data_1WC0 # _model_server_result.job_id HRQetBJYkrlMtj0KznoGxg _model_server_result.datetime_utc '2024-10-27 04:37:37' _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 1wc0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1500}' # _entry.id 1WC0 # _exptl.entry_id 1WC0 _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 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 1WC0 _cell.length_a 53.672 _cell.length_b 71.539 _cell.length_c 99.572 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WC0 _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 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,G,H _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 ? 2 C N N ? 2 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 A OD1 ASP 34 A ASP 1017 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A OD2 ASP 34 A ASP 1017 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc3 A O ILE 35 A ILE 1018 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc4 A OD2 ASP 78 A ASP 1061 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.331 ? metalc ? metalc5 A OD1 ASP 78 A ASP 1061 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc6 C O3G APC . A APC 1500 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc7 C O1B APC . A APC 1500 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc8 G O HOH . A HOH 2070 1_555 D CA CA . A CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc9 B OD2 ASP 34 B ASP 1017 1_555 F CA CA . B CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc10 B OD1 ASP 34 B ASP 1017 1_555 F CA CA . B CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc11 B O ILE 35 B ILE 1018 1_555 F CA CA . B CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc12 B OD2 ASP 78 B ASP 1061 1_555 F CA CA . B CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc13 E O1B APC . B APC 1500 1_555 F CA CA . B CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc14 E O3G APC . B APC 1500 1_555 F CA CA . B CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc15 H O HOH . B HOH 2070 1_555 F CA CA . B CA 2100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? # _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 1WC0 _atom_sites.fract_transf_matrix[1][1] 0.018632 _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] 0.013978 _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] 0.010043 _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 2 APC A 1 1500 1500 APC APC . D 3 CA A 1 2100 2100 CA CA . E 2 APC B 1 1500 1500 APC APC . F 3 CA B 1 2100 2100 CA CA . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . G 4 HOH A 21 2021 2021 HOH HOH . G 4 HOH A 22 2022 2022 HOH HOH . G 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH A 24 2024 2024 HOH HOH . G 4 HOH A 25 2025 2025 HOH HOH . G 4 HOH A 26 2026 2026 HOH HOH . G 4 HOH A 27 2027 2027 HOH HOH . G 4 HOH A 28 2028 2028 HOH HOH . G 4 HOH A 29 2029 2029 HOH HOH . G 4 HOH A 30 2030 2030 HOH HOH . G 4 HOH A 31 2031 2031 HOH HOH . G 4 HOH A 32 2032 2032 HOH HOH . G 4 HOH A 33 2033 2033 HOH HOH . G 4 HOH A 34 2034 2034 HOH HOH . G 4 HOH A 35 2035 2035 HOH HOH . G 4 HOH A 36 2036 2036 HOH HOH . G 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH A 38 2038 2038 HOH HOH . G 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH A 40 2040 2040 HOH HOH . G 4 HOH A 41 2041 2041 HOH HOH . G 4 HOH A 42 2042 2042 HOH HOH . G 4 HOH A 43 2043 2043 HOH HOH . G 4 HOH A 44 2044 2044 HOH HOH . G 4 HOH A 45 2045 2045 HOH HOH . G 4 HOH A 46 2046 2046 HOH HOH . G 4 HOH A 47 2047 2047 HOH HOH . G 4 HOH A 48 2048 2048 HOH HOH . G 4 HOH A 49 2049 2049 HOH HOH . G 4 HOH A 50 2050 2050 HOH HOH . G 4 HOH A 51 2051 2051 HOH HOH . G 4 HOH A 52 2052 2052 HOH HOH . G 4 HOH A 53 2053 2053 HOH HOH . G 4 HOH A 54 2054 2054 HOH HOH . G 4 HOH A 55 2055 2055 HOH HOH . G 4 HOH A 56 2056 2056 HOH HOH . G 4 HOH A 57 2057 2057 HOH HOH . G 4 HOH A 58 2058 2058 HOH HOH . G 4 HOH A 59 2059 2059 HOH HOH . G 4 HOH A 60 2060 2060 HOH HOH . G 4 HOH A 61 2061 2061 HOH HOH . G 4 HOH A 62 2062 2062 HOH HOH . G 4 HOH A 63 2063 2063 HOH HOH . G 4 HOH A 64 2064 2064 HOH HOH . G 4 HOH A 65 2065 2065 HOH HOH . G 4 HOH A 66 2066 2066 HOH HOH . G 4 HOH A 67 2067 2067 HOH HOH . G 4 HOH A 68 2068 2068 HOH HOH . G 4 HOH A 69 2069 2069 HOH HOH . G 4 HOH A 70 2070 2070 HOH HOH . G 4 HOH A 71 2071 2071 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 HOH HOH . H 4 HOH B 13 2013 2013 HOH HOH . H 4 HOH B 14 2014 2014 HOH HOH . H 4 HOH B 15 2015 2015 HOH HOH . H 4 HOH B 16 2016 2016 HOH HOH . H 4 HOH B 17 2017 2017 HOH HOH . H 4 HOH B 18 2018 2018 HOH HOH . H 4 HOH B 19 2019 2019 HOH HOH . H 4 HOH B 20 2020 2020 HOH HOH . H 4 HOH B 21 2021 2021 HOH HOH . H 4 HOH B 22 2022 2022 HOH HOH . H 4 HOH B 23 2023 2023 HOH HOH . H 4 HOH B 24 2024 2024 HOH HOH . H 4 HOH B 25 2025 2025 HOH HOH . H 4 HOH B 26 2026 2026 HOH HOH . H 4 HOH B 27 2027 2027 HOH HOH . H 4 HOH B 28 2028 2028 HOH HOH . H 4 HOH B 29 2029 2029 HOH HOH . H 4 HOH B 30 2030 2030 HOH HOH . H 4 HOH B 31 2031 2031 HOH HOH . H 4 HOH B 32 2032 2032 HOH HOH . H 4 HOH B 33 2033 2033 HOH HOH . H 4 HOH B 34 2034 2034 HOH HOH . H 4 HOH B 35 2035 2035 HOH HOH . H 4 HOH B 36 2036 2036 HOH HOH . H 4 HOH B 37 2037 2037 HOH HOH . H 4 HOH B 38 2038 2038 HOH HOH . H 4 HOH B 39 2039 2039 HOH HOH . H 4 HOH B 40 2040 2040 HOH HOH . H 4 HOH B 41 2041 2041 HOH HOH . H 4 HOH B 42 2042 2042 HOH HOH . H 4 HOH B 43 2043 2043 HOH HOH . H 4 HOH B 44 2044 2044 HOH HOH . H 4 HOH B 45 2045 2045 HOH HOH . H 4 HOH B 46 2046 2046 HOH HOH . H 4 HOH B 47 2047 2047 HOH HOH . H 4 HOH B 48 2048 2048 HOH HOH . H 4 HOH B 49 2049 2049 HOH HOH . H 4 HOH B 50 2050 2050 HOH HOH . H 4 HOH B 51 2051 2051 HOH HOH . H 4 HOH B 52 2052 2052 HOH HOH . H 4 HOH B 53 2053 2053 HOH HOH . H 4 HOH B 54 2054 2054 HOH HOH . H 4 HOH B 55 2055 2055 HOH HOH . H 4 HOH B 56 2056 2056 HOH HOH . H 4 HOH B 57 2057 2057 HOH HOH . H 4 HOH B 58 2058 2058 HOH HOH . H 4 HOH B 59 2059 2059 HOH HOH . H 4 HOH B 60 2060 2060 HOH HOH . H 4 HOH B 61 2061 2061 HOH HOH . H 4 HOH B 62 2062 2062 HOH HOH . H 4 HOH B 63 2063 2063 HOH HOH . H 4 HOH B 64 2064 2064 HOH HOH . H 4 HOH B 65 2065 2065 HOH HOH . H 4 HOH B 66 2066 2066 HOH HOH . H 4 HOH B 67 2067 2067 HOH HOH . H 4 HOH B 68 2068 2068 HOH HOH . H 4 HOH B 69 2069 2069 HOH HOH . H 4 HOH B 70 2070 2070 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 . . . C 2 15.238 5.296 55.842 1 41.77 ? PG APC 1500 A 1 HETATM 2 O O1G APC . . . C 2 15.452 4.596 57.202 1 41.88 ? O1G APC 1500 A 1 HETATM 3 O O2G APC . . . C 2 13.749 5.511 55.656 1 43.28 ? O2G APC 1500 A 1 HETATM 4 O O3G APC . . . C 2 15.75 4.39 54.76 1 44.13 ? O3G APC 1500 A 1 HETATM 5 P PB APC . . . C 2 17.524 6.951 55.99 1 36.81 ? PB APC 1500 A 1 HETATM 6 O O1B APC . . . C 2 18.343 6.078 54.998 1 37.16 ? O1B APC 1500 A 1 HETATM 7 O O2B APC . . . C 2 17.884 8.443 55.723 1 38.47 ? O2B APC 1500 A 1 HETATM 8 O O3B APC . . . C 2 15.949 6.763 55.779 1 39.52 ? O3B APC 1500 A 1 HETATM 9 P PA APC . . . C 2 19.618 6.735 58.082 1 35 ? PA APC 1500 A 1 HETATM 10 O O1A APC . . . C 2 20.542 5.801 57.251 1 29.4 ? O1A APC 1500 A 1 HETATM 11 O O2A APC . . . C 2 20.043 8.224 57.836 1 37.23 ? O2A APC 1500 A 1 HETATM 12 C C3A APC . . . C 2 17.891 6.527 57.684 1 34.12 ? C3A APC 1500 A 1 HETATM 13 O O5' APC . . . C 2 19.753 6.385 59.649 1 34.64 ? O5' APC 1500 A 1 HETATM 14 C C5' APC . . . C 2 19.602 5.068 60.078 1 29.68 ? C5' APC 1500 A 1 HETATM 15 C C4' APC . . . C 2 20.817 4.653 60.901 1 28 ? C4' APC 1500 A 1 HETATM 16 O O4' APC . . . C 2 20.591 3.407 61.603 1 28.01 ? O4' APC 1500 A 1 HETATM 17 C C3' APC . . . C 2 22.036 4.436 60.036 1 27.2 ? C3' APC 1500 A 1 HETATM 18 O O3' APC . . . C 2 23.182 4.942 60.792 1 26.94 ? O3' APC 1500 A 1 HETATM 19 C C2' APC . . . C 2 22.046 2.918 59.827 1 27.45 ? C2' APC 1500 A 1 HETATM 20 O O2' APC . . . C 2 23.375 2.496 59.46 1 30.03 ? O2' APC 1500 A 1 HETATM 21 C C1' APC . . . C 2 21.583 2.432 61.198 1 25.89 ? C1' APC 1500 A 1 HETATM 22 N N9 APC . . . C 2 20.904 1.124 61.181 1 20.8 ? N9 APC 1500 A 1 HETATM 23 C C8 APC . . . C 2 19.55 0.896 61.154 1 18.84 ? C8 APC 1500 A 1 HETATM 24 N N7 APC . . . C 2 19.192 -0.333 61.161 1 18.32 ? N7 APC 1500 A 1 HETATM 25 C C5 APC . . . C 2 20.419 -1.029 61.201 1 17.38 ? C5 APC 1500 A 1 HETATM 26 C C6 APC . . . C 2 20.71 -2.421 61.254 1 17.15 ? C6 APC 1500 A 1 HETATM 27 N N6 APC . . . C 2 19.779 -3.357 61.266 1 15.18 ? N6 APC 1500 A 1 HETATM 28 N N1 APC . . . C 2 22.024 -2.785 61.287 1 19.11 ? N1 APC 1500 A 1 HETATM 29 C C2 APC . . . C 2 22.989 -1.781 61.278 1 18.84 ? C2 APC 1500 A 1 HETATM 30 N N3 APC . . . C 2 22.81 -0.477 61.241 1 18.31 ? N3 APC 1500 A 1 HETATM 31 C C4 APC . . . C 2 21.476 -0.145 61.213 1 18.66 ? C4 APC 1500 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #