N9 ADP 504 A 1 HETATM 19 C C8 ADP . . . F 5 -49.487 19.192 68.186 1 67.27 ? C8 ADP 504 A 1 HETATM 20 N N7 ADP . . . F 5 -50.291 20.275 68.131 1 64.89 ? N7 ADP 504 A 1 HETATM 21 C C5 ADP . . . F 5 -49.696 21.169 67.318 1 64.41 ? C5 ADP 504 A 1 HETATM 22 C C6 ADP . . . F 5 -50.015 22.546 66.857 1 62.31 ? C6 ADP 504 A 1 HETATM 23 N N6 ADP . . . F 5 -51.146 23.186 67.244 1 59.95 ? N6 ADP 504 A 1 HETATM 24 N N1 ADP . . . F 5 -49.132 23.111 66.011 1 63.35 ? N1 ADP 504 A 1 HETATM 25 C C2 ADP . . . F 5 -47.983 22.49 65.611 1 62.47 ? C2 ADP 504 A 1 HETATM 26 N N3 ADP . . . F 5 -47.614 21.254 66.012 1 62.36 ? N3 ADP 504 A 1 HETATM 27 C C4 ADP . . . F 5 -48.432 20.553 66.846 1 65.46 ? C4 ADP 504 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #