data_7DYE # _model_server_result.job_id nJeB3ZtmV7Qzl6tI7tPDAQ _model_server_result.datetime_utc '2024-11-23 20:05:48' _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 7dye # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":602}' # _entry.id 7DYE # _exptl.entry_id 7DYE _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 4 _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 7DYE _cell.length_a 94.906 _cell.length_b 94.906 _cell.length_c 276.523 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DYE _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 94.906 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 47.453 82.191007 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 G N N ? 2 H N 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 OG1 THR 53 A THR 53 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc2 A OG1 THR 295 A THR 295 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc3 C O3G ATP . A ATP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc4 C O1B ATP . A ATP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc5 D O2G ATP . A ATP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc6 D O2B ATP . A ATP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc7 E MG MG . A MG 603 1_555 K O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc8 E MG MG . A MG 603 1_555 K O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc9 B OG1 THR 53 B THR 53 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc10 B OG1 THR 295 B THR 295 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc11 G O2G ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc12 G O3G ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc13 G O1B ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc14 H O2G ATP . B ATP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc15 H O2B ATP . B ATP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc16 I MG MG . B MG 603 1_555 L O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc17 I MG MG . B MG 603 1_555 L O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc18 J MG MG . B MG 604 1_555 L O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc19 J MG MG . B MG 604 1_555 L O HOH . B HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? # _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 7DYE _atom_sites.fract_transf_matrix[1][1] 0.010537 _atom_sites.fract_transf_matrix[1][2] 0.006083 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012167 _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] 0.003616 _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 2 ATP A 1 601 501 ATP ATP . D 2 ATP A 1 602 601 ATP ATP . E 3 MG A 1 603 1 MG MG . F 3 MG A 1 604 2 MG MG . G 2 ATP B 1 601 501 ATP ATP . H 2 ATP B 1 602 601 ATP ATP . I 3 MG B 1 603 3 MG MG . J 3 MG B 1 604 4 MG MG . K 4 HOH A 1 701 9 HOH HOH . K 4 HOH A 2 702 23 HOH HOH . K 4 HOH A 3 703 10 HOH HOH . K 4 HOH A 4 704 11 HOH HOH . K 4 HOH A 5 705 18 HOH HOH . K 4 HOH A 6 706 1 HOH HOH . K 4 HOH A 7 707 3 HOH HOH . K 4 HOH A 8 708 4 HOH HOH . K 4 HOH A 9 709 15 HOH HOH . L 4 HOH B 1 701 13 HOH HOH . L 4 HOH B 2 702 12 HOH HOH . L 4 HOH B 3 703 17 HOH HOH . L 4 HOH B 4 704 8 HOH HOH . L 4 HOH B 5 705 6 HOH HOH . L 4 HOH B 6 706 14 HOH HOH . L 4 HOH B 7 707 21 HOH HOH . L 4 HOH B 8 708 16 HOH HOH . L 4 HOH B 9 709 22 HOH HOH . L 4 HOH B 10 710 5 HOH HOH . L 4 HOH B 11 711 19 HOH HOH . L 4 HOH B 12 712 7 HOH HOH . L 4 HOH B 13 713 20 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 . . . H 2 31.113 47.95 -21.205 1 39.88 ? PG ATP 602 B 1 HETATM 2 O O1G ATP . . . H 2 32.349 47.146 -20.884 1 39.93 ? O1G ATP 602 B 1 HETATM 3 O O2G ATP . . . H 2 29.971 47.676 -20.255 1 39.36 ? O2G ATP 602 B 1 HETATM 4 O O3G ATP . . . H 2 31.401 49.421 -21.371 1 40.46 ? O3G ATP 602 B 1 HETATM 5 P PB ATP . . . H 2 29.174 47.392 -23.324 1 38.86 ? PB ATP 602 B 1 HETATM 6 O O1B ATP . . . H 2 29.258 46.623 -24.596 1 39.31 ? O1B ATP 602 B 1 HETATM 7 O O2B ATP . . . H 2 28.173 47.008 -22.287 1 38.81 ? O2B ATP 602 B 1 HETATM 8 O O3B ATP . . . H 2 30.625 47.44 -22.653 1 39.5 ? O3B ATP 602 B 1 HETATM 9 P PA ATP . . . H 2 27.807 49.706 -24.456 1 37.05 ? PA ATP 602 B 1 HETATM 10 O O1A ATP . . . H 2 27.707 51.078 -23.869 1 37.76 ? O1A ATP 602 B 1 HETATM 11 O O2A ATP . . . H 2 26.588 48.849 -24.463 1 37.38 ? O2A ATP 602 B 1 HETATM 12 O O3A ATP . . . H 2 28.979 48.933 -23.695 1 37.97 ? O3A ATP 602 B 1 HETATM 13 O O5' ATP . . . H 2 28.409 49.788 -25.938 1 36.91 ? O5' ATP 602 B 1 HETATM 14 C C5' ATP . . . H 2 28.692 51.11 -26.458 1 36.47 ? C5' ATP 602 B 1 HETATM 15 C C4' ATP . . . H 2 29.589 51.008 -27.663 1 35.83 ? C4' ATP 602 B 1 HETATM 16 O O4' ATP . . . H 2 28.797 51.213 -28.861 1 35.7 ? O4' ATP 602 B 1 HETATM 17 C C3' ATP . . . H 2 30.72 52.04 -27.723 1 35.66 ? C3' ATP 602 B 1 HETATM 18 O O3' ATP . . . H 2 31.912 51.484 -27.185 1 34.95 ? O3' ATP 602 B 1 HETATM 19 C C2' ATP . . . H 2 30.823 52.368 -29.216 1 36 ? C2' ATP 602 B 1 HETATM 20 O O2' ATP . . . H 2 31.679 51.5 -29.927 1 35.96 ? O2' ATP 602 B 1 HETATM 21 C C1' ATP . . . H 2 29.371 52.222 -29.662 1 36.15 ? C1' ATP 602 B 1 HETATM 22 N N9 ATP . . . H 2 28.59 53.437 -29.489 1 36.4 ? N9 ATP 602 B 1 HETATM 23 C C8 ATP . . . H 2 28.175 53.997 -28.306 1 36.63 ? C8 ATP 602 B 1 HETATM 24 N N7 ATP . . . H 2 27.491 55.102 -28.485 1 37.05 ? N7 ATP 602 B 1 HETATM 25 C C5 ATP . . . H 2 27.459 55.277 -29.862 1 36.95 ? C5 ATP 602 B 1 HETATM 26 C C6 ATP . . . H 2 26.882 56.268 -30.68 1 36.96 ? C6 ATP 602 B 1 HETATM 27 N N6 ATP . . . H 2 26.202 57.308 -30.204 1 36.68 ? N6 ATP 602 B 1 HETATM 28 N N1 ATP . . . H 2 27.041 56.14 -32.021 1 36.81 ? N1 ATP 602 B 1 HETATM 29 C C2 ATP . . . H 2 27.731 55.087 -32.487 1 36.64 ? C2 ATP 602 B 1 HETATM 30 N N3 ATP . . . H 2 28.312 54.095 -31.815 1 36.52 ? N3 ATP 602 B 1 HETATM 31 C C4 ATP . . . H 2 28.137 54.254 -30.491 1 36.69 ? C4 ATP 602 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 217 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 31 #