data_4CRJ # _model_server_result.job_id cNEaH_pypwV5bELoHoCnew _model_server_result.datetime_utc '2024-11-24 07:02:03' _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 4crj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1159}' # _entry.id 4CRJ # _exptl.entry_id 4CRJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 4CRJ _cell.length_a 82.48 _cell.length_b 82.48 _cell.length_c 52.173 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CRJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _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 _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 2 _struct_asym.id B _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 ASP 98 A ASP 95 1_555 C MG MG . A MG 1160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc2 A OD2 ASP 98 A ASP 95 1_555 D MG MG . A MG 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc3 A OD1 ASP 100 A ASP 97 1_555 C MG MG . A MG 1160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc4 A OD2 ASP 100 A ASP 97 1_555 D MG MG . A MG 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc5 B O1A APC . A APC 1159 1_555 C MG MG . A MG 1160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc6 B O1B APC . A APC 1159 1_555 C MG MG . A MG 1160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc7 B O1B APC . A APC 1159 1_555 D MG MG . A MG 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc8 B O1G APC . A APC 1159 1_555 D MG MG . A MG 1161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc9 C MG MG . A MG 1160 1_555 G O HOH . A HOH 2034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc10 C MG MG . A MG 1160 1_555 G O HOH . A HOH 2047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc11 D MG MG . A MG 1161 1_555 G O HOH . A HOH 2045 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc12 D MG MG . A MG 1161 1_555 G O HOH . A HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 4CRJ _atom_sites.fract_transf_matrix[1][1] 0.012124 _atom_sites.fract_transf_matrix[1][2] 0.007 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014 _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] 0.019167 _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 APC A 1 1159 1159 APC APC . C 3 MG A 1 1160 1160 MG MG . D 3 MG A 1 1161 1161 MG MG . E 4 NO3 A 1 1162 1162 NO3 NO3 . F 5 YH5 A 1 1163 1163 YH5 YH5 . G 6 HOH A 1 2001 2001 HOH HOH . G 6 HOH A 2 2002 2002 HOH HOH . G 6 HOH A 3 2003 2003 HOH HOH . G 6 HOH A 4 2004 2004 HOH HOH . G 6 HOH A 5 2005 2005 HOH HOH . G 6 HOH A 6 2006 2006 HOH HOH . G 6 HOH A 7 2007 2007 HOH HOH . G 6 HOH A 8 2008 2008 HOH HOH . G 6 HOH A 9 2009 2009 HOH HOH . G 6 HOH A 10 2010 2010 HOH HOH . G 6 HOH A 11 2011 2011 HOH HOH . G 6 HOH A 12 2012 2012 HOH HOH . G 6 HOH A 13 2013 2013 HOH HOH . G 6 HOH A 14 2014 2014 HOH HOH . G 6 HOH A 15 2015 2015 HOH HOH . G 6 HOH A 16 2016 2016 HOH HOH . G 6 HOH A 17 2017 2017 HOH HOH . G 6 HOH A 18 2018 2018 HOH HOH . G 6 HOH A 19 2019 2019 HOH HOH . G 6 HOH A 20 2020 2020 HOH HOH . G 6 HOH A 21 2021 2021 HOH HOH . G 6 HOH A 22 2022 2022 HOH HOH . G 6 HOH A 23 2023 2023 HOH HOH . G 6 HOH A 24 2024 2024 HOH HOH . G 6 HOH A 25 2025 2025 HOH HOH . G 6 HOH A 26 2026 2026 HOH HOH . G 6 HOH A 27 2027 2027 HOH HOH . G 6 HOH A 28 2028 2028 HOH HOH . G 6 HOH A 29 2029 2029 HOH HOH . G 6 HOH A 30 2030 2030 HOH HOH . G 6 HOH A 31 2031 2031 HOH HOH . G 6 HOH A 32 2032 2032 HOH HOH . G 6 HOH A 33 2033 2033 HOH HOH . G 6 HOH A 34 2034 2034 HOH HOH . G 6 HOH A 35 2035 2035 HOH HOH . G 6 HOH A 36 2036 2036 HOH HOH . G 6 HOH A 37 2037 2037 HOH HOH . G 6 HOH A 38 2038 2038 HOH HOH . G 6 HOH A 39 2039 2039 HOH HOH . G 6 HOH A 40 2040 2040 HOH HOH . G 6 HOH A 41 2041 2041 HOH HOH . G 6 HOH A 42 2042 2042 HOH HOH . G 6 HOH A 43 2043 2043 HOH HOH . G 6 HOH A 44 2044 2044 HOH HOH . G 6 HOH A 45 2045 2045 HOH HOH . G 6 HOH A 46 2046 2046 HOH HOH . G 6 HOH A 47 2047 2047 HOH HOH . G 6 HOH A 48 2048 2048 HOH HOH . G 6 HOH A 49 2049 2049 HOH HOH . G 6 HOH A 50 2050 2050 HOH HOH . G 6 HOH A 51 2051 2051 HOH HOH . G 6 HOH A 52 2052 2052 HOH HOH . G 6 HOH A 53 2053 2053 HOH HOH . G 6 HOH A 54 2054 2054 HOH HOH . G 6 HOH A 55 2055 2055 HOH HOH . G 6 HOH A 56 2056 2056 HOH HOH . G 6 HOH A 57 2057 2057 HOH HOH . G 6 HOH A 58 2058 2058 HOH HOH . G 6 HOH A 59 2059 2059 HOH HOH . G 6 HOH A 60 2060 2060 HOH HOH . G 6 HOH A 61 2061 2061 HOH HOH . G 6 HOH A 62 2062 2062 HOH HOH . G 6 HOH A 63 2063 2063 HOH HOH . G 6 HOH A 64 2064 2064 HOH HOH . G 6 HOH A 65 2065 2065 HOH HOH . G 6 HOH A 66 2066 2066 HOH HOH . G 6 HOH A 67 2067 2067 HOH HOH . G 6 HOH A 68 2068 2068 HOH HOH . G 6 HOH A 69 2069 2069 HOH HOH . G 6 HOH A 70 2070 2070 HOH HOH . G 6 HOH A 71 2071 2071 HOH HOH . G 6 HOH A 72 2072 2072 HOH HOH . G 6 HOH A 73 2073 2073 HOH HOH . G 6 HOH A 74 2074 2074 HOH HOH . G 6 HOH A 75 2075 2075 HOH HOH . G 6 HOH A 76 2076 2076 HOH HOH . G 6 HOH A 77 2077 2077 HOH HOH . G 6 HOH A 78 2078 2078 HOH HOH . G 6 HOH A 79 2079 2079 HOH HOH . G 6 HOH A 80 2080 2080 HOH HOH . G 6 HOH A 81 2081 2081 HOH HOH . G 6 HOH A 82 2082 2082 HOH HOH . G 6 HOH A 83 2083 2083 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 APC . . . B 2 31.599 -26.606 2.096 1 19.11 ? PG APC 1159 A 1 HETATM 2 O O1G APC . . . B 2 30.726 -27.654 1.435 1 19.4 ? O1G APC 1159 A 1 HETATM 3 O O2G APC . . . B 2 33.048 -27.07 2.228 1 19.09 ? O2G APC 1159 A 1 HETATM 4 O O3G APC . . . B 2 31.454 -25.238 1.512 1 21.18 ? O3G APC 1159 A 1 HETATM 5 P PB APC . . . B 2 29.623 -25.841 3.945 1 20.62 ? PB APC 1159 A 1 HETATM 6 O O1B APC . . . B 2 28.782 -25.799 2.71 1 17.88 ? O1B APC 1159 A 1 HETATM 7 O O2B APC . . . B 2 29.011 -26.782 5.068 1 19.25 ? O2B APC 1159 A 1 HETATM 8 O O3B APC . . . B 2 31.071 -26.488 3.605 1 19.88 ? O3B APC 1159 A 1 HETATM 9 P PA APC . . . B 2 28.541 -23.213 4.93 1 20.87 ? PA APC 1159 A 1 HETATM 10 O O1A APC . . . B 2 27.543 -23.445 3.859 1 20.66 ? O1A APC 1159 A 1 HETATM 11 O O2A APC . . . B 2 27.993 -23.433 6.397 1 20.17 ? O2A APC 1159 A 1 HETATM 12 C C3A APC . . . B 2 30.004 -24.225 4.644 1 19.67 ? C3A APC 1159 A 1 HETATM 13 O O5' APC . . . B 2 29.046 -21.701 4.93 1 23.46 ? O5' APC 1159 A 1 HETATM 14 C C5' APC . . . B 2 28.831 -20.859 3.838 1 25.46 ? C5' APC 1159 A 1 HETATM 15 C C4' APC . . . B 2 30.03 -19.937 3.768 1 25.34 ? C4' APC 1159 A 1 HETATM 16 O O4' APC . . . B 2 31.155 -20.547 3.132 1 25.04 ? O4' APC 1159 A 1 HETATM 17 C C3' APC . . . B 2 29.612 -18.77 2.935 1 26.37 ? C3' APC 1159 A 1 HETATM 18 O O3' APC . . . B 2 29.066 -17.801 3.831 1 27.35 ? O3' APC 1159 A 1 HETATM 19 C C2' APC . . . B 2 30.876 -18.375 2.194 1 26.98 ? C2' APC 1159 A 1 HETATM 20 O O2' APC . . . B 2 31.476 -17.221 2.802 1 28.17 ? O2' APC 1159 A 1 HETATM 21 C C1' APC . . . B 2 31.797 -19.592 2.305 1 25.55 ? C1' APC 1159 A 1 HETATM 22 N N9 APC . . . B 2 32.114 -20.133 0.958 1 25 ? N9 APC 1159 A 1 HETATM 23 C C8 APC . . . B 2 33.367 -20.227 0.473 1 25.19 ? C8 APC 1159 A 1 HETATM 24 N N7 APC . . . B 2 33.367 -20.729 -0.784 1 23.52 ? N7 APC 1159 A 1 HETATM 25 C C5 APC . . . B 2 32.08 -20.962 -1.111 1 22.21 ? C5 APC 1159 A 1 HETATM 26 C C6 APC . . . B 2 31.376 -21.501 -2.295 1 21.15 ? C6 APC 1159 A 1 HETATM 27 N N6 APC . . . B 2 32.107 -21.872 -3.373 1 19.92 ? N6 APC 1159 A 1 HETATM 28 N N1 APC . . . B 2 30.013 -21.602 -2.25 1 19.81 ? N1 APC 1159 A 1 HETATM 29 C C2 APC . . . B 2 29.314 -21.222 -1.159 1 20.83 ? C2 APC 1159 A 1 HETATM 30 N N3 APC . . . B 2 29.9 -20.725 -0.047 1 22.31 ? N3 APC 1159 A 1 HETATM 31 C C4 APC . . . B 2 31.254 -20.576 0.037 1 22.94 ? C4 APC 1159 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #