data_4D2I # _model_server_result.job_id hiLNrdmspYc6meIPDMqSZQ _model_server_result.datetime_utc '2025-02-27 21:26:55' _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 4d2i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1477}' # _entry.id 4D2I # _exptl.entry_id 4D2I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE 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 120 _cell.entry_id 4D2I _cell.length_a 150.21 _cell.length_b 150.21 _cell.length_c 140.54 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D2I _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 1,2,3 # 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' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 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 OG SER 155 A SER 155 1_555 D MG MG . A MG 1478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc2 C O2B ANP . A ANP 1477 1_555 D MG MG . A MG 1478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 C O2G ANP . A ANP 1477 1_555 D MG MG . A MG 1478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc4 D MG MG . A MG 1478 1_555 G O HOH . A HOH 2029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc5 D MG MG . A MG 1478 1_555 G O HOH . A HOH 2030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc6 D MG MG . A MG 1478 1_555 G O HOH . A HOH 2031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc7 B OG SER 155 B SER 155 1_555 F MG MG . B MG 1479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc8 E O2G ANP . B ANP 1478 1_555 F MG MG . B MG 1479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc9 E O2B ANP . B ANP 1478 1_555 F MG MG . B MG 1479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc10 F MG MG . B MG 1479 1_555 H O HOH . B HOH 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc11 F MG MG . B MG 1479 1_555 H O HOH . B HOH 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc12 F MG MG . B MG 1479 1_555 H O HOH . B HOH 2014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 4D2I _atom_sites.fract_transf_matrix[1][1] 0.006657 _atom_sites.fract_transf_matrix[1][2] 0.003844 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007687 _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] 0.007115 _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 ANP A 1 1477 1477 ANP ANP . D 3 MG A 1 1478 1478 MG MG . E 2 ANP B 1 1478 1478 ANP ANP . F 3 MG B 1 1479 1479 MG MG . 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 . G 4 HOH A 72 2072 2072 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 . # 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 ANP . . . C 2 -27.815 -16.919 0.348 1 37.16 ? PG ANP 1477 A 1 HETATM 2 O O1G ANP . . . C 2 -26.553 -16.187 0.947 1 39.7 ? O1G ANP 1477 A 1 HETATM 3 O O2G ANP . . . C 2 -28.449 -16.057 -0.816 1 41.15 ? O2G ANP 1477 A 1 HETATM 4 O O3G ANP . . . C 2 -27.409 -18.267 -0.161 1 42.82 ? O3G ANP 1477 A 1 HETATM 5 P PB ANP . . . C 2 -29.824 -15.665 1.804 1 41.13 ? PB ANP 1477 A 1 HETATM 6 O O1B ANP . . . C 2 -28.971 -14.565 2.346 1 36.7 ? O1B ANP 1477 A 1 HETATM 7 O O2B ANP . . . C 2 -30.421 -15.217 0.438 1 43.51 ? O2B ANP 1477 A 1 HETATM 8 N N3B ANP . . . C 2 -28.977 -17.097 1.563 1 44.9 ? N3B ANP 1477 A 1 HETATM 9 P PA ANP . . . C 2 -32.324 -16.532 2.447 1 45.84 ? PA ANP 1477 A 1 HETATM 10 O O1A ANP . . . C 2 -32.196 -16.902 0.965 1 67.04 ? O1A ANP 1477 A 1 HETATM 11 O O2A ANP . . . C 2 -33.382 -15.548 2.756 1 42.1 ? O2A ANP 1477 A 1 HETATM 12 O O3A ANP . . . C 2 -30.925 -15.945 2.867 1 49.25 ? O3A ANP 1477 A 1 HETATM 13 O O5' ANP . . . C 2 -32.541 -17.825 3.344 1 48.96 ? O5' ANP 1477 A 1 HETATM 14 C C5' ANP . . . C 2 -31.695 -18.137 4.477 1 48.85 ? C5' ANP 1477 A 1 HETATM 15 C C4' ANP . . . C 2 -32.467 -18.935 5.505 1 50.53 ? C4' ANP 1477 A 1 HETATM 16 O O4' ANP . . . C 2 -32.857 -18.067 6.595 1 51.8 ? O4' ANP 1477 A 1 HETATM 17 C C3' ANP . . . C 2 -33.753 -19.592 5.006 1 49.89 ? C3' ANP 1477 A 1 HETATM 18 O O3' ANP . . . C 2 -34.006 -20.838 5.646 1 52.61 ? O3' ANP 1477 A 1 HETATM 19 C C2' ANP . . . C 2 -34.823 -18.568 5.381 1 57.94 ? C2' ANP 1477 A 1 HETATM 20 O O2' ANP . . . C 2 -36.087 -19.188 5.588 1 57.9 ? O2' ANP 1477 A 1 HETATM 21 C C1' ANP . . . C 2 -34.266 -17.991 6.686 1 50.05 ? C1' ANP 1477 A 1 HETATM 22 N N9 ANP . . . C 2 -34.647 -16.6 6.895 1 46.8 ? N9 ANP 1477 A 1 HETATM 23 C C8 ANP . . . C 2 -34.293 -15.521 6.124 1 46.74 ? C8 ANP 1477 A 1 HETATM 24 N N7 ANP . . . C 2 -34.804 -14.384 6.527 1 42.12 ? N7 ANP 1477 A 1 HETATM 25 C C5 ANP . . . C 2 -35.563 -14.738 7.635 1 43.4 ? C5 ANP 1477 A 1 HETATM 26 C C6 ANP . . . C 2 -36.361 -13.986 8.514 1 40.79 ? C6 ANP 1477 A 1 HETATM 27 N N6 ANP . . . C 2 -36.536 -12.667 8.418 1 40.02 ? N6 ANP 1477 A 1 HETATM 28 N N1 ANP . . . C 2 -36.983 -14.65 9.515 1 45.09 ? N1 ANP 1477 A 1 HETATM 29 C C2 ANP . . . C 2 -36.809 -15.97 9.619 1 47.6 ? C2 ANP 1477 A 1 HETATM 30 N N3 ANP . . . C 2 -36.083 -16.783 8.849 1 55.66 ? N3 ANP 1477 A 1 HETATM 31 C C4 ANP . . . C 2 -35.478 -16.1 7.864 1 48.19 ? C4 ANP 1477 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 488 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 31 #