data_5MB9 # _model_server_result.job_id g6QXxK5e2uokIq2nlHDzRQ _model_server_result.datetime_utc '2025-04-04 05:10:16' _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 5mb9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":700}' # _entry.id 5MB9 # _exptl.entry_id 5MB9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5MB9 _cell.length_a 93.918 _cell.length_b 179.359 _cell.length_c 155.455 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MB9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,J 1 1 B,C,G,H,I,K 2 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 ? 3 E N N ? 3 G 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 E O2B ATP . A ATP 700 1_555 F MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc2 F MG MG . A MG 701 1_555 J O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc3 F MG MG . A MG 701 1_555 J O HOH . A HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc4 F MG MG . A MG 701 1_555 J O HOH . A HOH 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc5 F MG MG . A MG 701 1_555 J O HOH . A HOH 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc6 G O1B ATP . B ATP 601 1_555 H MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc7 H MG MG . B MG 602 1_555 K O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc8 H MG MG . B MG 602 1_555 K O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc9 H MG MG . B MG 602 1_555 K O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc10 H MG MG . B MG 602 1_555 K O HOH . B HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? # _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 5MB9 _atom_sites.fract_transf_matrix[1][1] 0.010648 _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] 0.005575 _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] 0.006433 _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 3 ATP A 1 700 700 ATP ATP . F 4 MG A 1 701 701 MG MG . G 3 ATP B 1 601 700 ATP ATP . H 4 MG B 1 602 701 MG MG . I 5 GOL B 1 603 1 GOL GOL . J 6 HOH A 1 801 2009 HOH HOH . J 6 HOH A 2 802 2008 HOH HOH . J 6 HOH A 3 803 2006 HOH HOH . J 6 HOH A 4 804 2007 HOH HOH . K 6 HOH B 1 701 2009 HOH HOH . K 6 HOH B 2 702 2008 HOH HOH . K 6 HOH B 3 703 2006 HOH HOH . K 6 HOH B 4 704 2007 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 3 -17.3 -9.066 24.728 1 80.3 ? PG ATP 700 A 1 HETATM 2 O O1G ATP . . . E 3 -17.455 -9.206 23.235 1 94.56 ? O1G ATP 700 A 1 HETATM 3 O O2G ATP . . . E 3 -17.76 -10.254 25.537 1 88.45 ? O2G ATP 700 A 1 HETATM 4 O O3G ATP . . . E 3 -17.784 -7.748 25.277 1 73.72 ? O3G ATP 700 A 1 HETATM 5 P PB ATP . . . E 3 -14.759 -10.216 25.239 1 67.89 ? PB ATP 700 A 1 HETATM 6 O O1B ATP . . . E 3 -13.484 -9.978 24.464 1 72.61 ? O1B ATP 700 A 1 HETATM 7 O O2B ATP . . . E 3 -15.505 -11.516 25.091 1 70.38 ? O2B ATP 700 A 1 HETATM 8 O O3B ATP . . . E 3 -15.719 -8.951 24.981 1 73.46 ? O3B ATP 700 A 1 HETATM 9 P PA ATP . . . E 3 -13.437 -10.801 27.691 1 62 ? PA ATP 700 A 1 HETATM 10 O O1A ATP . . . E 3 -12.04 -10.628 27.141 1 57.13 ? O1A ATP 700 A 1 HETATM 11 O O2A ATP . . . E 3 -14.025 -12.164 27.95 1 69.76 ? O2A ATP 700 A 1 HETATM 12 O O3A ATP . . . E 3 -14.441 -9.938 26.784 1 66.36 ? O3A ATP 700 A 1 HETATM 13 O O5' ATP . . . E 3 -13.589 -9.851 28.975 1 64.69 ? O5' ATP 700 A 1 HETATM 14 C C5' ATP . . . E 3 -13.166 -8.501 28.796 1 71.22 ? C5' ATP 700 A 1 HETATM 15 C C4' ATP . . . E 3 -13.734 -7.617 29.886 1 66.88 ? C4' ATP 700 A 1 HETATM 16 O O4' ATP . . . E 3 -13.32 -8.175 31.134 1 73.01 ? O4' ATP 700 A 1 HETATM 17 C C3' ATP . . . E 3 -13.146 -6.216 29.81 1 59.79 ? C3' ATP 700 A 1 HETATM 18 O O3' ATP . . . E 3 -14.098 -5.261 30.279 1 58.12 ? O3' ATP 700 A 1 HETATM 19 C C2' ATP . . . E 3 -11.967 -6.288 30.749 1 56.04 ? C2' ATP 700 A 1 HETATM 20 O O2' ATP . . . E 3 -11.7 -5.007 31.325 1 56.55 ? O2' ATP 700 A 1 HETATM 21 C C1' ATP . . . E 3 -12.482 -7.245 31.808 1 60.29 ? C1' ATP 700 A 1 HETATM 22 N N9 ATP . . . E 3 -11.362 -7.941 32.476 1 58.71 ? N9 ATP 700 A 1 HETATM 23 C C8 ATP . . . E 3 -10.354 -8.6 31.878 1 59.35 ? C8 ATP 700 A 1 HETATM 24 N N7 ATP . . . E 3 -9.508 -9.115 32.806 1 67.99 ? N7 ATP 700 A 1 HETATM 25 C C5 ATP . . . E 3 -9.982 -8.776 34.019 1 64.26 ? C5 ATP 700 A 1 HETATM 26 C C6 ATP . . . E 3 -9.579 -8.991 35.424 1 57.34 ? C6 ATP 700 A 1 HETATM 27 N N6 ATP . . . E 3 -8.465 -9.693 35.735 1 66.62 ? N6 ATP 700 A 1 HETATM 28 N N1 ATP . . . E 3 -10.366 -8.464 36.385 1 58.15 ? N1 ATP 700 A 1 HETATM 29 C C2 ATP . . . E 3 -11.477 -7.765 36.096 1 66.37 ? C2 ATP 700 A 1 HETATM 30 N N3 ATP . . . E 3 -11.903 -7.529 34.848 1 68.66 ? N3 ATP 700 A 1 HETATM 31 C C4 ATP . . . E 3 -11.206 -8.002 33.79 1 67.27 ? C4 ATP 700 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #