data_2Z08 # _model_server_result.job_id x4TKf6ALPq8PHPgD2DyN9g _model_server_result.datetime_utc '2024-11-28 22:08:05' _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 2z08 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 2Z08 # _exptl.entry_id 2Z08 _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 90 _cell.entry_id 2Z08 _cell.length_a 33.1 _cell.length_b 75.05 _cell.length_c 88.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Z08 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 33.1 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 33.1 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _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 metalc ? metalc1 D O2A ATP . A ATP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc2 D O3G ATP . A ATP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc3 D O2B ATP . A ATP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc4 B MG MG . A MG 2001 1_555 E O HOH . A HOH 2034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 B MG MG . A MG 2001 1_555 E O HOH . A HOH 2035 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc6 B MG MG . A MG 2001 1_555 E O HOH . A HOH 2050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc7 C MG MG . A MG 2002 1_555 E O HOH . A HOH 2058 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc8 C MG MG . A MG 2002 1_555 E O HOH . A HOH 2059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? # _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 54 n n PG O2G ATP sing 55 n n PG O3G ATP sing 56 n n PG O3B ATP sing 57 n n O2G HOG2 ATP sing 58 n n O3G HOG3 ATP sing 59 n n PB O1B ATP doub 60 n n PB O2B ATP sing 61 n n PB O3B ATP sing 62 n n PB O3A ATP sing 63 n n O2B HOB2 ATP sing 64 n n PA O1A ATP doub 65 n n PA O2A ATP sing 66 n n PA O3A ATP sing 67 n n PA O5' ATP sing 68 n n O2A HOA2 ATP sing 69 n n O5' C5' ATP sing 70 n n C5' C4' ATP sing 71 n n C5' "H5'1" ATP sing 72 n n C5' "H5'2" ATP sing 73 n n C4' O4' ATP sing 74 n n C4' C3' ATP sing 75 n n C4' H4' ATP sing 76 n n O4' C1' ATP sing 77 n n C3' O3' ATP sing 78 n n C3' C2' ATP sing 79 n n C3' H3' ATP sing 80 n n O3' HO3' ATP sing 81 n n C2' O2' ATP sing 82 n n C2' C1' ATP sing 83 n n C2' H2' ATP sing 84 n n O2' HO2' ATP sing 85 n n C1' N9 ATP sing 86 n n C1' H1' ATP sing 87 n n N9 C8 ATP sing 88 n y N9 C4 ATP sing 89 n y C8 N7 ATP doub 90 n y C8 H8 ATP sing 91 n n N7 C5 ATP sing 92 n y C5 C6 ATP sing 93 n y C5 C4 ATP doub 94 n y C6 N6 ATP sing 95 n n C6 N1 ATP doub 96 n y N6 HN61 ATP sing 97 n n N6 HN62 ATP sing 98 n n N1 C2 ATP sing 99 n y C2 N3 ATP doub 100 n y C2 H2 ATP sing 101 n n N3 C4 ATP sing 102 n y # _atom_sites.entry_id 2Z08 _atom_sites.fract_transf_matrix[1][1] 0.030211 _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] 0.013324 _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] 0.011276 _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 2001 2001 MG MG . C 2 MG A 1 2002 2002 MG MG . D 3 ATP A 1 1001 1001 ATP ATP . E 4 HOH A 1 2003 1 HOH HOH . E 4 HOH A 2 2004 2 HOH HOH . E 4 HOH A 3 2005 3 HOH HOH . E 4 HOH A 4 2006 4 HOH HOH . E 4 HOH A 5 2007 5 HOH HOH . E 4 HOH A 6 2008 6 HOH HOH . E 4 HOH A 7 2009 7 HOH HOH . E 4 HOH A 8 2010 8 HOH HOH . E 4 HOH A 9 2011 9 HOH HOH . E 4 HOH A 10 2012 10 HOH HOH . E 4 HOH A 11 2013 11 HOH HOH . E 4 HOH A 12 2014 12 HOH HOH . E 4 HOH A 13 2015 13 HOH HOH . E 4 HOH A 14 2016 14 HOH HOH . E 4 HOH A 15 2017 15 HOH HOH . E 4 HOH A 16 2018 16 HOH HOH . E 4 HOH A 17 2019 17 HOH HOH . E 4 HOH A 18 2020 18 HOH HOH . E 4 HOH A 19 2021 19 HOH HOH . E 4 HOH A 20 2022 20 HOH HOH . E 4 HOH A 21 2023 21 HOH HOH . E 4 HOH A 22 2024 22 HOH HOH . E 4 HOH A 23 2025 23 HOH HOH . E 4 HOH A 24 2026 24 HOH HOH . E 4 HOH A 25 2027 25 HOH HOH . E 4 HOH A 26 2028 26 HOH HOH . E 4 HOH A 27 2029 27 HOH HOH . E 4 HOH A 28 2030 28 HOH HOH . E 4 HOH A 29 2031 29 HOH HOH . E 4 HOH A 30 2032 30 HOH HOH . E 4 HOH A 31 2033 31 HOH HOH . E 4 HOH A 32 2034 32 HOH HOH . E 4 HOH A 33 2035 33 HOH HOH . E 4 HOH A 34 2036 34 HOH HOH . E 4 HOH A 35 2037 35 HOH HOH . E 4 HOH A 36 2038 36 HOH HOH . E 4 HOH A 37 2039 37 HOH HOH . E 4 HOH A 38 2040 38 HOH HOH . E 4 HOH A 39 2041 39 HOH HOH . E 4 HOH A 40 2042 40 HOH HOH . E 4 HOH A 41 2043 41 HOH HOH . E 4 HOH A 42 2044 42 HOH HOH . E 4 HOH A 43 2045 43 HOH HOH . E 4 HOH A 44 2046 44 HOH HOH . E 4 HOH A 45 2047 45 HOH HOH . E 4 HOH A 46 2048 46 HOH HOH . E 4 HOH A 47 2049 47 HOH HOH . E 4 HOH A 48 2050 48 HOH HOH . E 4 HOH A 49 2051 49 HOH HOH . E 4 HOH A 50 2052 50 HOH HOH . E 4 HOH A 51 2053 51 HOH HOH . E 4 HOH A 52 2054 52 HOH HOH . E 4 HOH A 53 2055 53 HOH HOH . E 4 HOH A 54 2056 54 HOH HOH . E 4 HOH A 55 2057 55 HOH HOH . E 4 HOH A 56 2058 56 HOH HOH . E 4 HOH A 57 2059 57 HOH HOH . E 4 HOH A 58 2060 58 HOH HOH . E 4 HOH A 59 2061 59 HOH HOH . E 4 HOH A 60 2062 60 HOH HOH . E 4 HOH A 61 2063 61 HOH HOH . E 4 HOH A 62 2064 62 HOH HOH . E 4 HOH A 63 2065 63 HOH HOH . E 4 HOH A 64 2066 64 HOH HOH . E 4 HOH A 65 2067 65 HOH HOH . E 4 HOH A 66 2068 66 HOH HOH . E 4 HOH A 67 2069 67 HOH HOH . E 4 HOH A 68 2070 68 HOH HOH . E 4 HOH A 69 2071 69 HOH HOH . E 4 HOH A 70 2072 70 HOH HOH . E 4 HOH A 71 2073 71 HOH HOH . E 4 HOH A 72 2074 72 HOH HOH . E 4 HOH A 73 2075 73 HOH HOH . E 4 HOH A 74 2076 74 HOH HOH . E 4 HOH A 75 2077 75 HOH HOH . E 4 HOH A 76 2078 76 HOH HOH . E 4 HOH A 77 2079 77 HOH HOH . E 4 HOH A 78 2080 78 HOH HOH . E 4 HOH A 79 2081 79 HOH HOH . E 4 HOH A 80 2082 80 HOH HOH . E 4 HOH A 81 2083 81 HOH HOH . E 4 HOH A 82 2084 82 HOH HOH . E 4 HOH A 83 2085 83 HOH HOH . E 4 HOH A 84 2086 84 HOH HOH . E 4 HOH A 85 2087 85 HOH HOH . E 4 HOH A 86 2088 86 HOH HOH . E 4 HOH A 87 2089 87 HOH HOH . E 4 HOH A 88 2090 88 HOH HOH . E 4 HOH A 89 2091 89 HOH HOH . E 4 HOH A 90 2092 90 HOH HOH . E 4 HOH A 91 2093 91 HOH HOH . E 4 HOH A 92 2094 92 HOH HOH . E 4 HOH A 93 2095 93 HOH HOH . E 4 HOH A 94 2096 94 HOH HOH . E 4 HOH A 95 2097 95 HOH HOH . E 4 HOH A 96 2098 96 HOH HOH . E 4 HOH A 97 2099 97 HOH HOH . E 4 HOH A 98 2100 98 HOH HOH . E 4 HOH A 99 2101 99 HOH HOH . E 4 HOH A 100 2102 100 HOH HOH . E 4 HOH A 101 2103 101 HOH HOH . E 4 HOH A 102 2104 102 HOH HOH . E 4 HOH A 103 2105 103 HOH HOH . E 4 HOH A 104 2106 104 HOH HOH . E 4 HOH A 105 2107 105 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 3 19.536 2.837 12.025 1 14.27 ? PG ATP 1001 A 1 HETATM 2 O O1G ATP . . . D 3 20.212 1.668 12.646 1 16.61 ? O1G ATP 1001 A 1 HETATM 3 O O2G ATP . . . D 3 18.612 2.529 10.752 1 18.37 ? O2G ATP 1001 A 1 HETATM 4 O O3G ATP . . . D 3 18.872 3.893 13.007 1 12.74 ? O3G ATP 1001 A 1 HETATM 5 P PB ATP . . . D 3 21.245 5.088 11.351 1 12.24 ? PB ATP 1001 A 1 HETATM 6 O O1B ATP . . . D 3 22.524 5.302 10.639 1 12.25 ? O1B ATP 1001 A 1 HETATM 7 O O2B ATP . . . D 3 21.055 5.626 12.841 1 12.37 ? O2B ATP 1001 A 1 HETATM 8 O O3B ATP . . . D 3 20.729 3.577 11.268 1 13.46 ? O3B ATP 1001 A 1 HETATM 9 P PA ATP . . . D 3 18.87 6.761 10.847 1 10.43 ? PA ATP 1001 A 1 HETATM 10 O O1A ATP . . . D 3 17.901 6.601 9.755 1 9.82 ? O1A ATP 1001 A 1 HETATM 11 O O2A ATP . . . D 3 18.456 6.591 12.352 1 10.61 ? O2A ATP 1001 A 1 HETATM 12 O O3A ATP . . . D 3 20.193 5.907 10.456 1 10.66 ? O3A ATP 1001 A 1 HETATM 13 O O5' ATP . . . D 3 19.483 8.245 10.714 1 10.85 ? O5' ATP 1001 A 1 HETATM 14 C C5' ATP . . . D 3 19.207 9.184 9.665 1 9.7 ? C5' ATP 1001 A 1 HETATM 15 C C4' ATP . . . D 3 18.627 10.463 10.266 1 8.31 ? C4' ATP 1001 A 1 HETATM 16 O O4' ATP . . . D 3 17.349 10.151 10.855 1 9.9 ? O4' ATP 1001 A 1 HETATM 17 C C3' ATP . . . D 3 19.445 11.051 11.415 1 9.58 ? C3' ATP 1001 A 1 HETATM 18 O O3' ATP . . . D 3 20.578 11.764 10.898 1 10.99 ? O3' ATP 1001 A 1 HETATM 19 C C2' ATP . . . D 3 18.387 12.019 11.949 1 9.09 ? C2' ATP 1001 A 1 HETATM 20 O O2' ATP . . . D 3 18.293 13.144 11.067 1 9.35 ? O2' ATP 1001 A 1 HETATM 21 C C1' ATP . . . D 3 17.108 11.174 11.84 1 9.17 ? C1' ATP 1001 A 1 HETATM 22 N N9 ATP . . . D 3 16.851 10.451 13.102 1 9.82 ? N9 ATP 1001 A 1 HETATM 23 C C8 ATP . . . D 3 17.205 9.213 13.443 1 9.26 ? C8 ATP 1001 A 1 HETATM 24 N N7 ATP . . . D 3 16.796 8.949 14.686 1 10.17 ? N7 ATP 1001 A 1 HETATM 25 C C5 ATP . . . D 3 16.153 10.025 15.141 1 9.86 ? C5 ATP 1001 A 1 HETATM 26 C C6 ATP . . . D 3 15.523 10.337 16.342 1 9.08 ? C6 ATP 1001 A 1 HETATM 27 N N6 ATP . . . D 3 15.499 9.517 17.398 1 11.55 ? N6 ATP 1001 A 1 HETATM 28 N N1 ATP . . . D 3 14.958 11.548 16.415 1 9.83 ? N1 ATP 1001 A 1 HETATM 29 C C2 ATP . . . D 3 14.984 12.432 15.428 1 9.34 ? C2 ATP 1001 A 1 HETATM 30 N N3 ATP . . . D 3 15.595 12.181 14.276 1 9.11 ? N3 ATP 1001 A 1 HETATM 31 C C4 ATP . . . D 3 16.173 10.974 14.128 1 10.98 ? C4 ATP 1001 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #