data_7JV1 # _model_server_result.job_id r6-eJM5wRZddH1TftjyvaA _model_server_result.datetime_utc '2024-11-25 13:38:58' _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 7jv1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 7JV1 # _exptl.entry_id 7JV1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _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 7JV1 _cell.length_a 137 _cell.length_b 137 _cell.length_c 221 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JV1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 3 C N N ? 3 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 covale ? covale1 B NZ LYS 88 C LYS 97 1_555 E O1A ANP . C ANP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? metalc ? metalc1 A OD1 ASN 173 D ASN 738 1_555 D MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc2 A OD2 ASP 185 D ASP 750 1_555 D MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc3 C O2A ANP . D ANP 901 1_555 D MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? # _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 7JV1 _atom_sites.fract_transf_matrix[1][1] 0.007299 _atom_sites.fract_transf_matrix[1][2] 0.004214 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008428 _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] 0.004525 _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 3 ANP D 1 901 901 ANP ANP . D 4 MG D 1 902 1001 MG MG . E 3 ANP C 1 401 401 ANP ANP . F 5 VKG C 1 402 501 VKG 951 . # 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 . . . E 3 -20.854 40.66 3.071 1 212.96 ? PG ANP 401 C 1 HETATM 2 O O1G ANP . . . E 3 -21.4 41.287 4.316 1 206.5 ? O1G ANP 401 C 1 HETATM 3 O O2G ANP . . . E 3 -20.185 41.762 2.161 1 210.53 ? O2G ANP 401 C 1 HETATM 4 O O3G ANP . . . E 3 -19.783 39.563 3.46 1 209.05 ? O3G ANP 401 C 1 HETATM 5 P PB ANP . . . E 3 -21.4 38.764 1.191 1 211.09 ? PB ANP 401 C 1 HETATM 6 O O1B ANP . . . E 3 -22.033 38.842 -0.16 1 208.68 ? O1B ANP 401 C 1 HETATM 7 O O2B ANP . . . E 3 -21.613 37.348 1.8 1 209.61 ? O2B ANP 401 C 1 HETATM 8 N N3B ANP . . . E 3 -22.089 39.903 2.203 1 207.77 ? N3B ANP 401 C 1 HETATM 9 P PA ANP . . . E 3 -18.892 37.846 0.81 1 221.88 ? PA ANP 401 C 1 HETATM 10 O O1A ANP . . . E 3 -18.412 37.281 2.097 1 213.83 ? O1A ANP 401 C 1 HETATM 11 O O2A ANP . . . E 3 -17.785 38.356 -0.115 1 215.93 ? O2A ANP 401 C 1 HETATM 12 O O3A ANP . . . E 3 -19.875 39.057 1.065 1 217.1 ? O3A ANP 401 C 1 HETATM 13 O O5' ANP . . . E 3 -19.799 36.779 0.072 1 215.06 ? O5' ANP 401 C 1 HETATM 14 C C5' ANP . . . E 3 -19.816 36.654 -1.37 1 213.61 ? C5' ANP 401 C 1 HETATM 15 C C4' ANP . . . E 3 -20.866 35.642 -1.761 1 212.33 ? C4' ANP 401 C 1 HETATM 16 O O4' ANP . . . E 3 -20.269 34.328 -1.793 1 215.48 ? O4' ANP 401 C 1 HETATM 17 C C3' ANP . . . E 3 -22.069 35.571 -0.82 1 207.08 ? C3' ANP 401 C 1 HETATM 18 O O3' ANP . . . E 3 -23.193 36.224 -1.399 1 204.33 ? O3' ANP 401 C 1 HETATM 19 C C2' ANP . . . E 3 -22.325 34.068 -0.65 1 207.6 ? C2' ANP 401 C 1 HETATM 20 O O2' ANP . . . E 3 -23.297 33.587 -1.573 1 207.37 ? O2' ANP 401 C 1 HETATM 21 C C1' ANP . . . E 3 -20.954 33.448 -0.926 1 211.45 ? C1' ANP 401 C 1 HETATM 22 N N9 ANP . . . E 3 -20.125 33.217 0.257 1 209.04 ? N9 ANP 401 C 1 HETATM 23 C C8 ANP . . . E 3 -19.709 34.142 1.179 1 206.87 ? C8 ANP 401 C 1 HETATM 24 N N7 ANP . . . E 3 -18.958 33.644 2.132 1 204.22 ? N7 ANP 401 C 1 HETATM 25 C C5 ANP . . . E 3 -18.869 32.298 1.812 1 202.78 ? C5 ANP 401 C 1 HETATM 26 C C6 ANP . . . E 3 -18.213 31.216 2.431 1 198.48 ? C6 ANP 401 C 1 HETATM 27 N N6 ANP . . . E 3 -17.489 31.329 3.547 1 193.12 ? N6 ANP 401 C 1 HETATM 28 N N1 ANP . . . E 3 -18.326 29.998 1.853 1 191.1 ? N1 ANP 401 C 1 HETATM 29 C C2 ANP . . . E 3 -19.051 29.881 0.737 1 190.22 ? C2 ANP 401 C 1 HETATM 30 N N3 ANP . . . E 3 -19.711 30.827 0.063 1 192.78 ? N3 ANP 401 C 1 HETATM 31 C C4 ANP . . . E 3 -19.582 32.02 0.657 1 201.72 ? C4 ANP 401 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #