data_2V9J # _model_server_result.job_id h2ASD2-kPrv2pAzmxmlL2w _model_server_result.datetime_utc '2025-01-09 21:06:50' _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 2v9j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1328}' # _entry.id 2V9J # _exptl.entry_id 2V9J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _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 2V9J _cell.length_a 48.79 _cell.length_b 120.685 _cell.length_c 127.069 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2V9J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 4 D N N ? 4 E 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 D O2B ATP . E ATP 1327 1_555 G MG MG . E MG 1330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc2 D O1G ATP . E ATP 1327 1_555 G MG MG . E MG 1330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc3 E O2B ATP . E ATP 1328 1_555 H MG MG . E MG 1331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc4 E O1G ATP . E ATP 1328 1_555 H MG MG . E MG 1331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc5 G MG MG . E MG 1330 1_555 K O HOH . E HOH 2074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc6 G MG MG . E MG 1330 1_555 K O HOH . E HOH 2077 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc7 H MG MG . E MG 1331 1_555 K O HOH . E HOH 2078 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? # _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 2V9J _atom_sites.fract_transf_matrix[1][1] 0.020496 _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] 0.008286 _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] 0.00787 _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 D 4 ATP E 1 1327 1327 ATP ATP . E 4 ATP E 1 1328 1328 ATP ATP . F 5 AMP E 1 1329 1329 AMP AMP . G 6 MG E 1 1330 1330 MG MG . H 6 MG E 1 1331 1331 MG MG . I 7 HOH A 1 2001 2001 HOH HOH . I 7 HOH A 2 2002 2002 HOH HOH . I 7 HOH A 3 2003 2003 HOH HOH . I 7 HOH A 4 2004 2004 HOH HOH . I 7 HOH A 5 2005 2005 HOH HOH . I 7 HOH A 6 2006 2006 HOH HOH . I 7 HOH A 7 2007 2007 HOH HOH . I 7 HOH A 8 2008 2008 HOH HOH . I 7 HOH A 9 2009 2009 HOH HOH . I 7 HOH A 10 2010 2010 HOH HOH . I 7 HOH A 11 2011 2011 HOH HOH . I 7 HOH A 12 2012 2012 HOH HOH . I 7 HOH A 13 2013 2013 HOH HOH . I 7 HOH A 14 2014 2014 HOH HOH . I 7 HOH A 15 2015 2015 HOH HOH . I 7 HOH A 16 2016 2016 HOH HOH . I 7 HOH A 17 2017 2017 HOH HOH . I 7 HOH A 18 2018 2018 HOH HOH . I 7 HOH A 19 2019 2019 HOH HOH . I 7 HOH A 20 2020 2020 HOH HOH . I 7 HOH A 21 2021 2021 HOH HOH . I 7 HOH A 22 2022 2022 HOH HOH . I 7 HOH A 23 2023 2023 HOH HOH . I 7 HOH A 24 2024 2024 HOH HOH . I 7 HOH A 25 2025 2025 HOH HOH . I 7 HOH A 26 2026 2026 HOH HOH . I 7 HOH A 27 2027 2027 HOH HOH . I 7 HOH A 28 2028 2028 HOH HOH . I 7 HOH A 29 2029 2029 HOH HOH . I 7 HOH A 30 2030 2030 HOH HOH . I 7 HOH A 31 2031 2031 HOH HOH . I 7 HOH A 32 2032 2032 HOH HOH . I 7 HOH A 33 2033 2033 HOH HOH . I 7 HOH A 34 2034 2034 HOH HOH . I 7 HOH A 35 2035 2035 HOH HOH . J 7 HOH B 1 2001 2001 HOH HOH . J 7 HOH B 2 2002 2002 HOH HOH . J 7 HOH B 3 2003 2003 HOH HOH . J 7 HOH B 4 2004 2004 HOH HOH . J 7 HOH B 5 2005 2005 HOH HOH . J 7 HOH B 6 2006 2006 HOH HOH . J 7 HOH B 7 2007 2007 HOH HOH . J 7 HOH B 8 2008 2008 HOH HOH . J 7 HOH B 9 2009 2009 HOH HOH . J 7 HOH B 10 2010 2010 HOH HOH . J 7 HOH B 11 2011 2011 HOH HOH . J 7 HOH B 12 2012 2012 HOH HOH . J 7 HOH B 13 2013 2013 HOH HOH . J 7 HOH B 14 2014 2014 HOH HOH . J 7 HOH B 15 2015 2015 HOH HOH . J 7 HOH B 16 2016 2016 HOH HOH . J 7 HOH B 17 2017 2017 HOH HOH . J 7 HOH B 18 2018 2018 HOH HOH . J 7 HOH B 19 2019 2019 HOH HOH . J 7 HOH B 20 2020 2020 HOH HOH . J 7 HOH B 21 2021 2021 HOH HOH . J 7 HOH B 22 2022 2022 HOH HOH . J 7 HOH B 23 2023 2023 HOH HOH . J 7 HOH B 24 2024 2024 HOH HOH . J 7 HOH B 25 2025 2025 HOH HOH . J 7 HOH B 26 2026 2026 HOH HOH . J 7 HOH B 27 2027 2027 HOH HOH . K 7 HOH E 1 2001 2001 HOH HOH . K 7 HOH E 2 2002 2002 HOH HOH . K 7 HOH E 3 2003 2003 HOH HOH . K 7 HOH E 4 2004 2004 HOH HOH . K 7 HOH E 5 2005 2005 HOH HOH . K 7 HOH E 6 2006 2006 HOH HOH . K 7 HOH E 7 2007 2007 HOH HOH . K 7 HOH E 8 2008 2008 HOH HOH . K 7 HOH E 9 2009 2009 HOH HOH . K 7 HOH E 10 2010 2010 HOH HOH . K 7 HOH E 11 2011 2011 HOH HOH . K 7 HOH E 12 2012 2012 HOH HOH . K 7 HOH E 13 2013 2013 HOH HOH . K 7 HOH E 14 2014 2014 HOH HOH . K 7 HOH E 15 2015 2015 HOH HOH . K 7 HOH E 16 2016 2016 HOH HOH . K 7 HOH E 17 2017 2017 HOH HOH . K 7 HOH E 18 2018 2018 HOH HOH . K 7 HOH E 19 2019 2019 HOH HOH . K 7 HOH E 20 2020 2020 HOH HOH . K 7 HOH E 21 2021 2021 HOH HOH . K 7 HOH E 22 2022 2022 HOH HOH . K 7 HOH E 23 2023 2023 HOH HOH . K 7 HOH E 24 2024 2024 HOH HOH . K 7 HOH E 25 2025 2025 HOH HOH . K 7 HOH E 26 2026 2026 HOH HOH . K 7 HOH E 27 2027 2027 HOH HOH . K 7 HOH E 28 2028 2028 HOH HOH . K 7 HOH E 29 2029 2029 HOH HOH . K 7 HOH E 30 2030 2030 HOH HOH . K 7 HOH E 31 2031 2031 HOH HOH . K 7 HOH E 32 2032 2032 HOH HOH . K 7 HOH E 33 2033 2033 HOH HOH . K 7 HOH E 34 2034 2034 HOH HOH . K 7 HOH E 35 2035 2035 HOH HOH . K 7 HOH E 36 2036 2036 HOH HOH . K 7 HOH E 37 2037 2037 HOH HOH . K 7 HOH E 38 2038 2038 HOH HOH . K 7 HOH E 39 2039 2039 HOH HOH . K 7 HOH E 40 2040 2040 HOH HOH . K 7 HOH E 41 2041 2041 HOH HOH . K 7 HOH E 42 2042 2042 HOH HOH . K 7 HOH E 43 2043 2043 HOH HOH . K 7 HOH E 44 2044 2044 HOH HOH . K 7 HOH E 45 2045 2045 HOH HOH . K 7 HOH E 46 2046 2046 HOH HOH . K 7 HOH E 47 2047 2047 HOH HOH . K 7 HOH E 48 2048 2048 HOH HOH . K 7 HOH E 49 2049 2049 HOH HOH . K 7 HOH E 50 2050 2050 HOH HOH . K 7 HOH E 51 2051 2051 HOH HOH . K 7 HOH E 52 2052 2052 HOH HOH . K 7 HOH E 53 2053 2053 HOH HOH . K 7 HOH E 54 2054 2054 HOH HOH . K 7 HOH E 55 2055 2055 HOH HOH . K 7 HOH E 56 2056 2056 HOH HOH . K 7 HOH E 57 2057 2057 HOH HOH . K 7 HOH E 58 2058 2058 HOH HOH . K 7 HOH E 59 2059 2059 HOH HOH . K 7 HOH E 60 2060 2060 HOH HOH . K 7 HOH E 61 2061 2061 HOH HOH . K 7 HOH E 62 2062 2062 HOH HOH . K 7 HOH E 63 2063 2063 HOH HOH . K 7 HOH E 64 2064 2064 HOH HOH . K 7 HOH E 65 2065 2065 HOH HOH . K 7 HOH E 66 2066 2066 HOH HOH . K 7 HOH E 67 2067 2067 HOH HOH . K 7 HOH E 68 2068 2068 HOH HOH . K 7 HOH E 69 2069 2069 HOH HOH . K 7 HOH E 70 2070 2070 HOH HOH . K 7 HOH E 71 2071 2071 HOH HOH . K 7 HOH E 72 2072 2072 HOH HOH . K 7 HOH E 73 2073 2073 HOH HOH . K 7 HOH E 74 2074 2074 HOH HOH . K 7 HOH E 75 2075 2075 HOH HOH . K 7 HOH E 76 2076 2076 HOH HOH . K 7 HOH E 77 2077 2077 HOH HOH . K 7 HOH E 78 2078 2078 HOH HOH . K 7 HOH E 79 2079 2079 HOH HOH . K 7 HOH E 80 2080 2080 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 4 26.316 8.566 22.704 1 62.07 ? PG ATP 1328 E 1 HETATM 2 O O1G ATP . . . E 4 26.29 7.039 22.169 1 61.46 ? O1G ATP 1328 E 1 HETATM 3 O O2G ATP . . . E 4 24.909 8.95 23.12 1 62.32 ? O2G ATP 1328 E 1 HETATM 4 O O3G ATP . . . E 4 27.043 9.374 21.653 1 63.76 ? O3G ATP 1328 E 1 HETATM 5 P PB ATP . . . E 4 26.894 7.836 25.399 1 53.88 ? PB ATP 1328 E 1 HETATM 6 O O1B ATP . . . E 4 25.455 8.202 25.964 1 56.82 ? O1B ATP 1328 E 1 HETATM 7 O O2B ATP . . . E 4 26.965 6.242 25.185 1 57.08 ? O2B ATP 1328 E 1 HETATM 8 O O3B ATP . . . E 4 27.281 8.528 23.993 1 58.58 ? O3B ATP 1328 E 1 HETATM 9 P PA ATP . . . E 4 27.49 9.901 27.082 1 39.75 ? PA ATP 1328 E 1 HETATM 10 O O1A ATP . . . E 4 26.483 9.609 28.146 1 42.39 ? O1A ATP 1328 E 1 HETATM 11 O O2A ATP . . . E 4 27.145 10.939 26.077 1 41.89 ? O2A ATP 1328 E 1 HETATM 12 O O3A ATP . . . E 4 27.928 8.485 26.425 1 47.83 ? O3A ATP 1328 E 1 HETATM 13 O O5' ATP . . . E 4 28.939 10.266 27.654 1 39.92 ? O5' ATP 1328 E 1 HETATM 14 C C5' ATP . . . E 4 29.257 11.485 28.305 1 36.14 ? C5' ATP 1328 E 1 HETATM 15 C C4' ATP . . . E 4 30.28 11.244 29.415 1 32.38 ? C4' ATP 1328 E 1 HETATM 16 O O4' ATP . . . E 4 29.68 11.629 30.645 1 31.07 ? O4' ATP 1328 E 1 HETATM 17 C C3' ATP . . . E 4 30.708 9.8 29.617 1 31.99 ? C3' ATP 1328 E 1 HETATM 18 O O3' ATP . . . E 4 32.076 9.78 30.042 1 33.91 ? O3' ATP 1328 E 1 HETATM 19 C C2' ATP . . . E 4 29.901 9.278 30.779 1 29.67 ? C2' ATP 1328 E 1 HETATM 20 O O2' ATP . . . E 4 30.693 8.453 31.641 1 29.29 ? O2' ATP 1328 E 1 HETATM 21 C C1' ATP . . . E 4 29.479 10.521 31.531 1 25.99 ? C1' ATP 1328 E 1 HETATM 22 N N9 ATP . . . E 4 28.038 10.433 31.843 1 23.39 ? N9 ATP 1328 E 1 HETATM 23 C C8 ATP . . . E 4 27.085 9.894 31.052 1 21.92 ? C8 ATP 1328 E 1 HETATM 24 N N7 ATP . . . E 4 25.871 9.995 31.641 1 21.67 ? N7 ATP 1328 E 1 HETATM 25 C C5 ATP . . . E 4 26.039 10.621 32.823 1 21.23 ? C5 ATP 1328 E 1 HETATM 26 C C6 ATP . . . E 4 25.176 11.064 33.941 1 21.8 ? C6 ATP 1328 E 1 HETATM 27 N N6 ATP . . . E 4 23.847 10.837 33.929 1 21.77 ? N6 ATP 1328 E 1 HETATM 28 N N1 ATP . . . E 4 25.755 11.686 34.996 1 22.26 ? N1 ATP 1328 E 1 HETATM 29 C C2 ATP . . . E 4 27.08 11.917 35.029 1 22 ? C2 ATP 1328 E 1 HETATM 30 N N3 ATP . . . E 4 27.921 11.555 34.042 1 21.28 ? N3 ATP 1328 E 1 HETATM 31 C C4 ATP . . . E 4 27.472 10.91 32.944 1 21.49 ? C4 ATP 1328 E 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #