data_5IUJ # _model_server_result.job_id GdY2FY7Mia8ysTsjw9xkZg _model_server_result.datetime_utc '2024-10-19 08:21:20' _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 5iuj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 5IUJ # _exptl.entry_id 5IUJ _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.44 _cell.angle_gamma 90 _cell.entry_id 5IUJ _cell.length_a 87.82 _cell.length_b 114.619 _cell.length_c 91.597 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IUJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,K,Q,R,S 1 1 D,E,F,L,M,N,O,P,T,U,V 2 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 G N N ? 3 I N N ? 3 L N N ? 3 N 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 OE2 GLU 137 A GLU 289 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc2 A OD1 ASN 141 A ASN 293 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc3 G O1G ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc4 G O2B ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc5 G O2A ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc6 H MG MG . A MG 402 1_555 Q O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc7 B OE2 GLU 137 B GLU 289 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc8 B OD1 ASN 141 B ASN 293 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc9 I O1G ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc10 I O1B ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc11 I O2A ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc12 J MG MG . B MG 402 1_555 R O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc13 C O ASN 26 C ASN 22 1_555 K K K . C K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc14 C O GLU 28 C GLU 24 1_555 K K K . C K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc15 C O MET 31 C MET 27 1_555 K K K . C K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc16 D OE2 GLU 137 D GLU 289 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc17 D OD1 ASN 141 D ASN 293 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc18 L O1G ACP . D ACP 401 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc19 L O2B ACP . D ACP 401 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc20 L O2A ACP . D ACP 401 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc21 M MG MG . D MG 402 1_555 T O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc22 E OE2 GLU 137 E GLU 289 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc23 E OD1 ASN 141 E ASN 293 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc24 N O1G ACP . E ACP 401 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc25 N O1B ACP . E ACP 401 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc26 N O1A ACP . E ACP 401 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc27 O MG MG . E MG 402 1_555 U O HOH . E HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc28 F O ASN 26 F ASN 22 1_555 P K K . F K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.182 ? metalc ? metalc29 F O GLU 28 F GLU 24 1_555 P K K . F K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc30 F O MET 31 F MET 27 1_555 P K K . F K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? # _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 5IUJ _atom_sites.fract_transf_matrix[1][1] 0.011387 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005662 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008725 _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] 0.012193 _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 G 3 ACP A 1 401 401 ACP ACP . H 4 MG A 1 402 501 MG MG . I 3 ACP B 1 401 401 ACP ACP . J 4 MG B 1 402 501 MG MG . K 5 K C 1 201 1 K K . L 3 ACP D 1 401 401 ACP ACP . M 4 MG D 1 402 501 MG MG . N 3 ACP E 1 401 401 ACP ACP . O 4 MG E 1 402 501 MG MG . P 5 K F 1 201 2 K K . Q 6 HOH A 1 501 16 HOH HOH . Q 6 HOH A 2 502 11 HOH HOH . Q 6 HOH A 3 503 2 HOH HOH . Q 6 HOH A 4 504 12 HOH HOH . R 6 HOH B 1 501 17 HOH HOH . R 6 HOH B 2 502 18 HOH HOH . S 6 HOH C 1 301 5 HOH HOH . S 6 HOH C 2 302 10 HOH HOH . S 6 HOH C 3 303 3 HOH HOH . T 6 HOH D 1 501 19 HOH HOH . T 6 HOH D 2 502 15 HOH HOH . T 6 HOH D 3 503 13 HOH HOH . U 6 HOH E 1 501 6 HOH HOH . V 6 HOH F 1 301 14 HOH HOH . V 6 HOH F 2 302 8 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 . . . N 3 -77.517 -15.442 131.986 1 94.95 ? PG ACP 401 E 1 HETATM 2 O O1G ACP . . . N 3 -78.638 -14.997 131.016 1 93.31 ? O1G ACP 401 E 1 HETATM 3 O O2G ACP . . . N 3 -76.216 -15.574 131.158 1 93.65 ? O2G ACP 401 E 1 HETATM 4 O O3G ACP . . . N 3 -77.382 -14.518 133.155 1 96.3 ? O3G ACP 401 E 1 HETATM 5 P PB ACP . . . N 3 -79.139 -18.088 131.765 1 92.91 ? PB ACP 401 E 1 HETATM 6 O O1B ACP . . . N 3 -78.947 -17.887 130.24 1 88.41 ? O1B ACP 401 E 1 HETATM 7 O O2B ACP . . . N 3 -79.136 -19.561 132.029 1 97.08 ? O2B ACP 401 E 1 HETATM 8 C C3B ACP . . . N 3 -77.891 -17.094 132.595 1 95.86 ? C3B ACP 401 E 1 HETATM 9 P PA ACP . . . N 3 -81.881 -17.138 131.367 1 90.18 ? PA ACP 401 E 1 HETATM 10 O O1A ACP . . . N 3 -81.492 -16.27 130.224 1 84.48 ? O1A ACP 401 E 1 HETATM 11 O O2A ACP . . . N 3 -82.87 -16.405 132.333 1 89.31 ? O2A ACP 401 E 1 HETATM 12 O O3A ACP . . . N 3 -80.566 -17.505 132.191 1 93.07 ? O3A ACP 401 E 1 HETATM 13 O O5' ACP . . . N 3 -82.52 -18.552 130.88 1 93.7 ? O5' ACP 401 E 1 HETATM 14 C C5' ACP . . . N 3 -83.121 -19.467 131.824 1 99.4 ? C5' ACP 401 E 1 HETATM 15 C C4' ACP . . . N 3 -82.998 -20.904 131.377 1 102.11 ? C4' ACP 401 E 1 HETATM 16 O O4' ACP . . . N 3 -83.825 -21.149 130.222 1 101.5 ? O4' ACP 401 E 1 HETATM 17 C C3' ACP . . . N 3 -81.612 -21.357 130.957 1 103.18 ? C3' ACP 401 E 1 HETATM 18 O O3' ACP . . . N 3 -80.842 -21.697 132.104 1 107.63 ? O3' ACP 401 E 1 HETATM 19 C C2' ACP . . . N 3 -81.918 -22.57 130.077 1 106.07 ? C2' ACP 401 E 1 HETATM 20 O O2' ACP . . . N 3 -82.033 -23.769 130.837 1 112.91 ? O2' ACP 401 E 1 HETATM 21 C C1' ACP . . . N 3 -83.255 -22.179 129.432 1 103.67 ? C1' ACP 401 E 1 HETATM 22 N N9 ACP . . . N 3 -83.146 -21.707 128.054 1 101.41 ? N9 ACP 401 E 1 HETATM 23 C C8 ACP . . . N 3 -83.149 -20.403 127.632 1 98.94 ? C8 ACP 401 E 1 HETATM 24 N N7 ACP . . . N 3 -83.042 -20.259 126.332 1 97.92 ? N7 ACP 401 E 1 HETATM 25 C C5 ACP . . . N 3 -82.961 -21.561 125.863 1 100.65 ? C5 ACP 401 E 1 HETATM 26 C C6 ACP . . . N 3 -82.84 -22.098 124.564 1 100.75 ? C6 ACP 401 E 1 HETATM 27 N N6 ACP . . . N 3 -82.674 -21.357 123.465 1 97.84 ? N6 ACP 401 E 1 HETATM 28 N N1 ACP . . . N 3 -82.833 -23.444 124.437 1 104.55 ? N1 ACP 401 E 1 HETATM 29 C C2 ACP . . . N 3 -82.9 -24.193 125.543 1 107.98 ? C2 ACP 401 E 1 HETATM 30 N N3 ACP . . . N 3 -82.998 -23.802 126.82 1 108.61 ? N3 ACP 401 E 1 HETATM 31 C C4 ACP . . . N 3 -83.029 -22.466 126.914 1 103.81 ? C4 ACP 401 E 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #