data_2YCH # _model_server_result.job_id nl-n1cLQ-Vksut93yQa15Q _model_server_result.datetime_utc '2024-11-21 22:36:16' _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 2ych # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 2YCH # _exptl.entry_id 2YCH _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 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 90 _cell.entry_id 2YCH _cell.length_a 50.78 _cell.length_b 50.78 _cell.length_c 366.117 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YCH _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 4 _struct_asym.id D _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 A C LEU 50 A LEU 50 1_555 A N MSE 51 A MSE 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C MSE 51 A MSE 51 1_555 A N GLU 52 A GLU 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale3 A C GLY 53 A GLY 53 1_555 A N MSE 54 A MSE 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 A C MSE 54 A MSE 54 1_555 A N VAL 55 A VAL 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale5 A C LYS 97 A LYS 97 1_555 A N MSE 98 A MSE 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 A C MSE 98 A MSE 98 1_555 A N PRO 99 A PRO 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale7 A C GLU 102 A GLU 102 1_555 A N MSE 103 A MSE 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale8 A C MSE 103 A MSE 103 1_555 A N GLU 104 A GLU 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale9 A C VAL 143 A VAL 143 1_555 A N MSE 144 A MSE 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale10 A C MSE 144 A MSE 144 1_555 A N VAL 145 A VAL 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.309 ? metalc ? metalc1 A OE2 GLU 19 A GLU 19 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc2 C MG MG . A MG 501 1_555 D O3G ATP . A ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc3 C MG MG . A MG 501 1_555 D O2B ATP . A ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc4 C MG MG . A MG 501 1_555 E O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 C MG MG . A MG 501 1_555 E O HOH . A HOH 2049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc6 C MG MG . A MG 501 1_555 E O HOH . A HOH 2050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? # _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 2YCH _atom_sites.fract_transf_matrix[1][1] 0.019693 _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] 0.019693 _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] 0.002731 _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 3 MG A 1 501 501 MG MG . D 4 ATP A 1 502 502 ATP ATP . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 HOH HOH . E 5 HOH A 80 2080 2080 HOH HOH . E 5 HOH A 81 2081 2081 HOH HOH . F 5 HOH B 1 2001 2001 HOH HOH . F 5 HOH B 2 2002 2002 HOH HOH . F 5 HOH B 3 2003 2003 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 . . . D 4 15.039 5.606 22.533 1 27.35 ? PG ATP 502 A 1 HETATM 2 O O1G ATP . . . D 4 15.945 5.945 23.707 1 28.84 ? O1G ATP 502 A 1 HETATM 3 O O2G ATP . . . D 4 14.707 6.862 21.786 1 27.77 ? O2G ATP 502 A 1 HETATM 4 O O3G ATP . . . D 4 13.877 4.767 22.881 1 26.06 ? O3G ATP 502 A 1 HETATM 5 P PB ATP . . . D 4 15.762 3.624 20.47 1 25.06 ? PB ATP 502 A 1 HETATM 6 O O1B ATP . . . D 4 16.171 4.316 19.194 1 25.11 ? O1B ATP 502 A 1 HETATM 7 O O2B ATP . . . D 4 14.321 3.227 20.541 1 18.93 ? O2B ATP 502 A 1 HETATM 8 O O3B ATP . . . D 4 16.121 4.72 21.629 1 26.38 ? O3B ATP 502 A 1 HETATM 9 P PA ATP . . . D 4 16.699 0.894 20.419 1 25.39 ? PA ATP 502 A 1 HETATM 10 O O1A ATP . . . D 4 16.299 0.997 18.945 1 27.23 ? O1A ATP 502 A 1 HETATM 11 O O2A ATP . . . D 4 15.906 0.052 21.369 1 25.03 ? O2A ATP 502 A 1 HETATM 12 O O3A ATP . . . D 4 16.772 2.452 20.852 1 24.42 ? O3A ATP 502 A 1 HETATM 13 O O5' ATP . . . D 4 18.145 0.429 20.723 1 28.52 ? O5' ATP 502 A 1 HETATM 14 C C5' ATP . . . D 4 19.201 1.174 20.184 1 28.28 ? C5' ATP 502 A 1 HETATM 15 C C4' ATP . . . D 4 20.374 1.069 21.183 1 28.95 ? C4' ATP 502 A 1 HETATM 16 O O4' ATP . . . D 4 20.773 -0.254 21.507 1 28.02 ? O4' ATP 502 A 1 HETATM 17 C C3' ATP . . . D 4 21.593 1.696 20.549 1 30.71 ? C3' ATP 502 A 1 HETATM 18 O O3' ATP . . . D 4 22.125 2.434 21.612 1 29.78 ? O3' ATP 502 A 1 HETATM 19 C C2' ATP . . . D 4 22.543 0.589 20.201 1 29.73 ? C2' ATP 502 A 1 HETATM 20 O O2' ATP . . . D 4 23.891 1.002 20.265 1 33.92 ? O2' ATP 502 A 1 HETATM 21 C C1' ATP . . . D 4 22.21 -0.362 21.31 1 29.32 ? C1' ATP 502 A 1 HETATM 22 N N9 ATP . . . D 4 22.467 -1.716 20.839 1 29.39 ? N9 ATP 502 A 1 HETATM 23 C C8 ATP . . . D 4 21.793 -2.259 19.781 1 28.82 ? C8 ATP 502 A 1 HETATM 24 N N7 ATP . . . D 4 22.178 -3.538 19.63 1 25.28 ? N7 ATP 502 A 1 HETATM 25 C C5 ATP . . . D 4 23.121 -3.814 20.509 1 27.24 ? C5 ATP 502 A 1 HETATM 26 C C6 ATP . . . D 4 23.968 -4.986 20.76 1 30.44 ? C6 ATP 502 A 1 HETATM 27 N N6 ATP . . . D 4 23.849 -6.113 20.054 1 34.42 ? N6 ATP 502 A 1 HETATM 28 N N1 ATP . . . D 4 24.859 -4.9 21.743 1 32.48 ? N1 ATP 502 A 1 HETATM 29 C C2 ATP . . . D 4 24.987 -3.746 22.481 1 30.56 ? C2 ATP 502 A 1 HETATM 30 N N3 ATP . . . D 4 24.278 -2.614 22.283 1 28.72 ? N3 ATP 502 A 1 HETATM 31 C C4 ATP . . . D 4 23.336 -2.602 21.307 1 28.94 ? C4 ATP 502 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #