data_5DN3 # _model_server_result.job_id aRkwD6DmmtqOs9BRaEE5DQ _model_server_result.datetime_utc '2024-10-10 11:20:52' _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 5dn3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 5DN3 # _exptl.entry_id 5DN3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 5 _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 5DN3 _cell.length_a 81.65 _cell.length_b 81.65 _cell.length_c 136.91 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DN3 _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 5 _struct_asym.id E _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale2 A C TPO 169 A TPO 288 1_555 A N LEU 170 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OD1 ASN 142 A ASN 261 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc2 A OD2 ASP 155 A ASP 274 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc3 B MG MG . A MG 401 1_555 E O2B ATP . A ATP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc4 B MG MG . A MG 401 1_555 E O2A ATP . A ATP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc5 B MG MG . A MG 401 1_555 F O HOH . A HOH 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? # _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 102 n n PG O2G ATP sing 103 n n PG O3G ATP sing 104 n n PG O3B ATP sing 105 n n O2G HOG2 ATP sing 106 n n O3G HOG3 ATP sing 107 n n PB O1B ATP doub 108 n n PB O2B ATP sing 109 n n PB O3B ATP sing 110 n n PB O3A ATP sing 111 n n O2B HOB2 ATP sing 112 n n PA O1A ATP doub 113 n n PA O2A ATP sing 114 n n PA O3A ATP sing 115 n n PA O5' ATP sing 116 n n O2A HOA2 ATP sing 117 n n O5' C5' ATP sing 118 n n C5' C4' ATP sing 119 n n C5' "H5'1" ATP sing 120 n n C5' "H5'2" ATP sing 121 n n C4' O4' ATP sing 122 n n C4' C3' ATP sing 123 n n C4' H4' ATP sing 124 n n O4' C1' ATP sing 125 n n C3' O3' ATP sing 126 n n C3' C2' ATP sing 127 n n C3' H3' ATP sing 128 n n O3' HO3' ATP sing 129 n n C2' O2' ATP sing 130 n n C2' C1' ATP sing 131 n n C2' H2' ATP sing 132 n n O2' HO2' ATP sing 133 n n C1' N9 ATP sing 134 n n C1' H1' ATP sing 135 n n N9 C8 ATP sing 136 n y N9 C4 ATP sing 137 n y C8 N7 ATP doub 138 n y C8 H8 ATP sing 139 n n N7 C5 ATP sing 140 n y C5 C6 ATP sing 141 n y C5 C4 ATP doub 142 n y C6 N6 ATP sing 143 n n C6 N1 ATP doub 144 n y N6 HN61 ATP sing 145 n n N6 HN62 ATP sing 146 n n N1 C2 ATP sing 147 n y C2 N3 ATP doub 148 n y C2 H2 ATP sing 149 n n N3 C4 ATP sing 150 n y # _atom_sites.entry_id 5DN3 _atom_sites.fract_transf_matrix[1][1] 0.012247 _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] 0.012247 _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] 0.007304 _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 5DN A 1 402 1 5DN 035 . D 4 SO4 A 1 403 1 SO4 SO4 . E 5 ATP A 1 404 1 ATP ATP . F 6 HOH A 1 501 56 HOH HOH . F 6 HOH A 2 502 1 HOH HOH . F 6 HOH A 3 503 37 HOH HOH . F 6 HOH A 4 504 38 HOH HOH . F 6 HOH A 5 505 121 HOH HOH . F 6 HOH A 6 506 54 HOH HOH . F 6 HOH A 7 507 36 HOH HOH . F 6 HOH A 8 508 51 HOH HOH . F 6 HOH A 9 509 71 HOH HOH . F 6 HOH A 10 510 40 HOH HOH . F 6 HOH A 11 511 39 HOH HOH . F 6 HOH A 12 512 57 HOH HOH . F 6 HOH A 13 513 91 HOH HOH . F 6 HOH A 14 514 46 HOH HOH . F 6 HOH A 15 515 124 HOH HOH . F 6 HOH A 16 516 22 HOH HOH . F 6 HOH A 17 517 73 HOH HOH . F 6 HOH A 18 518 8 HOH HOH . F 6 HOH A 19 519 17 HOH HOH . F 6 HOH A 20 520 60 HOH HOH . F 6 HOH A 21 521 114 HOH HOH . F 6 HOH A 22 522 14 HOH HOH . F 6 HOH A 23 523 118 HOH HOH . F 6 HOH A 24 524 2 HOH HOH . F 6 HOH A 25 525 16 HOH HOH . F 6 HOH A 26 526 101 HOH HOH . F 6 HOH A 27 527 112 HOH HOH . F 6 HOH A 28 528 92 HOH HOH . F 6 HOH A 29 529 48 HOH HOH . F 6 HOH A 30 530 28 HOH HOH . F 6 HOH A 31 531 136 HOH HOH . F 6 HOH A 32 532 138 HOH HOH . F 6 HOH A 33 533 117 HOH HOH . F 6 HOH A 34 534 94 HOH HOH . F 6 HOH A 35 535 27 HOH HOH . F 6 HOH A 36 536 20 HOH HOH . F 6 HOH A 37 537 19 HOH HOH . F 6 HOH A 38 538 55 HOH HOH . F 6 HOH A 39 539 89 HOH HOH . F 6 HOH A 40 540 66 HOH HOH . F 6 HOH A 41 541 135 HOH HOH . F 6 HOH A 42 542 5 HOH HOH . F 6 HOH A 43 543 25 HOH HOH . F 6 HOH A 44 544 146 HOH HOH . F 6 HOH A 45 545 145 HOH HOH . F 6 HOH A 46 546 30 HOH HOH . F 6 HOH A 47 547 147 HOH HOH . F 6 HOH A 48 548 125 HOH HOH . F 6 HOH A 49 549 130 HOH HOH . F 6 HOH A 50 550 132 HOH HOH . F 6 HOH A 51 551 62 HOH HOH . F 6 HOH A 52 552 4 HOH HOH . F 6 HOH A 53 553 104 HOH HOH . F 6 HOH A 54 554 58 HOH HOH . F 6 HOH A 55 555 139 HOH HOH . F 6 HOH A 56 556 11 HOH HOH . F 6 HOH A 57 557 64 HOH HOH . F 6 HOH A 58 558 3 HOH HOH . F 6 HOH A 59 559 103 HOH HOH . F 6 HOH A 60 560 67 HOH HOH . F 6 HOH A 61 561 6 HOH HOH . F 6 HOH A 62 562 102 HOH HOH . F 6 HOH A 63 563 65 HOH HOH . F 6 HOH A 64 564 68 HOH HOH . F 6 HOH A 65 565 50 HOH HOH . F 6 HOH A 66 566 142 HOH HOH . F 6 HOH A 67 567 123 HOH HOH . F 6 HOH A 68 568 110 HOH HOH . F 6 HOH A 69 569 88 HOH HOH . F 6 HOH A 70 570 29 HOH HOH . F 6 HOH A 71 571 13 HOH HOH . F 6 HOH A 72 572 86 HOH HOH . F 6 HOH A 73 573 59 HOH HOH . F 6 HOH A 74 574 21 HOH HOH . F 6 HOH A 75 575 41 HOH HOH . F 6 HOH A 76 576 47 HOH HOH . F 6 HOH A 77 577 23 HOH HOH . F 6 HOH A 78 578 95 HOH HOH . F 6 HOH A 79 579 133 HOH HOH . F 6 HOH A 80 580 74 HOH HOH . F 6 HOH A 81 581 80 HOH HOH . F 6 HOH A 82 582 32 HOH HOH . F 6 HOH A 83 583 126 HOH HOH . F 6 HOH A 84 584 9 HOH HOH . F 6 HOH A 85 585 116 HOH HOH . F 6 HOH A 86 586 18 HOH HOH . F 6 HOH A 87 587 111 HOH HOH . F 6 HOH A 88 588 70 HOH HOH . F 6 HOH A 89 589 63 HOH HOH . F 6 HOH A 90 590 44 HOH HOH . F 6 HOH A 91 591 33 HOH HOH . F 6 HOH A 92 592 143 HOH HOH . F 6 HOH A 93 593 24 HOH HOH . F 6 HOH A 94 594 69 HOH HOH . F 6 HOH A 95 595 109 HOH HOH . F 6 HOH A 96 596 113 HOH HOH . F 6 HOH A 97 597 31 HOH HOH . F 6 HOH A 98 598 49 HOH HOH . F 6 HOH A 99 599 12 HOH HOH . F 6 HOH A 100 600 15 HOH HOH . F 6 HOH A 101 601 141 HOH HOH . F 6 HOH A 102 602 128 HOH HOH . F 6 HOH A 103 603 10 HOH HOH . F 6 HOH A 104 604 119 HOH HOH . F 6 HOH A 105 605 134 HOH HOH . F 6 HOH A 106 606 43 HOH HOH . F 6 HOH A 107 607 115 HOH HOH . F 6 HOH A 108 608 45 HOH HOH . F 6 HOH A 109 609 81 HOH HOH . F 6 HOH A 110 610 87 HOH HOH . F 6 HOH A 111 611 53 HOH HOH . F 6 HOH A 112 612 107 HOH HOH . F 6 HOH A 113 613 106 HOH HOH . F 6 HOH A 114 614 79 HOH HOH . F 6 HOH A 115 615 108 HOH HOH . F 6 HOH A 116 616 140 HOH HOH . F 6 HOH A 117 617 42 HOH HOH . F 6 HOH A 118 618 105 HOH HOH . F 6 HOH A 119 619 127 HOH HOH . F 6 HOH A 120 620 129 HOH HOH . F 6 HOH A 121 621 144 HOH HOH . F 6 HOH A 122 622 75 HOH HOH . F 6 HOH A 123 623 84 HOH HOH . F 6 HOH A 124 624 35 HOH HOH . F 6 HOH A 125 625 76 HOH HOH . F 6 HOH A 126 626 120 HOH HOH . F 6 HOH A 127 627 131 HOH HOH . F 6 HOH A 128 628 34 HOH HOH . F 6 HOH A 129 629 137 HOH HOH . F 6 HOH A 130 630 122 HOH HOH . F 6 HOH A 131 631 78 HOH HOH . F 6 HOH A 132 632 26 HOH HOH . F 6 HOH A 133 633 100 HOH HOH . F 6 HOH A 134 634 61 HOH HOH . F 6 HOH A 135 635 96 HOH HOH . F 6 HOH A 136 636 99 HOH HOH . F 6 HOH A 137 637 98 HOH HOH . F 6 HOH A 138 638 93 HOH HOH . F 6 HOH A 139 639 7 HOH HOH . F 6 HOH A 140 640 97 HOH HOH . F 6 HOH A 141 641 72 HOH HOH . F 6 HOH A 142 642 90 HOH HOH . F 6 HOH A 143 643 83 HOH HOH . F 6 HOH A 144 644 82 HOH HOH . F 6 HOH A 145 645 52 HOH HOH . F 6 HOH A 146 646 77 HOH HOH . F 6 HOH A 147 647 85 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 . . . E 5 26.906 85.274 4.088 1 55.63 ? PG ATP 404 A 1 HETATM 2 O O1G ATP . . . E 5 26.456 85.389 2.548 1 56.43 ? O1G ATP 404 A 1 HETATM 3 O O2G ATP . . . E 5 26.109 86.31 4.962 1 48.65 ? O2G ATP 404 A 1 HETATM 4 O O3G ATP . . . E 5 28.421 85.462 4.04 1 54.46 ? O3G ATP 404 A 1 HETATM 5 P PB ATP . . . E 5 25.36 83.053 5.312 1 30.66 ? PB ATP 404 A 1 HETATM 6 O O1B ATP . . . E 5 24.5 82.469 4.221 1 31.15 ? O1B ATP 404 A 1 HETATM 7 O O2B ATP . . . E 5 24.511 83.784 6.279 1 25.42 ? O2B ATP 404 A 1 HETATM 8 O O3B ATP . . . E 5 26.627 83.828 4.74 1 34.4 ? O3B ATP 404 A 1 HETATM 9 P PA ATP . . . E 5 26.588 81.604 7.529 1 28.68 ? PA ATP 404 A 1 HETATM 10 O O1A ATP . . . E 5 28.082 81.522 7.485 1 29.39 ? O1A ATP 404 A 1 HETATM 11 O O2A ATP . . . E 5 26.164 82.697 8.425 1 24.93 ? O2A ATP 404 A 1 HETATM 12 O O3A ATP . . . E 5 25.93 81.773 6.088 1 31.26 ? O3A ATP 404 A 1 HETATM 13 O O5' ATP . . . E 5 25.986 80.163 8.041 1 30.77 ? O5' ATP 404 A 1 HETATM 14 C C5' ATP . . . E 5 24.557 79.908 8.069 1 27.61 ? C5' ATP 404 A 1 HETATM 15 C C4' ATP . . . E 5 24.168 79.26 9.376 1 27.01 ? C4' ATP 404 A 1 HETATM 16 O O4' ATP . . . E 5 24.853 77.985 9.514 1 27.36 ? O4' ATP 404 A 1 HETATM 17 C C3' ATP . . . E 5 24.54 80.035 10.636 1 27.03 ? C3' ATP 404 A 1 HETATM 18 O O3' ATP . . . E 5 23.587 81.04 10.957 1 27.66 ? O3' ATP 404 A 1 HETATM 19 C C2' ATP . . . E 5 24.602 78.913 11.68 1 27.18 ? C2' ATP 404 A 1 HETATM 20 O O2' ATP . . . E 5 23.27 78.558 12.024 1 27.32 ? O2' ATP 404 A 1 HETATM 21 C C1' ATP . . . E 5 25.231 77.77 10.862 1 27.58 ? C1' ATP 404 A 1 HETATM 22 N N9 ATP . . . E 5 26.688 77.736 10.926 1 28.72 ? N9 ATP 404 A 1 HETATM 23 C C8 ATP . . . E 5 27.554 78.471 10.16 1 28.99 ? C8 ATP 404 A 1 HETATM 24 N N7 ATP . . . E 5 28.818 78.233 10.404 1 29.35 ? N7 ATP 404 A 1 HETATM 25 C C5 ATP . . . E 5 28.784 77.278 11.41 1 28.63 ? C5 ATP 404 A 1 HETATM 26 C C6 ATP . . . E 5 29.805 76.63 12.131 1 27.48 ? C6 ATP 404 A 1 HETATM 27 N N6 ATP . . . E 5 31.1 76.755 11.833 1 26.46 ? N6 ATP 404 A 1 HETATM 28 N N1 ATP . . . E 5 29.438 75.805 13.14 1 28.96 ? N1 ATP 404 A 1 HETATM 29 C C2 ATP . . . E 5 28.134 75.614 13.374 1 28.03 ? C2 ATP 404 A 1 HETATM 30 N N3 ATP . . . E 5 27.083 76.133 12.729 1 32.02 ? N3 ATP 404 A 1 HETATM 31 C C4 ATP . . . E 5 27.48 76.973 11.754 1 30.41 ? C4 ATP 404 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #