data_2NVU # _model_server_result.job_id q1LJcDlxQ3-wSFyC5g_j5Q _model_server_result.datetime_utc '2024-10-14 00:24:27' _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 2nvu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":103}' # _entry.id 2NVU # _exptl.entry_id 2NVU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 7 _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 2NVU _cell.length_a 156.494 _cell.length_b 156.494 _cell.length_c 190.485 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NVU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 # _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 7 _struct_asym.id H _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 B SG CYS 579 B CYS 2216 1_555 E C GLY 81 J GLY 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? metalc ? metalc1 J O HOH . B HOH 45 1_555 F MG MG . B MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc2 F MG MG . B MG 101 1_555 H O3G ATP . B ATP 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc3 F MG MG . B MG 101 1_555 H O2B ATP . B ATP 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? metalc ? metalc4 F MG MG . B MG 101 1_555 B OD2 ASP 509 B ASP 2146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc5 G ZN ZN . B ZN 102 1_555 B SG CYS 562 B CYS 2199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc6 G ZN ZN . B ZN 102 1_555 B SG CYS 565 B CYS 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc7 G ZN ZN . B ZN 102 1_555 B SG CYS 706 B CYS 2343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc8 G ZN ZN . B ZN 102 1_555 B SG CYS 709 B CYS 2346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? # _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 2NVU _atom_sites.fract_transf_matrix[1][1] 0.00639 _atom_sites.fract_transf_matrix[1][2] 0.003689 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007379 _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] 0.00525 _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 F 5 MG B 1 101 101 MG MG . G 6 ZN B 1 102 102 ZN ZN . H 7 ATP B 1 103 103 ATP ATP . I 8 HOH A 1 535 2 HOH HOH . I 8 HOH A 2 536 4 HOH HOH . I 8 HOH A 3 537 11 HOH HOH . I 8 HOH A 4 538 12 HOH HOH . I 8 HOH A 5 539 13 HOH HOH . I 8 HOH A 6 540 19 HOH HOH . I 8 HOH A 7 541 23 HOH HOH . I 8 HOH A 8 542 25 HOH HOH . I 8 HOH A 9 543 35 HOH HOH . I 8 HOH A 10 544 36 HOH HOH . I 8 HOH A 11 545 39 HOH HOH . J 8 HOH B 1 1 1 HOH HOH . J 8 HOH B 2 3 3 HOH HOH . J 8 HOH B 3 5 5 HOH HOH . J 8 HOH B 4 6 6 HOH HOH . J 8 HOH B 5 7 7 HOH HOH . J 8 HOH B 6 8 8 HOH HOH . J 8 HOH B 7 9 9 HOH HOH . J 8 HOH B 8 14 14 HOH HOH . J 8 HOH B 9 15 15 HOH HOH . J 8 HOH B 10 16 16 HOH HOH . J 8 HOH B 11 17 17 HOH HOH . J 8 HOH B 12 18 18 HOH HOH . J 8 HOH B 13 20 20 HOH HOH . J 8 HOH B 14 21 21 HOH HOH . J 8 HOH B 15 22 22 HOH HOH . J 8 HOH B 16 24 24 HOH HOH . J 8 HOH B 17 27 27 HOH HOH . J 8 HOH B 18 28 28 HOH HOH . J 8 HOH B 19 29 29 HOH HOH . J 8 HOH B 20 31 31 HOH HOH . J 8 HOH B 21 32 32 HOH HOH . J 8 HOH B 22 37 37 HOH HOH . J 8 HOH B 23 40 40 HOH HOH . J 8 HOH B 24 41 41 HOH HOH . J 8 HOH B 25 42 42 HOH HOH . J 8 HOH B 26 44 44 HOH HOH . J 8 HOH B 27 45 45 HOH HOH . K 8 HOH C 1 184 10 HOH HOH . K 8 HOH C 2 185 26 HOH HOH . K 8 HOH C 3 186 30 HOH HOH . K 8 HOH C 4 187 43 HOH HOH . L 8 HOH I 1 77 33 HOH HOH . L 8 HOH I 2 78 34 HOH HOH . L 8 HOH I 3 79 38 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 7 84.869 -28.165 -19.671 1 65.56 ? PG ATP 103 B 1 HETATM 2 O O1G ATP . . . H 7 85.546 -27.632 -20.88 1 70.8 ? O1G ATP 103 B 1 HETATM 3 O O2G ATP . . . H 7 83.354 -27.928 -19.683 1 70.1 ? O2G ATP 103 B 1 HETATM 4 O O3G ATP . . . H 7 85.168 -29.641 -19.597 1 69.95 ? O3G ATP 103 B 1 HETATM 5 P PB ATP . . . H 7 86.918 -27.299 -17.771 1 70.18 ? PB ATP 103 B 1 HETATM 6 O O1B ATP . . . H 7 87.703 -26.481 -18.718 1 69.45 ? O1B ATP 103 B 1 HETATM 7 O O2B ATP . . . H 7 87.571 -28.623 -17.422 1 73.77 ? O2B ATP 103 B 1 HETATM 8 O O3B ATP . . . H 7 85.446 -27.44 -18.352 1 69.84 ? O3B ATP 103 B 1 HETATM 9 P PA ATP . . . H 7 85.765 -26.712 -15.235 1 62.71 ? PA ATP 103 B 1 HETATM 10 O O1A ATP . . . H 7 84.885 -25.587 -14.988 1 63.53 ? O1A ATP 103 B 1 HETATM 11 O O2A ATP . . . H 7 85.008 -28.024 -15.378 1 67.62 ? O2A ATP 103 B 1 HETATM 12 O O3A ATP . . . H 7 86.579 -26.4 -16.529 1 64.27 ? O3A ATP 103 B 1 HETATM 13 O O5' ATP . . . H 7 86.905 -26.73 -14.159 1 63.37 ? O5' ATP 103 B 1 HETATM 14 C C5' ATP . . . H 7 87.248 -27.845 -13.387 1 61.3 ? C5' ATP 103 B 1 HETATM 15 C C4' ATP . . . H 7 88.765 -27.801 -13.269 1 62.21 ? C4' ATP 103 B 1 HETATM 16 O O4' ATP . . . H 7 89.234 -28.877 -12.5 1 62.93 ? O4' ATP 103 B 1 HETATM 17 C C3' ATP . . . H 7 89.42 -27.882 -14.625 1 61.87 ? C3' ATP 103 B 1 HETATM 18 O O3' ATP . . . H 7 90.112 -26.659 -14.854 1 60.07 ? O3' ATP 103 B 1 HETATM 19 C C2' ATP . . . H 7 90.282 -29.101 -14.527 1 61.78 ? C2' ATP 103 B 1 HETATM 20 O O2' ATP . . . H 7 91.455 -29.151 -15.225 1 61.92 ? O2' ATP 103 B 1 HETATM 21 C C1' ATP . . . H 7 90.471 -29.273 -13.055 1 61.56 ? C1' ATP 103 B 1 HETATM 22 N N9 ATP . . . H 7 90.719 -30.672 -12.552 1 64.29 ? N9 ATP 103 B 1 HETATM 23 C C8 ATP . . . H 7 89.88 -31.761 -12.746 1 63.05 ? C8 ATP 103 B 1 HETATM 24 N N7 ATP . . . H 7 90.445 -32.806 -12.181 1 62.85 ? N7 ATP 103 B 1 HETATM 25 C C5 ATP . . . H 7 91.622 -32.468 -11.595 1 61.73 ? C5 ATP 103 B 1 HETATM 26 C C6 ATP . . . H 7 92.68 -33.112 -10.894 1 61.62 ? C6 ATP 103 B 1 HETATM 27 N N6 ATP . . . H 7 92.72 -34.375 -10.554 1 62.24 ? N6 ATP 103 B 1 HETATM 28 N N1 ATP . . . H 7 93.775 -32.37 -10.459 1 61.7 ? N1 ATP 103 B 1 HETATM 29 C C2 ATP . . . H 7 93.895 -31.019 -10.73 1 60.69 ? C2 ATP 103 B 1 HETATM 30 N N3 ATP . . . H 7 92.898 -30.375 -11.423 1 61 ? N3 ATP 103 B 1 HETATM 31 C C4 ATP . . . H 7 91.8 -31.086 -11.872 1 63.01 ? C4 ATP 103 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #