data_1GKZ # _model_server_result.job_id HXM6rcrj3yXLby2dsltvew _model_server_result.datetime_utc '2024-11-15 04:02:33' _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 1gkz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 1GKZ # _exptl.entry_id 1GKZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 1GKZ _cell.length_a 128.917 _cell.length_b 128.917 _cell.length_c 74.105 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GKZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 5 _struct_asym.id F _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 A OD1 ASN 249 A ASN 249 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc2 A O VAL 298 A VAL 298 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc3 A O ASP 300 A ASP 300 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc4 A O PHE 303 A PHE 303 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc5 A O GLY 337 A GLY 337 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O2B ADP . A ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc7 B MG MG . A MG 401 1_555 F O1A ADP . A ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc8 B MG MG . A MG 401 1_555 J O HOH . A HOH 2072 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc9 B MG MG . A MG 401 1_555 J O HOH . A HOH 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc10 B MG MG . A MG 401 1_555 J O HOH . A HOH 2124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc11 C K K . A K 402 1_555 F O2A ADP . A ADP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1GKZ _atom_sites.fract_transf_matrix[1][1] 0.007757 _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] 0.007757 _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] 0.013494 _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 1 401 401 MG MG . C 3 K A 1 402 402 K K . D 4 XE A 1 501 501 XE XE . E 4 XE A 1 502 502 XE XE . F 5 ADP A 1 601 601 ADP ADP . G 6 CL A 1 701 701 CL CL . H 6 CL A 1 702 702 CL CL . I 6 CL A 1 703 703 CL CL . J 7 HOH A 1 2001 2001 HOH HOH . J 7 HOH A 2 2002 2002 HOH HOH . J 7 HOH A 3 2003 2003 HOH HOH . J 7 HOH A 4 2004 2004 HOH HOH . J 7 HOH A 5 2005 2005 HOH HOH . J 7 HOH A 6 2006 2006 HOH HOH . J 7 HOH A 7 2007 2007 HOH HOH . J 7 HOH A 8 2008 2008 HOH HOH . J 7 HOH A 9 2009 2009 HOH HOH . J 7 HOH A 10 2010 2010 HOH HOH . J 7 HOH A 11 2011 2011 HOH HOH . J 7 HOH A 12 2012 2012 HOH HOH . J 7 HOH A 13 2013 2013 HOH HOH . J 7 HOH A 14 2014 2014 HOH HOH . J 7 HOH A 15 2015 2015 HOH HOH . J 7 HOH A 16 2016 2016 HOH HOH . J 7 HOH A 17 2017 2017 HOH HOH . J 7 HOH A 18 2018 2018 HOH HOH . J 7 HOH A 19 2019 2019 HOH HOH . J 7 HOH A 20 2020 2020 HOH HOH . J 7 HOH A 21 2021 2021 HOH HOH . J 7 HOH A 22 2022 2022 HOH HOH . J 7 HOH A 23 2023 2023 HOH HOH . J 7 HOH A 24 2024 2024 HOH HOH . J 7 HOH A 25 2025 2025 HOH HOH . J 7 HOH A 26 2026 2026 HOH HOH . J 7 HOH A 27 2027 2027 HOH HOH . J 7 HOH A 28 2028 2028 HOH HOH . J 7 HOH A 29 2029 2029 HOH HOH . J 7 HOH A 30 2030 2030 HOH HOH . J 7 HOH A 31 2031 2031 HOH HOH . J 7 HOH A 32 2032 2032 HOH HOH . J 7 HOH A 33 2033 2033 HOH HOH . J 7 HOH A 34 2034 2034 HOH HOH . J 7 HOH A 35 2035 2035 HOH HOH . J 7 HOH A 36 2036 2036 HOH HOH . J 7 HOH A 37 2037 2037 HOH HOH . J 7 HOH A 38 2038 2038 HOH HOH . J 7 HOH A 39 2039 2039 HOH HOH . J 7 HOH A 40 2040 2040 HOH HOH . J 7 HOH A 41 2041 2041 HOH HOH . J 7 HOH A 42 2042 2042 HOH HOH . J 7 HOH A 43 2043 2043 HOH HOH . J 7 HOH A 44 2044 2044 HOH HOH . J 7 HOH A 45 2045 2045 HOH HOH . J 7 HOH A 46 2046 2046 HOH HOH . J 7 HOH A 47 2047 2047 HOH HOH . J 7 HOH A 48 2048 2048 HOH HOH . J 7 HOH A 49 2049 2049 HOH HOH . J 7 HOH A 50 2050 2050 HOH HOH . J 7 HOH A 51 2051 2051 HOH HOH . J 7 HOH A 52 2052 2052 HOH HOH . J 7 HOH A 53 2053 2053 HOH HOH . J 7 HOH A 54 2054 2054 HOH HOH . J 7 HOH A 55 2055 2055 HOH HOH . J 7 HOH A 56 2056 2056 HOH HOH . J 7 HOH A 57 2057 2057 HOH HOH . J 7 HOH A 58 2058 2058 HOH HOH . J 7 HOH A 59 2059 2059 HOH HOH . J 7 HOH A 60 2060 2060 HOH HOH . J 7 HOH A 61 2061 2061 HOH HOH . J 7 HOH A 62 2062 2062 HOH HOH . J 7 HOH A 63 2063 2063 HOH HOH . J 7 HOH A 64 2064 2064 HOH HOH . J 7 HOH A 65 2065 2065 HOH HOH . J 7 HOH A 66 2066 2066 HOH HOH . J 7 HOH A 67 2067 2067 HOH HOH . J 7 HOH A 68 2068 2068 HOH HOH . J 7 HOH A 69 2069 2069 HOH HOH . J 7 HOH A 70 2070 2070 HOH HOH . J 7 HOH A 71 2071 2071 HOH HOH . J 7 HOH A 72 2072 2072 HOH HOH . J 7 HOH A 73 2073 2073 HOH HOH . J 7 HOH A 74 2074 2074 HOH HOH . J 7 HOH A 75 2075 2075 HOH HOH . J 7 HOH A 76 2076 2076 HOH HOH . J 7 HOH A 77 2077 2077 HOH HOH . J 7 HOH A 78 2078 2078 HOH HOH . J 7 HOH A 79 2079 2079 HOH HOH . J 7 HOH A 80 2080 2080 HOH HOH . J 7 HOH A 81 2081 2081 HOH HOH . J 7 HOH A 82 2082 2082 HOH HOH . J 7 HOH A 83 2083 2083 HOH HOH . J 7 HOH A 84 2084 2084 HOH HOH . J 7 HOH A 85 2085 2085 HOH HOH . J 7 HOH A 86 2086 2086 HOH HOH . J 7 HOH A 87 2087 2087 HOH HOH . J 7 HOH A 88 2088 2088 HOH HOH . J 7 HOH A 89 2089 2089 HOH HOH . J 7 HOH A 90 2090 2090 HOH HOH . J 7 HOH A 91 2091 2091 HOH HOH . J 7 HOH A 92 2092 2092 HOH HOH . J 7 HOH A 93 2093 2093 HOH HOH . J 7 HOH A 94 2094 2094 HOH HOH . J 7 HOH A 95 2095 2095 HOH HOH . J 7 HOH A 96 2096 2096 HOH HOH . J 7 HOH A 97 2097 2097 HOH HOH . J 7 HOH A 98 2098 2098 HOH HOH . J 7 HOH A 99 2099 2099 HOH HOH . J 7 HOH A 100 2100 2100 HOH HOH . J 7 HOH A 101 2101 2101 HOH HOH . J 7 HOH A 102 2102 2102 HOH HOH . J 7 HOH A 103 2103 2103 HOH HOH . J 7 HOH A 104 2104 2104 HOH HOH . J 7 HOH A 105 2105 2105 HOH HOH . J 7 HOH A 106 2106 2106 HOH HOH . J 7 HOH A 107 2107 2107 HOH HOH . J 7 HOH A 108 2108 2108 HOH HOH . J 7 HOH A 109 2109 2109 HOH HOH . J 7 HOH A 110 2110 2110 HOH HOH . J 7 HOH A 111 2111 2111 HOH HOH . J 7 HOH A 112 2112 2112 HOH HOH . J 7 HOH A 113 2113 2113 HOH HOH . J 7 HOH A 114 2114 2114 HOH HOH . J 7 HOH A 115 2115 2115 HOH HOH . J 7 HOH A 116 2116 2116 HOH HOH . J 7 HOH A 117 2117 2117 HOH HOH . J 7 HOH A 118 2118 2118 HOH HOH . J 7 HOH A 119 2119 2119 HOH HOH . J 7 HOH A 120 2120 2120 HOH HOH . J 7 HOH A 121 2121 2121 HOH HOH . J 7 HOH A 122 2122 2122 HOH HOH . J 7 HOH A 123 2123 2123 HOH HOH . J 7 HOH A 124 2124 2124 HOH HOH . J 7 HOH A 125 2125 2125 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 PB ADP . . . F 5 95.859 123.777 32.253 1 58.77 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . F 5 96.196 123.822 30.8 1 57.86 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . F 5 95.218 122.524 32.779 1 57.23 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . F 5 94.976 124.837 32.837 1 59.23 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . F 5 98.28 123.098 33.717 1 51.63 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . F 5 97.596 122.259 34.705 1 53.7 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . F 5 99.383 123.916 34.139 1 51.97 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . F 5 97.248 124.066 32.985 1 55.97 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . F 5 98.61 122.121 32.491 1 51.43 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . F 5 99.514 122.493 31.445 1 51.53 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . F 5 99.332 121.58 30.248 1 51.45 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . F 5 100.066 120.345 30.483 1 51.38 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . F 5 97.917 121.095 29.966 1 51.46 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . F 5 97.189 122.09 29.255 1 52.3 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . F 5 98.189 119.843 29.128 1 52.66 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . F 5 98.709 120.112 27.824 1 54.42 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . F 5 99.369 119.254 29.891 1 50.34 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . F 5 99.061 118.241 30.906 1 48.59 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . F 5 99.051 118.35 32.283 1 47.7 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . F 5 98.826 117.203 32.897 1 45.98 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . F 5 98.649 116.299 31.863 1 43.48 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . F 5 98.396 114.943 31.865 1 42.14 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . F 5 98.223 114.272 32.987 1 41.78 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . F 5 98.299 114.293 30.66 1 41.13 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . F 5 98.403 115.011 29.553 1 44.36 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . F 5 98.63 116.335 29.424 1 47.06 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . F 5 98.761 116.919 30.635 1 46.1 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #