data_4AYT # _model_server_result.job_id twAask0TFWtEJLdGfxuNFg _model_server_result.datetime_utc '2024-11-23 15:50:20' _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 4ayt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":900}' # _entry.id 4AYT # _exptl.entry_id 4AYT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE 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 4AYT _cell.length_a 175.11 _cell.length_b 175.11 _cell.length_c 49.55 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AYT _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _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,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 16.516667 # _struct_asym.details ? _struct_asym.entity_id 4 _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 A OG SER 384 A SER 534 1_555 C MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 A OE1 GLN 425 A GLN 575 1_555 C MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc3 C MG MG . A MG 801 1_555 D O3G ACP . A ACP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc4 C MG MG . A MG 801 1_555 D O2B ACP . A ACP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 4AYT _atom_sites.fract_transf_matrix[1][1] 0.005711 _atom_sites.fract_transf_matrix[1][2] 0.003297 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006594 _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] 0.020182 _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 GLY A 1 1717 1717 GLY GLY . C 3 MG A 1 801 801 MG MG . D 4 ACP A 1 900 900 ACP ACP . E 5 LMT A 1 1720 1720 LMT LMT . F 6 CDL A 1 1721 1721 CDL CDL . G 5 LMT A 1 1723 1723 LMT LMT . H 5 LMT A 1 1724 1724 LMT LMT . I 6 CDL A 1 1727 1727 CDL CDL . 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 . # 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 ACP . . . D 4 -16.984 22.833 7.176 1 101.64 ? PG ACP 900 A 1 HETATM 2 O O1G ACP . . . D 4 -15.791 21.932 7.102 1 101.83 ? O1G ACP 900 A 1 HETATM 3 O O2G ACP . . . D 4 -16.68 24.179 7.874 1 101.11 ? O2G ACP 900 A 1 HETATM 4 O O3G ACP . . . D 4 -18.202 22.188 7.883 1 102.98 ? O3G ACP 900 A 1 HETATM 5 P PB ACP . . . D 4 -18.4 22.008 4.782 1 94.72 ? PB ACP 900 A 1 HETATM 6 O O1B ACP . . . D 4 -17.648 20.905 4.053 1 93.66 ? O1B ACP 900 A 1 HETATM 7 O O2B ACP . . . D 4 -19.608 21.553 5.668 1 94.7 ? O2B ACP 900 A 1 HETATM 8 C C3B ACP . . . D 4 -17.471 23.221 5.551 1 98.57 ? C3B ACP 900 A 1 HETATM 9 P PA ACP . . . D 4 -20.465 23.429 3.275 1 90.26 ? PA ACP 900 A 1 HETATM 10 O O1A ACP . . . D 4 -20.959 24.221 4.425 1 90.38 ? O1A ACP 900 A 1 HETATM 11 O O2A ACP . . . D 4 -21.442 22.474 2.603 1 90.1 ? O2A ACP 900 A 1 HETATM 12 O O3A ACP . . . D 4 -19.131 22.597 3.479 1 92.51 ? O3A ACP 900 A 1 HETATM 13 O O5' ACP . . . D 4 -20.29 24.375 1.971 1 88.21 ? O5' ACP 900 A 1 HETATM 14 C C5' ACP . . . D 4 -19.417 24.157 0.843 1 87.77 ? C5' ACP 900 A 1 HETATM 15 C C4' ACP . . . D 4 -19.091 25.488 0.205 1 87.44 ? C4' ACP 900 A 1 HETATM 16 O O4' ACP . . . D 4 -20.308 26.201 -0.117 1 85.65 ? O4' ACP 900 A 1 HETATM 17 C C3' ACP . . . D 4 -18.221 26.446 1.024 1 88.2 ? C3' ACP 900 A 1 HETATM 18 O O3' ACP . . . D 4 -17.129 26.948 0.257 1 89.79 ? O3' ACP 900 A 1 HETATM 19 C C2' ACP . . . D 4 -19.213 27.522 1.491 1 85.9 ? C2' ACP 900 A 1 HETATM 20 O O2' ACP . . . D 4 -18.618 28.802 1.68 1 85.92 ? O2' ACP 900 A 1 HETATM 21 C C1' ACP . . . D 4 -20.223 27.536 0.344 1 83.22 ? C1' ACP 900 A 1 HETATM 22 N N9 ACP . . . D 4 -21.567 27.991 0.704 1 77.87 ? N9 ACP 900 A 1 HETATM 23 C C8 ACP . . . D 4 -22.313 27.591 1.781 1 74.37 ? C8 ACP 900 A 1 HETATM 24 N N7 ACP . . . D 4 -23.515 28.116 1.827 1 72.34 ? N7 ACP 900 A 1 HETATM 25 C C5 ACP . . . D 4 -23.567 28.918 0.697 1 72.38 ? C5 ACP 900 A 1 HETATM 26 C C6 ACP . . . D 4 -24.589 29.718 0.144 1 71.14 ? C6 ACP 900 A 1 HETATM 27 N N6 ACP . . . D 4 -25.801 29.855 0.692 1 69.61 ? N6 ACP 900 A 1 HETATM 28 N N1 ACP . . . D 4 -24.326 30.371 -1.014 1 71.31 ? N1 ACP 900 A 1 HETATM 29 C C2 ACP . . . D 4 -23.114 30.236 -1.568 1 71.47 ? C2 ACP 900 A 1 HETATM 30 N N3 ACP . . . D 4 -22.075 29.509 -1.143 1 73.18 ? N3 ACP 900 A 1 HETATM 31 C C4 ACP . . . D 4 -22.369 28.861 0 1 74.88 ? C4 ACP 900 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #