data_3DV3 # _model_server_result.job_id UerubrNwvnWMGWJZ551v2w _model_server_result.datetime_utc '2024-11-26 12:42:22' _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 3dv3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":9000}' # _entry.id 3DV3 # _exptl.entry_id 3DV3 _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 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 120 _cell.entry_id 3DV3 _cell.length_a 81.596 _cell.length_b 81.596 _cell.length_c 129.966 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DV3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # 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 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1,2 A,B,C,D,E,F 2 1 # 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' 4_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 81.596 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 B MG MG . A MG 1 1_555 A OD1 ASN 135 A ASN 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc2 B MG MG . A MG 1 1_555 A OD2 ASP 148 A ASP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc3 B MG MG . A MG 1 1_555 C O1B ATP . A ATP 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? metalc ? metalc4 B MG MG . A MG 1 1_555 C O2A ATP . A ATP 9000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc5 B MG MG . A MG 1 1_555 F O HOH . A HOH 9020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc6 B MG MG . A MG 1 1_555 F O HOH . A HOH 9078 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? # _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 3DV3 _atom_sites.fract_transf_matrix[1][1] 0.012256 _atom_sites.fract_transf_matrix[1][2] 0.007076 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014151 _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] 0.007694 _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 1 1 MG MG . C 3 ATP A 1 9000 9000 ATP ATP . D 4 MEK A 1 9001 1 MEK MEK . E 5 GOL A 1 9003 9003 GOL GOL . F 6 HOH A 1 9004 1 HOH HOH . F 6 HOH A 2 9005 2 HOH HOH . F 6 HOH A 3 9006 3 HOH HOH . F 6 HOH A 4 9007 4 HOH HOH . F 6 HOH A 5 9008 5 HOH HOH . F 6 HOH A 6 9009 6 HOH HOH . F 6 HOH A 7 9010 7 HOH HOH . F 6 HOH A 8 9011 8 HOH HOH . F 6 HOH A 9 9012 9 HOH HOH . F 6 HOH A 10 9013 10 HOH HOH . F 6 HOH A 11 9014 11 HOH HOH . F 6 HOH A 12 9015 12 HOH HOH . F 6 HOH A 13 9016 13 HOH HOH . F 6 HOH A 14 9017 14 HOH HOH . F 6 HOH A 15 9018 15 HOH HOH . F 6 HOH A 16 9019 16 HOH HOH . F 6 HOH A 17 9020 17 HOH HOH . F 6 HOH A 18 9021 18 HOH HOH . F 6 HOH A 19 9022 19 HOH HOH . F 6 HOH A 20 9023 20 HOH HOH . F 6 HOH A 21 9024 21 HOH HOH . F 6 HOH A 22 9025 22 HOH HOH . F 6 HOH A 23 9026 23 HOH HOH . F 6 HOH A 24 9027 24 HOH HOH . F 6 HOH A 25 9028 25 HOH HOH . F 6 HOH A 26 9029 27 HOH HOH . F 6 HOH A 27 9030 28 HOH HOH . F 6 HOH A 28 9031 31 HOH HOH . F 6 HOH A 29 9032 32 HOH HOH . F 6 HOH A 30 9033 33 HOH HOH . F 6 HOH A 31 9034 34 HOH HOH . F 6 HOH A 32 9035 35 HOH HOH . F 6 HOH A 33 9036 36 HOH HOH . F 6 HOH A 34 9037 37 HOH HOH . F 6 HOH A 35 9038 38 HOH HOH . F 6 HOH A 36 9039 39 HOH HOH . F 6 HOH A 37 9040 40 HOH HOH . F 6 HOH A 38 9041 41 HOH HOH . F 6 HOH A 39 9042 42 HOH HOH . F 6 HOH A 40 9043 44 HOH HOH . F 6 HOH A 41 9044 45 HOH HOH . F 6 HOH A 42 9045 46 HOH HOH . F 6 HOH A 43 9046 47 HOH HOH . F 6 HOH A 44 9047 48 HOH HOH . F 6 HOH A 45 9048 49 HOH HOH . F 6 HOH A 46 9049 50 HOH HOH . F 6 HOH A 47 9050 51 HOH HOH . F 6 HOH A 48 9051 52 HOH HOH . F 6 HOH A 49 9052 53 HOH HOH . F 6 HOH A 50 9053 54 HOH HOH . F 6 HOH A 51 9054 55 HOH HOH . F 6 HOH A 52 9055 56 HOH HOH . F 6 HOH A 53 9056 57 HOH HOH . F 6 HOH A 54 9057 59 HOH HOH . F 6 HOH A 55 9058 60 HOH HOH . F 6 HOH A 56 9059 61 HOH HOH . F 6 HOH A 57 9060 62 HOH HOH . F 6 HOH A 58 9061 65 HOH HOH . F 6 HOH A 59 9062 66 HOH HOH . F 6 HOH A 60 9063 67 HOH HOH . F 6 HOH A 61 9064 69 HOH HOH . F 6 HOH A 62 9065 70 HOH HOH . F 6 HOH A 63 9066 71 HOH HOH . F 6 HOH A 64 9067 73 HOH HOH . F 6 HOH A 65 9068 74 HOH HOH . F 6 HOH A 66 9069 75 HOH HOH . F 6 HOH A 67 9070 76 HOH HOH . F 6 HOH A 68 9071 77 HOH HOH . F 6 HOH A 69 9072 78 HOH HOH . F 6 HOH A 70 9073 79 HOH HOH . F 6 HOH A 71 9074 80 HOH HOH . F 6 HOH A 72 9075 81 HOH HOH . F 6 HOH A 73 9076 82 HOH HOH . F 6 HOH A 74 9077 83 HOH HOH . F 6 HOH A 75 9078 84 HOH HOH . F 6 HOH A 76 9079 85 HOH HOH . F 6 HOH A 77 9080 86 HOH HOH . F 6 HOH A 78 9081 87 HOH HOH . F 6 HOH A 79 9082 88 HOH HOH . F 6 HOH A 80 9083 89 HOH HOH . F 6 HOH A 81 9084 90 HOH HOH . F 6 HOH A 82 9085 91 HOH HOH . F 6 HOH A 83 9086 92 HOH HOH . F 6 HOH A 84 9087 93 HOH HOH . F 6 HOH A 85 9088 94 HOH HOH . F 6 HOH A 86 9089 95 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 . . . C 3 44.974 -6.738 -2.239 1 60.19 ? PG ATP 9000 A 1 HETATM 2 O O1G ATP . . . C 3 44.511 -7.902 -3.01 1 60.46 ? O1G ATP 9000 A 1 HETATM 3 O O2G ATP . . . C 3 44.102 -6.442 -1.104 1 61.24 ? O2G ATP 9000 A 1 HETATM 4 O O3G ATP . . . C 3 45.326 -5.563 -3.037 1 60.57 ? O3G ATP 9000 A 1 HETATM 5 P PB ATP . . . C 3 46.972 -8.091 -0.672 1 45.39 ? PB ATP 9000 A 1 HETATM 6 O O1B ATP . . . C 3 46.549 -9.48 -0.872 1 45.65 ? O1B ATP 9000 A 1 HETATM 7 O O2B ATP . . . C 3 48.355 -7.716 -0.632 1 43.99 ? O2B ATP 9000 A 1 HETATM 8 O O3B ATP . . . C 3 46.436 -7.13 -1.767 1 52.56 ? O3B ATP 9000 A 1 HETATM 9 P PA ATP . . . C 3 45.718 -8.579 1.77 1 44.41 ? PA ATP 9000 A 1 HETATM 10 O O1A ATP . . . C 3 44.82 -7.791 2.561 1 44.65 ? O1A ATP 9000 A 1 HETATM 11 O O2A ATP . . . C 3 45.21 -9.827 1.198 1 46.42 ? O2A ATP 9000 A 1 HETATM 12 O O3A ATP . . . C 3 46.276 -7.662 0.64 1 43.17 ? O3A ATP 9000 A 1 HETATM 13 O O5' ATP . . . C 3 46.962 -8.925 2.632 1 45.82 ? O5' ATP 9000 A 1 HETATM 14 C C5' ATP . . . C 3 47.943 -7.976 2.958 1 53.12 ? C5' ATP 9000 A 1 HETATM 15 C C4' ATP . . . C 3 49.286 -8.593 3.276 1 55.26 ? C4' ATP 9000 A 1 HETATM 16 O O4' ATP . . . C 3 49.238 -9.345 4.466 1 55.27 ? O4' ATP 9000 A 1 HETATM 17 C C3' ATP . . . C 3 49.75 -9.559 2.239 1 55.52 ? C3' ATP 9000 A 1 HETATM 18 O O3' ATP . . . C 3 50.595 -8.924 1.313 1 57.47 ? O3' ATP 9000 A 1 HETATM 19 C C2' ATP . . . C 3 50.616 -10.489 3.02 1 54.75 ? C2' ATP 9000 A 1 HETATM 20 O O2' ATP . . . C 3 51.909 -9.955 2.918 1 58.01 ? O2' ATP 9000 A 1 HETATM 21 C C1' ATP . . . C 3 50.177 -10.384 4.445 1 49.33 ? C1' ATP 9000 A 1 HETATM 22 N N9 ATP . . . C 3 49.491 -11.618 4.835 1 49.53 ? N9 ATP 9000 A 1 HETATM 23 C C8 ATP . . . C 3 48.257 -11.902 4.504 1 46.22 ? C8 ATP 9000 A 1 HETATM 24 N N7 ATP . . . C 3 47.888 -13.077 4.99 1 44.55 ? N7 ATP 9000 A 1 HETATM 25 C C5 ATP . . . C 3 48.906 -13.578 5.661 1 47.38 ? C5 ATP 9000 A 1 HETATM 26 C C6 ATP . . . C 3 49.188 -14.805 6.423 1 45.67 ? C6 ATP 9000 A 1 HETATM 27 N N6 ATP . . . C 3 48.274 -15.748 6.568 1 45.06 ? N6 ATP 9000 A 1 HETATM 28 N N1 ATP . . . C 3 50.383 -14.946 6.968 1 45.35 ? N1 ATP 9000 A 1 HETATM 29 C C2 ATP . . . C 3 51.307 -14.023 6.827 1 44.86 ? C2 ATP 9000 A 1 HETATM 30 N N3 ATP . . . C 3 51.125 -12.903 6.16 1 48.21 ? N3 ATP 9000 A 1 HETATM 31 C C4 ATP . . . C 3 49.968 -12.61 5.559 1 48.32 ? C4 ATP 9000 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #