data_3GIG # _model_server_result.job_id YGYkSbUdAgB9eI-bFBtxww _model_server_result.datetime_utc '2024-12-03 21:55:12' _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 3gig # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1303}' # _entry.id 3GIG # _exptl.entry_id 3GIG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC 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 3GIG _cell.length_a 94.63 _cell.length_b 94.63 _cell.length_c 162.46 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GIG _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 _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 C LEU 35 B LEU 187 1_555 B N NEP 36 B NEP 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale2 B C NEP 36 B NEP 188 1_555 B N ASP 37 B ASP 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 D MG MG . A MG 1 1_555 A OE2 GLU 137 A GLU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 D MG MG . A MG 1 1_555 A OD1 ASN 141 A ASN 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 D MG MG . A MG 1 1_555 C O3G ACP . A ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc4 D MG MG . A MG 1 1_555 C O2B ACP . A ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc5 D MG MG . A MG 1 1_555 C O1A ACP . A ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc6 D MG MG . A MG 1 1_555 C O3A ACP . A ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc7 D MG MG . A MG 1 1_555 C O1G ACP . A ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc8 F MG MG . B MG 1 1_555 B OE2 GLU 137 B GLU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc9 F MG MG . B MG 1 1_555 B OD1 ASN 141 B ASN 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc10 F MG MG . B MG 1 1_555 E O3G ACP . B ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc11 F MG MG . B MG 1 1_555 E O2B ACP . B ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc12 F MG MG . B MG 1 1_555 E O1A ACP . B ACP 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? # _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 3GIG _atom_sites.fract_transf_matrix[1][1] 0.010567 _atom_sites.fract_transf_matrix[1][2] 0.006101 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012202 _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] 0.006155 _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 ACP A 1 1303 1303 ACP ACP . D 4 MG A 1 1 1 MG MG . E 3 ACP B 1 1303 1303 ACP ACP . F 4 MG B 1 1 1 MG MG . # 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 . . . E 3 11.427 46.643 13.005 1 194.78 ? PG ACP 1303 B 1 HETATM 2 O O1G ACP . . . E 3 11.408 47.757 14.018 1 243.93 ? O1G ACP 1303 B 1 HETATM 3 O O2G ACP . . . E 3 11.185 47.144 11.61 1 173.23 ? O2G ACP 1303 B 1 HETATM 4 O O3G ACP . . . E 3 10.653 45.395 13.361 1 179.33 ? O3G ACP 1303 B 1 HETATM 5 P PB ACP . . . E 3 13.424 44.428 13.567 1 195.78 ? PB ACP 1303 B 1 HETATM 6 O O1B ACP . . . E 3 14.913 44.196 13.54 1 211.25 ? O1B ACP 1303 B 1 HETATM 7 O O2B ACP . . . E 3 12.552 43.545 12.719 1 170.71 ? O2B ACP 1303 B 1 HETATM 8 C C3B ACP . . . E 3 13.16 46.127 12.977 1 164.3 ? C3B ACP 1303 B 1 HETATM 9 P PA ACP . . . E 3 12.244 42.803 15.603 1 169.82 ? PA ACP 1303 B 1 HETATM 10 O O1A ACP . . . E 3 11.295 42.309 14.544 1 147.79 ? O1A ACP 1303 B 1 HETATM 11 O O2A ACP . . . E 3 11.824 43.01 17.031 1 153.71 ? O2A ACP 1303 B 1 HETATM 12 O O3A ACP . . . E 3 12.985 44.154 15.1 1 160.45 ? O3A ACP 1303 B 1 HETATM 13 O O5' ACP . . . E 3 13.375 41.698 15.726 1 165.76 ? O5' ACP 1303 B 1 HETATM 14 C C5' ACP . . . E 3 14.149 41.766 16.915 1 169.16 ? C5' ACP 1303 B 1 HETATM 15 C C4' ACP . . . E 3 15.454 41.014 16.69 1 158.2 ? C4' ACP 1303 B 1 HETATM 16 O O4' ACP . . . E 3 15.259 39.609 16.927 1 162.84 ? O4' ACP 1303 B 1 HETATM 17 C C3' ACP . . . E 3 15.944 41.207 15.257 1 156.49 ? C3' ACP 1303 B 1 HETATM 18 O O3' ACP . . . E 3 17.026 42.158 15.19 1 169.88 ? O3' ACP 1303 B 1 HETATM 19 C C2' ACP . . . E 3 16.384 39.819 14.841 1 163.27 ? C2' ACP 1303 B 1 HETATM 20 O O2' ACP . . . E 3 17.806 39.765 14.977 1 170.98 ? O2' ACP 1303 B 1 HETATM 21 C C1' ACP . . . E 3 15.735 38.844 15.821 1 185.59 ? C1' ACP 1303 B 1 HETATM 22 N N9 ACP . . . E 3 14.564 38.162 15.225 1 168.26 ? N9 ACP 1303 B 1 HETATM 23 C C8 ACP . . . E 3 13.299 38.596 15.314 1 159.67 ? C8 ACP 1303 B 1 HETATM 24 N N7 ACP . . . E 3 12.473 37.739 14.662 1 158.89 ? N7 ACP 1303 B 1 HETATM 25 C C5 ACP . . . E 3 13.205 36.727 14.141 1 178.86 ? C5 ACP 1303 B 1 HETATM 26 C C6 ACP . . . E 3 12.953 35.489 13.342 1 159.24 ? C6 ACP 1303 B 1 HETATM 27 N N6 ACP . . . E 3 11.711 35.125 12.941 1 167.22 ? N6 ACP 1303 B 1 HETATM 28 N N1 ACP . . . E 3 14.012 34.723 13.015 1 191.36 ? N1 ACP 1303 B 1 HETATM 29 C C2 ACP . . . E 3 15.256 35.061 13.399 1 169.57 ? C2 ACP 1303 B 1 HETATM 30 N N3 ACP . . . E 3 15.556 36.157 14.124 1 173.19 ? N3 ACP 1303 B 1 HETATM 31 C C4 ACP . . . E 3 14.592 37.021 14.523 1 173.84 ? C4 ACP 1303 B 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #