data_5DNR # _model_server_result.job_id HCmebVq8M7aedwvUzlWkjw _model_server_result.datetime_utc '2024-10-10 11:17:12' _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 5dnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5DNR # _exptl.entry_id 5DNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 90 _cell.entry_id 5DNR _cell.length_a 81.46 _cell.length_b 81.46 _cell.length_c 137.38 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 covale ? covale1 A C THR 168 A THR 287 1_555 A N TPO 169 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C TPO 169 A TPO 288 1_555 A N LEU 170 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OE1 GLU 62 A GLU 181 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc2 A OD1 ASN 142 A ASN 261 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc3 A OD2 ASP 155 A ASP 274 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc4 B MG MG . A MG 401 1_555 D O2B ATP . A ATP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc5 B MG MG . A MG 401 1_555 D O2A ATP . A ATP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.761 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O HOH . A HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc7 B MG MG . A MG 401 1_555 F O HOH . A HOH 599 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc8 D O3G ATP . A ATP 403 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 5DNR _atom_sites.fract_transf_matrix[1][1] 0.012276 _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] 0.012276 _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] 0.007279 _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 B 2 MG A 1 401 1 MG MG . C 3 SO4 A 1 402 1 SO4 SO4 . D 4 ATP A 1 403 1 ATP ATP . E 2 MG A 1 404 1 MG MG . F 5 HOH A 1 501 93 HOH HOH . F 5 HOH A 2 502 49 HOH HOH . F 5 HOH A 3 503 95 HOH HOH . F 5 HOH A 4 504 44 HOH HOH . F 5 HOH A 5 505 32 HOH HOH . F 5 HOH A 6 506 63 HOH HOH . F 5 HOH A 7 507 50 HOH HOH . F 5 HOH A 8 508 31 HOH HOH . F 5 HOH A 9 509 120 HOH HOH . F 5 HOH A 10 510 92 HOH HOH . F 5 HOH A 11 511 13 HOH HOH . F 5 HOH A 12 512 34 HOH HOH . F 5 HOH A 13 513 33 HOH HOH . F 5 HOH A 14 514 103 HOH HOH . F 5 HOH A 15 515 40 HOH HOH . F 5 HOH A 16 516 69 HOH HOH . F 5 HOH A 17 517 91 HOH HOH . F 5 HOH A 18 518 47 HOH HOH . F 5 HOH A 19 519 97 HOH HOH . F 5 HOH A 20 520 104 HOH HOH . F 5 HOH A 21 521 111 HOH HOH . F 5 HOH A 22 522 118 HOH HOH . F 5 HOH A 23 523 7 HOH HOH . F 5 HOH A 24 524 96 HOH HOH . F 5 HOH A 25 525 1 HOH HOH . F 5 HOH A 26 526 65 HOH HOH . F 5 HOH A 27 527 15 HOH HOH . F 5 HOH A 28 528 19 HOH HOH . F 5 HOH A 29 529 90 HOH HOH . F 5 HOH A 30 530 115 HOH HOH . F 5 HOH A 31 531 80 HOH HOH . F 5 HOH A 32 532 94 HOH HOH . F 5 HOH A 33 533 27 HOH HOH . F 5 HOH A 34 534 2 HOH HOH . F 5 HOH A 35 535 20 HOH HOH . F 5 HOH A 36 536 16 HOH HOH . F 5 HOH A 37 537 46 HOH HOH . F 5 HOH A 38 538 59 HOH HOH . F 5 HOH A 39 539 51 HOH HOH . F 5 HOH A 40 540 53 HOH HOH . F 5 HOH A 41 541 10 HOH HOH . F 5 HOH A 42 542 24 HOH HOH . F 5 HOH A 43 543 25 HOH HOH . F 5 HOH A 44 544 41 HOH HOH . F 5 HOH A 45 545 82 HOH HOH . F 5 HOH A 46 546 99 HOH HOH . F 5 HOH A 47 547 61 HOH HOH . F 5 HOH A 48 548 57 HOH HOH . F 5 HOH A 49 549 60 HOH HOH . F 5 HOH A 50 550 76 HOH HOH . F 5 HOH A 51 551 48 HOH HOH . F 5 HOH A 52 552 21 HOH HOH . F 5 HOH A 53 553 3 HOH HOH . F 5 HOH A 54 554 87 HOH HOH . F 5 HOH A 55 555 5 HOH HOH . F 5 HOH A 56 556 6 HOH HOH . F 5 HOH A 57 557 12 HOH HOH . F 5 HOH A 58 558 18 HOH HOH . F 5 HOH A 59 559 42 HOH HOH . F 5 HOH A 60 560 107 HOH HOH . F 5 HOH A 61 561 55 HOH HOH . F 5 HOH A 62 562 17 HOH HOH . F 5 HOH A 63 563 8 HOH HOH . F 5 HOH A 64 564 66 HOH HOH . F 5 HOH A 65 565 114 HOH HOH . F 5 HOH A 66 566 35 HOH HOH . F 5 HOH A 67 567 22 HOH HOH . F 5 HOH A 68 568 72 HOH HOH . F 5 HOH A 69 569 52 HOH HOH . F 5 HOH A 70 570 78 HOH HOH . F 5 HOH A 71 571 117 HOH HOH . F 5 HOH A 72 572 62 HOH HOH . F 5 HOH A 73 573 4 HOH HOH . F 5 HOH A 74 574 113 HOH HOH . F 5 HOH A 75 575 28 HOH HOH . F 5 HOH A 76 576 37 HOH HOH . F 5 HOH A 77 577 102 HOH HOH . F 5 HOH A 78 578 11 HOH HOH . F 5 HOH A 79 579 26 HOH HOH . F 5 HOH A 80 580 56 HOH HOH . F 5 HOH A 81 581 43 HOH HOH . F 5 HOH A 82 582 116 HOH HOH . F 5 HOH A 83 583 100 HOH HOH . F 5 HOH A 84 584 58 HOH HOH . F 5 HOH A 85 585 101 HOH HOH . F 5 HOH A 86 586 109 HOH HOH . F 5 HOH A 87 587 105 HOH HOH . F 5 HOH A 88 588 38 HOH HOH . F 5 HOH A 89 589 81 HOH HOH . F 5 HOH A 90 590 36 HOH HOH . F 5 HOH A 91 591 71 HOH HOH . F 5 HOH A 92 592 9 HOH HOH . F 5 HOH A 93 593 108 HOH HOH . F 5 HOH A 94 594 23 HOH HOH . F 5 HOH A 95 595 54 HOH HOH . F 5 HOH A 96 596 29 HOH HOH . F 5 HOH A 97 597 77 HOH HOH . F 5 HOH A 98 598 30 HOH HOH . F 5 HOH A 99 599 106 HOH HOH . F 5 HOH A 100 600 73 HOH HOH . F 5 HOH A 101 601 84 HOH HOH . F 5 HOH A 102 602 83 HOH HOH . F 5 HOH A 103 603 39 HOH HOH . F 5 HOH A 104 604 89 HOH HOH . F 5 HOH A 105 605 88 HOH HOH . F 5 HOH A 106 606 110 HOH HOH . F 5 HOH A 107 607 75 HOH HOH . F 5 HOH A 108 608 67 HOH HOH . F 5 HOH A 109 609 112 HOH HOH . F 5 HOH A 110 610 119 HOH HOH . F 5 HOH A 111 611 68 HOH HOH . F 5 HOH A 112 612 86 HOH HOH . F 5 HOH A 113 613 14 HOH HOH . F 5 HOH A 114 614 79 HOH HOH . F 5 HOH A 115 615 85 HOH HOH . F 5 HOH A 116 616 98 HOH HOH . F 5 HOH A 117 617 64 HOH HOH . F 5 HOH A 118 618 74 HOH HOH . F 5 HOH A 119 619 45 HOH HOH . F 5 HOH A 120 620 70 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 PG ATP . . . D 4 26.672 84.906 4.355 1 50.83 ? PG ATP 403 A 1 HETATM 2 O O1G ATP . . . D 4 25.937 84.667 3.058 1 51.22 ? O1G ATP 403 A 1 HETATM 3 O O2G ATP . . . D 4 25.96 85.83 5.314 1 45.47 ? O2G ATP 403 A 1 HETATM 4 O O3G ATP . . . D 4 28.146 85.193 4.192 1 53.15 ? O3G ATP 403 A 1 HETATM 5 P PB ATP . . . D 4 25.228 82.795 5.482 1 27.04 ? PB ATP 403 A 1 HETATM 6 O O1B ATP . . . D 4 24.535 82.379 4.206 1 27.62 ? O1B ATP 403 A 1 HETATM 7 O O2B ATP . . . D 4 24.521 83.698 6.463 1 22.15 ? O2B ATP 403 A 1 HETATM 8 O O3B ATP . . . D 4 26.634 83.476 5.092 1 28.68 ? O3B ATP 403 A 1 HETATM 9 P PA ATP . . . D 4 26.466 81.567 7.667 1 25.96 ? PA ATP 403 A 1 HETATM 10 O O1A ATP . . . D 4 27.933 81.314 7.413 1 25.46 ? O1A ATP 403 A 1 HETATM 11 O O2A ATP . . . D 4 26.03 82.838 8.357 1 23.04 ? O2A ATP 403 A 1 HETATM 12 O O3A ATP . . . D 4 25.686 81.463 6.263 1 28.31 ? O3A ATP 403 A 1 HETATM 13 O O5' ATP . . . D 4 25.874 80.318 8.492 1 24.91 ? O5' ATP 403 A 1 HETATM 14 C C5' ATP . . . D 4 24.701 79.644 8.041 1 24.47 ? C5' ATP 403 A 1 HETATM 15 C C4' ATP . . . D 4 24.026 78.956 9.221 1 25.22 ? C4' ATP 403 A 1 HETATM 16 O O4' ATP . . . D 4 24.728 77.753 9.545 1 25.71 ? O4' ATP 403 A 1 HETATM 17 C C3' ATP . . . D 4 24.031 79.845 10.454 1 25.78 ? C3' ATP 403 A 1 HETATM 18 O O3' ATP . . . D 4 22.689 80.097 10.882 1 25.34 ? O3' ATP 403 A 1 HETATM 19 C C2' ATP . . . D 4 24.783 79.081 11.525 1 23.89 ? C2' ATP 403 A 1 HETATM 20 O O2' ATP . . . D 4 23.93 78.842 12.648 1 26.19 ? O2' ATP 403 A 1 HETATM 21 C C1' ATP . . . D 4 25.197 77.761 10.896 1 24.07 ? C1' ATP 403 A 1 HETATM 22 N N9 ATP . . . D 4 26.677 77.641 10.912 1 25 ? N9 ATP 403 A 1 HETATM 23 C C8 ATP . . . D 4 27.526 78.261 10.072 1 27.15 ? C8 ATP 403 A 1 HETATM 24 N N7 ATP . . . D 4 28.815 77.941 10.353 1 26.41 ? N7 ATP 403 A 1 HETATM 25 C C5 ATP . . . D 4 28.802 77.094 11.399 1 25.03 ? C5 ATP 403 A 1 HETATM 26 C C6 ATP . . . D 4 29.817 76.371 12.201 1 25.77 ? C6 ATP 403 A 1 HETATM 27 N N6 ATP . . . D 4 31.14 76.494 11.932 1 25.6 ? N6 ATP 403 A 1 HETATM 28 N N1 ATP . . . D 4 29.379 75.585 13.209 1 25.35 ? N1 ATP 403 A 1 HETATM 29 C C2 ATP . . . D 4 28.068 75.454 13.486 1 22.82 ? C2 ATP 403 A 1 HETATM 30 N N3 ATP . . . D 4 27.094 76.08 12.801 1 27.1 ? N3 ATP 403 A 1 HETATM 31 C C4 ATP . . . D 4 27.39 76.899 11.764 1 25.67 ? C4 ATP 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #