data_9MDT # _model_server_result.job_id rEfNE8Pc7TkfDulRDTDswg _model_server_result.datetime_utc '2025-01-10 19:56:01' _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 9mdt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":502}' # _entry.id 9MDT # _exptl.entry_id 9MDT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 9MDT _cell.length_a 87.109 _cell.length_b 87.109 _cell.length_c 478.237 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9MDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 L N N ? 2 M N N # _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 109 n n PG O2G ATP sing 110 n n PG O3G ATP sing 111 n n PG O3B ATP sing 112 n n O2G HOG2 ATP sing 113 n n O3G HOG3 ATP sing 114 n n PB O1B ATP doub 115 n n PB O2B ATP sing 116 n n PB O3B ATP sing 117 n n PB O3A ATP sing 118 n n O2B HOB2 ATP sing 119 n n PA O1A ATP doub 120 n n PA O2A ATP sing 121 n n PA O3A ATP sing 122 n n PA O5' ATP sing 123 n n O2A HOA2 ATP sing 124 n n O5' C5' ATP sing 125 n n C5' C4' ATP sing 126 n n C5' "H5'1" ATP sing 127 n n C5' "H5'2" ATP sing 128 n n C4' O4' ATP sing 129 n n C4' C3' ATP sing 130 n n C4' H4' ATP sing 131 n n O4' C1' ATP sing 132 n n C3' O3' ATP sing 133 n n C3' C2' ATP sing 134 n n C3' H3' ATP sing 135 n n O3' HO3' ATP sing 136 n n C2' O2' ATP sing 137 n n C2' C1' ATP sing 138 n n C2' H2' ATP sing 139 n n O2' HO2' ATP sing 140 n n C1' N9 ATP sing 141 n n C1' H1' ATP sing 142 n n N9 C8 ATP sing 143 n y N9 C4 ATP sing 144 n y C8 N7 ATP doub 145 n y C8 H8 ATP sing 146 n n N7 C5 ATP sing 147 n y C5 C6 ATP sing 148 n y C5 C4 ATP doub 149 n y C6 N6 ATP sing 150 n n C6 N1 ATP doub 151 n y N6 HN61 ATP sing 152 n n N6 HN62 ATP sing 153 n n N1 C2 ATP sing 154 n y C2 N3 ATP doub 155 n y C2 H2 ATP sing 156 n n N3 C4 ATP sing 157 n y # _atom_sites.entry_id 9MDT _atom_sites.fract_transf_matrix[1][1] 0.01148 _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] 0.01148 _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] 0.002091 _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 E 2 ATP A 1 501 101 ATP ATP . F 3 PPV A 1 502 201 PPV PPV . G 4 AMP A 1 503 301 AMP AMP . H 5 PO4 A 1 504 403 PO4 PO4 . I 5 PO4 A 1 505 405 PO4 PO4 . J 6 CL A 1 506 501 CL CL . K 6 CL A 1 507 505 CL CL . L 2 ATP B 1 501 102 ATP ATP . M 2 ATP B 1 502 103 ATP ATP . N 3 PPV B 1 503 202 PPV PPV . O 5 PO4 B 1 504 404 PO4 PO4 . P 5 PO4 B 1 505 406 PO4 PO4 . Q 6 CL B 1 506 502 CL CL . R 6 CL B 1 507 503 CL CL . S 6 CL B 1 508 1 CL CL . T 3 PPV C 1 501 203 PPV PPV . U 5 PO4 C 1 502 401 PO4 PO4 . V 5 PO4 C 1 503 408 PO4 PO4 . W 3 PPV D 1 501 204 PPV PPV . X 5 PO4 D 1 502 402 PO4 PO4 . Y 5 PO4 D 1 503 407 PO4 PO4 . Z 6 CL D 1 504 504 CL CL . AA 6 CL D 1 505 2 CL CL . BA 7 HOH A 1 601 87 HOH HOH . BA 7 HOH A 2 602 78 HOH HOH . BA 7 HOH A 3 603 84 HOH HOH . BA 7 HOH A 4 604 60 HOH HOH . BA 7 HOH A 5 605 153 HOH HOH . BA 7 HOH A 6 606 120 HOH HOH . BA 7 HOH A 7 607 104 HOH HOH . BA 7 HOH A 8 608 88 HOH HOH . BA 7 HOH A 9 609 18 HOH HOH . BA 7 HOH A 10 610 160 HOH HOH . BA 7 HOH A 11 611 42 HOH HOH . BA 7 HOH A 12 612 57 HOH HOH . BA 7 HOH A 13 613 137 HOH HOH . BA 7 HOH A 14 614 67 HOH HOH . BA 7 HOH A 15 615 150 HOH HOH . BA 7 HOH A 16 616 50 HOH HOH . BA 7 HOH A 17 617 22 HOH HOH . BA 7 HOH A 18 618 28 HOH HOH . BA 7 HOH A 19 619 167 HOH HOH . BA 7 HOH A 20 620 23 HOH HOH . BA 7 HOH A 21 621 71 HOH HOH . BA 7 HOH A 22 622 72 HOH HOH . BA 7 HOH A 23 623 86 HOH HOH . BA 7 HOH A 24 624 136 HOH HOH . BA 7 HOH A 25 625 70 HOH HOH . BA 7 HOH A 26 626 12 HOH HOH . BA 7 HOH A 27 627 19 HOH HOH . BA 7 HOH A 28 628 47 HOH HOH . BA 7 HOH A 29 629 69 HOH HOH . BA 7 HOH A 30 630 125 HOH HOH . BA 7 HOH A 31 631 122 HOH HOH . BA 7 HOH A 32 632 8 HOH HOH . BA 7 HOH A 33 633 143 HOH HOH . BA 7 HOH A 34 634 10 HOH HOH . BA 7 HOH A 35 635 103 HOH HOH . BA 7 HOH A 36 636 21 HOH HOH . BA 7 HOH A 37 637 126 HOH HOH . BA 7 HOH A 38 638 108 HOH HOH . BA 7 HOH A 39 639 5 HOH HOH . BA 7 HOH A 40 640 121 HOH HOH . BA 7 HOH A 41 641 38 HOH HOH . BA 7 HOH A 42 642 119 HOH HOH . BA 7 HOH A 43 643 95 HOH HOH . BA 7 HOH A 44 644 68 HOH HOH . BA 7 HOH A 45 645 139 HOH HOH . BA 7 HOH A 46 646 177 HOH HOH . BA 7 HOH A 47 647 92 HOH HOH . BA 7 HOH A 48 648 1 HOH HOH . BA 7 HOH A 49 649 159 HOH HOH . BA 7 HOH A 50 650 131 HOH HOH . BA 7 HOH A 51 651 147 HOH HOH . BA 7 HOH A 52 652 146 HOH HOH . BA 7 HOH A 53 653 32 HOH HOH . BA 7 HOH A 54 654 144 HOH HOH . BA 7 HOH A 55 655 48 HOH HOH . CA 7 HOH B 1 601 133 HOH HOH . CA 7 HOH B 2 602 80 HOH HOH . CA 7 HOH B 3 603 29 HOH HOH . CA 7 HOH B 4 604 115 HOH HOH . CA 7 HOH B 5 605 41 HOH HOH . CA 7 HOH B 6 606 116 HOH HOH . CA 7 HOH B 7 607 112 HOH HOH . CA 7 HOH B 8 608 148 HOH HOH . CA 7 HOH B 9 609 49 HOH HOH . CA 7 HOH B 10 610 156 HOH HOH . CA 7 HOH B 11 611 62 HOH HOH . CA 7 HOH B 12 612 82 HOH HOH . CA 7 HOH B 13 613 17 HOH HOH . CA 7 HOH B 14 614 152 HOH HOH . CA 7 HOH B 15 615 79 HOH HOH . CA 7 HOH B 16 616 155 HOH HOH . CA 7 HOH B 17 617 2 HOH HOH . CA 7 HOH B 18 618 173 HOH HOH . CA 7 HOH B 19 619 9 HOH HOH . CA 7 HOH B 20 620 96 HOH HOH . CA 7 HOH B 21 621 52 HOH HOH . CA 7 HOH B 22 622 61 HOH HOH . CA 7 HOH B 23 623 36 HOH HOH . CA 7 HOH B 24 624 34 HOH HOH . CA 7 HOH B 25 625 53 HOH HOH . CA 7 HOH B 26 626 13 HOH HOH . CA 7 HOH B 27 627 151 HOH HOH . CA 7 HOH B 28 628 24 HOH HOH . CA 7 HOH B 29 629 6 HOH HOH . CA 7 HOH B 30 630 161 HOH HOH . CA 7 HOH B 31 631 117 HOH HOH . CA 7 HOH B 32 632 73 HOH HOH . CA 7 HOH B 33 633 44 HOH HOH . CA 7 HOH B 34 634 172 HOH HOH . CA 7 HOH B 35 635 54 HOH HOH . CA 7 HOH B 36 636 97 HOH HOH . CA 7 HOH B 37 637 157 HOH HOH . CA 7 HOH B 38 638 59 HOH HOH . CA 7 HOH B 39 639 30 HOH HOH . CA 7 HOH B 40 640 178 HOH HOH . CA 7 HOH B 41 641 55 HOH HOH . DA 7 HOH C 1 601 85 HOH HOH . DA 7 HOH C 2 602 16 HOH HOH . DA 7 HOH C 3 603 33 HOH HOH . DA 7 HOH C 4 604 51 HOH HOH . DA 7 HOH C 5 605 45 HOH HOH . DA 7 HOH C 6 606 77 HOH HOH . DA 7 HOH C 7 607 105 HOH HOH . DA 7 HOH C 8 608 4 HOH HOH . DA 7 HOH C 9 609 39 HOH HOH . DA 7 HOH C 10 610 20 HOH HOH . DA 7 HOH C 11 611 123 HOH HOH . DA 7 HOH C 12 612 37 HOH HOH . DA 7 HOH C 13 613 140 HOH HOH . DA 7 HOH C 14 614 109 HOH HOH . DA 7 HOH C 15 615 98 HOH HOH . DA 7 HOH C 16 616 7 HOH HOH . DA 7 HOH C 17 617 56 HOH HOH . DA 7 HOH C 18 618 106 HOH HOH . DA 7 HOH C 19 619 102 HOH HOH . DA 7 HOH C 20 620 101 HOH HOH . DA 7 HOH C 21 621 35 HOH HOH . DA 7 HOH C 22 622 135 HOH HOH . DA 7 HOH C 23 623 138 HOH HOH . DA 7 HOH C 24 624 100 HOH HOH . DA 7 HOH C 25 625 76 HOH HOH . DA 7 HOH C 26 626 14 HOH HOH . DA 7 HOH C 27 627 171 HOH HOH . DA 7 HOH C 28 628 154 HOH HOH . DA 7 HOH C 29 629 90 HOH HOH . DA 7 HOH C 30 630 142 HOH HOH . DA 7 HOH C 31 631 134 HOH HOH . DA 7 HOH C 32 632 107 HOH HOH . DA 7 HOH C 33 633 149 HOH HOH . DA 7 HOH C 34 634 40 HOH HOH . DA 7 HOH C 35 635 75 HOH HOH . DA 7 HOH C 36 636 11 HOH HOH . DA 7 HOH C 37 637 83 HOH HOH . DA 7 HOH C 38 638 99 HOH HOH . DA 7 HOH C 39 639 127 HOH HOH . DA 7 HOH C 40 640 27 HOH HOH . DA 7 HOH C 41 641 46 HOH HOH . DA 7 HOH C 42 642 91 HOH HOH . DA 7 HOH C 43 643 124 HOH HOH . DA 7 HOH C 44 644 129 HOH HOH . DA 7 HOH C 45 645 26 HOH HOH . DA 7 HOH C 46 646 74 HOH HOH . DA 7 HOH C 47 647 118 HOH HOH . EA 7 HOH D 1 601 63 HOH HOH . EA 7 HOH D 2 602 58 HOH HOH . EA 7 HOH D 3 603 132 HOH HOH . EA 7 HOH D 4 604 179 HOH HOH . EA 7 HOH D 5 605 165 HOH HOH . EA 7 HOH D 6 606 43 HOH HOH . EA 7 HOH D 7 607 164 HOH HOH . EA 7 HOH D 8 608 170 HOH HOH . EA 7 HOH D 9 609 66 HOH HOH . EA 7 HOH D 10 610 169 HOH HOH . EA 7 HOH D 11 611 166 HOH HOH . EA 7 HOH D 12 612 168 HOH HOH . EA 7 HOH D 13 613 110 HOH HOH . EA 7 HOH D 14 614 111 HOH HOH . EA 7 HOH D 15 615 65 HOH HOH . EA 7 HOH D 16 616 158 HOH HOH . EA 7 HOH D 17 617 141 HOH HOH . EA 7 HOH D 18 618 25 HOH HOH . EA 7 HOH D 19 619 81 HOH HOH . EA 7 HOH D 20 620 128 HOH HOH . EA 7 HOH D 21 621 114 HOH HOH . EA 7 HOH D 22 622 15 HOH HOH . EA 7 HOH D 23 623 174 HOH HOH . EA 7 HOH D 24 624 94 HOH HOH . EA 7 HOH D 25 625 163 HOH HOH . EA 7 HOH D 26 626 176 HOH HOH . EA 7 HOH D 27 627 93 HOH HOH . EA 7 HOH D 28 628 64 HOH HOH . EA 7 HOH D 29 629 3 HOH HOH . EA 7 HOH D 30 630 162 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 . . . M 2 17.27 -1.734 -60.806 1 122.23 ? PG ATP 502 B 1 HETATM 2 O O1G ATP . . . M 2 15.832 -2.115 -60.985 1 100.77 ? O1G ATP 502 B 1 HETATM 3 O O2G ATP . . . M 2 17.777 -0.766 -61.89 1 112.67 ? O2G ATP 502 B 1 HETATM 4 O O3G ATP . . . M 2 17.615 -1.155 -59.405 1 84.58 ? O3G ATP 502 B 1 HETATM 5 P PB ATP . . . M 2 19.731 -3.392 -61.271 1 115.04 ? PB ATP 502 B 1 HETATM 6 O O1B ATP . . . M 2 20.601 -3.24 -60.074 1 97.22 ? O1B ATP 502 B 1 HETATM 7 O O2B ATP . . . M 2 20.142 -2.58 -62.503 1 102 ? O2B ATP 502 B 1 HETATM 8 O O3B ATP . . . M 2 18.215 -3.022 -60.942 1 112.8 ? O3B ATP 502 B 1 HETATM 9 P PA ATP . . . M 2 19.836 -6.344 -61.06 1 81.61 ? PA ATP 502 B 1 HETATM 10 O O1A ATP . . . M 2 20.386 -7.309 -62.035 1 81.01 ? O1A ATP 502 B 1 HETATM 11 O O2A ATP . . . M 2 18.523 -6.757 -60.396 1 68.83 ? O2A ATP 502 B 1 HETATM 12 O O3A ATP . . . M 2 19.598 -4.914 -61.723 1 89.01 ? O3A ATP 502 B 1 HETATM 13 O O5' ATP . . . M 2 20.879 -6.02 -59.916 1 74.99 ? O5' ATP 502 B 1 HETATM 14 C C5' ATP . . . M 2 22.267 -5.735 -60.211 1 72.72 ? C5' ATP 502 B 1 HETATM 15 C C4' ATP . . . M 2 22.994 -5.493 -58.908 1 70.13 ? C4' ATP 502 B 1 HETATM 16 O O4' ATP . . . M 2 22.419 -4.308 -58.344 1 66.29 ? O4' ATP 502 B 1 HETATM 17 C C3' ATP . . . M 2 22.633 -6.611 -57.935 1 66.94 ? C3' ATP 502 B 1 HETATM 18 O O3' ATP . . . M 2 23.873 -7.152 -57.491 1 63.33 ? O3' ATP 502 B 1 HETATM 19 C C2' ATP . . . M 2 22.018 -5.884 -56.736 1 61.55 ? C2' ATP 502 B 1 HETATM 20 O O2' ATP . . . M 2 22.738 -6.323 -55.589 1 71.01 ? O2' ATP 502 B 1 HETATM 21 C C1' ATP . . . M 2 22.467 -4.451 -56.955 1 59.03 ? C1' ATP 502 B 1 HETATM 22 N N9 ATP . . . M 2 21.489 -3.515 -56.424 1 59.23 ? N9 ATP 502 B 1 HETATM 23 C C8 ATP . . . M 2 20.16 -3.431 -56.76 1 69.36 ? C8 ATP 502 B 1 HETATM 24 N N7 ATP . . . M 2 19.51 -2.474 -56.145 1 62.64 ? N7 ATP 502 B 1 HETATM 25 C C5 ATP . . . M 2 20.482 -1.876 -55.359 1 62.48 ? C5 ATP 502 B 1 HETATM 26 C C6 ATP . . . M 2 20.442 -0.789 -54.464 1 62.56 ? C6 ATP 502 B 1 HETATM 27 N N6 ATP . . . M 2 19.333 -0.086 -54.203 1 56.62 ? N6 ATP 502 B 1 HETATM 28 N N1 ATP . . . M 2 21.595 -0.446 -53.835 1 60.12 ? N1 ATP 502 B 1 HETATM 29 C C2 ATP . . . M 2 22.705 -1.144 -54.095 1 56.56 ? C2 ATP 502 B 1 HETATM 30 N N3 ATP . . . M 2 22.858 -2.185 -54.918 1 61.96 ? N3 ATP 502 B 1 HETATM 31 C C4 ATP . . . M 2 21.708 -2.504 -55.52 1 59.4 ? C4 ATP 502 B 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 42 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 459 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #