data_5IZL # _model_server_result.job_id xBQ9Icz5Wjpd_KHgBxlFig _model_server_result.datetime_utc '2024-11-22 14:46:31' _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 5izl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1002}' # _entry.id 5IZL # _exptl.entry_id 5IZL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE 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 90 _cell.entry_id 5IZL _cell.length_a 94.302 _cell.length_b 113.242 _cell.length_c 329.725 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IZL _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,G 1 1 B,E,F,H 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 D N N ? 3 F 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 OG1 THR 41 A THR 21 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 A OG1 THR 68 A THR 48 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc3 C MG MG . A MG 1001 1_555 D O1B GCP . A GCP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc4 C MG MG . A MG 1001 1_555 D O1G GCP . A GCP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc5 C MG MG . A MG 1001 1_555 G O HOH . A HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 C MG MG . A MG 1001 1_555 G O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc7 B OG1 THR 41 B THR 21 1_555 E MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc8 B OG1 THR 68 B THR 48 1_555 E MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc9 E MG MG . B MG 1001 1_555 F O1G GCP . B GCP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc10 E MG MG . B MG 1001 1_555 F O3G GCP . B GCP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc11 E MG MG . B MG 1001 1_555 F O1B GCP . B GCP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc12 E MG MG . B MG 1001 1_555 H O HOH . B HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? # _chem_comp.formula 'C11 H18 N5 O13 P3' _chem_comp.formula_weight 521.208 _chem_comp.id GCP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE 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 GCP doub 83 n n PG O2G GCP sing 84 n n PG O3G GCP sing 85 n n PG C3B GCP sing 86 n n O2G HOG2 GCP sing 87 n n O3G HOG3 GCP sing 88 n n C3B PB GCP sing 89 n n C3B H3B1 GCP sing 90 n n C3B H3B2 GCP sing 91 n n PB O1B GCP doub 92 n n PB O2B GCP sing 93 n n PB O3A GCP sing 94 n n O2B HOB2 GCP sing 95 n n O3A PA GCP sing 96 n n PA O1A GCP doub 97 n n PA O2A GCP sing 98 n n PA O5' GCP sing 99 n n O2A HOA2 GCP sing 100 n n O5' C5' GCP sing 101 n n C5' C4' GCP sing 102 n n C5' "H5'2" GCP sing 103 n n C5' "H5'1" GCP sing 104 n n C4' O4' GCP sing 105 n n C4' C3' GCP sing 106 n n C4' H4' GCP sing 107 n n O4' C1' GCP sing 108 n n C3' O3' GCP sing 109 n n C3' C2' GCP sing 110 n n C3' H3' GCP sing 111 n n O3' HO3' GCP sing 112 n n C2' O2' GCP sing 113 n n C2' C1' GCP sing 114 n n C2' H2' GCP sing 115 n n O2' HO2' GCP sing 116 n n C1' N9 GCP sing 117 n n C1' H1' GCP sing 118 n n N9 C8 GCP sing 119 n y N9 C4 GCP sing 120 n y C8 N7 GCP doub 121 n y C8 H8 GCP sing 122 n n N7 C5 GCP sing 123 n y C5 C6 GCP sing 124 n y C5 C4 GCP doub 125 n y C6 O6 GCP doub 126 n n C6 N1 GCP sing 127 n y N1 C2 GCP sing 128 n y N1 HN1 GCP sing 129 n n C2 N2 GCP sing 130 n n C2 N3 GCP doub 131 n y N2 HN21 GCP sing 132 n n N2 HN22 GCP sing 133 n n N3 C4 GCP sing 134 n y # _atom_sites.entry_id 5IZL _atom_sites.fract_transf_matrix[1][1] 0.010604 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008831 _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] 0.003033 _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 MG A 1 1001 1001 MG MG . D 3 GCP A 1 1002 2001 GCP GCP . E 2 MG B 1 1001 1001 MG MG . F 3 GCP B 1 1002 2001 GCP GCP . G 4 HOH A 1 1101 18 HOH HOH . G 4 HOH A 2 1102 2 HOH HOH . G 4 HOH A 3 1103 10 HOH HOH . G 4 HOH A 4 1104 12 HOH HOH . G 4 HOH A 5 1105 13 HOH HOH . G 4 HOH A 6 1106 6 HOH HOH . G 4 HOH A 7 1107 16 HOH HOH . G 4 HOH A 8 1108 3 HOH HOH . G 4 HOH A 9 1109 11 HOH HOH . G 4 HOH A 10 1110 15 HOH HOH . G 4 HOH A 11 1111 7 HOH HOH . G 4 HOH A 12 1112 17 HOH HOH . G 4 HOH A 13 1113 19 HOH HOH . G 4 HOH A 14 1114 4 HOH HOH . G 4 HOH A 15 1115 20 HOH HOH . G 4 HOH A 16 1116 5 HOH HOH . H 4 HOH B 1 1101 1 HOH HOH . H 4 HOH B 2 1102 28 HOH HOH . H 4 HOH B 3 1103 22 HOH HOH . H 4 HOH B 4 1104 21 HOH HOH . H 4 HOH B 5 1105 32 HOH HOH . H 4 HOH B 6 1106 14 HOH HOH . H 4 HOH B 7 1107 30 HOH HOH . H 4 HOH B 8 1108 29 HOH HOH . H 4 HOH B 9 1109 8 HOH HOH . H 4 HOH B 10 1110 26 HOH HOH . H 4 HOH B 11 1111 25 HOH HOH . H 4 HOH B 12 1112 31 HOH HOH . H 4 HOH B 13 1113 23 HOH HOH . H 4 HOH B 14 1114 24 HOH HOH . H 4 HOH B 15 1115 27 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 GCP . . . D 3 -16.256 -50.171 26.432 1 66.45 ? PG GCP 1002 A 1 HETATM 2 O O1G GCP . . . D 3 -15.811 -49.294 25.328 1 70.27 ? O1G GCP 1002 A 1 HETATM 3 O O2G GCP . . . D 3 -16.364 -51.679 25.887 1 85.68 ? O2G GCP 1002 A 1 HETATM 4 O O3G GCP . . . D 3 -15.508 -50.176 27.707 1 83.98 ? O3G GCP 1002 A 1 HETATM 5 C C3B GCP . . . D 3 -17.985 -49.785 26.796 1 73.74 ? C3B GCP 1002 A 1 HETATM 6 P PB GCP . . . D 3 -18.873 -49.436 25.237 1 58.55 ? PB GCP 1002 A 1 HETATM 7 O O1B GCP . . . D 3 -18.015 -48.265 24.519 1 70.02 ? O1B GCP 1002 A 1 HETATM 8 O O2B GCP . . . D 3 -20.277 -49.021 25.483 1 83.71 ? O2B GCP 1002 A 1 HETATM 9 O O3A GCP . . . D 3 -18.734 -50.75 24.316 1 83.55 ? O3A GCP 1002 A 1 HETATM 10 P PA GCP . . . D 3 -19.932 -51.172 23.333 1 67.83 ? PA GCP 1002 A 1 HETATM 11 O O1A GCP . . . D 3 -19.534 -52.385 22.587 1 92.95 ? O1A GCP 1002 A 1 HETATM 12 O O2A GCP . . . D 3 -20.388 -49.976 22.592 1 63.16 ? O2A GCP 1002 A 1 HETATM 13 O O5' GCP . . . D 3 -21.085 -51.583 24.378 1 108.81 ? O5' GCP 1002 A 1 HETATM 14 C C5' GCP . . . D 3 -21.073 -52.879 24.983 1 88.26 ? C5' GCP 1002 A 1 HETATM 15 C C4' GCP . . . D 3 -22.372 -53.613 24.643 1 87.53 ? C4' GCP 1002 A 1 HETATM 16 O O4' GCP . . . D 3 -23.466 -52.685 24.663 1 82.47 ? O4' GCP 1002 A 1 HETATM 17 C C3' GCP . . . D 3 -22.322 -54.092 23.201 1 90.48 ? C3' GCP 1002 A 1 HETATM 18 O O3' GCP . . . D 3 -21.98 -55.485 23.171 1 123.32 ? O3' GCP 1002 A 1 HETATM 19 C C2' GCP . . . D 3 -23.746 -53.908 22.701 1 89.48 ? C2' GCP 1002 A 1 HETATM 20 O O2' GCP . . . D 3 -24.301 -55.186 22.356 1 97.04 ? O2' GCP 1002 A 1 HETATM 21 C C1' GCP . . . D 3 -24.489 -53.339 23.899 1 84.16 ? C1' GCP 1002 A 1 HETATM 22 N N9 GCP . . . D 3 -25.5 -52.345 23.474 1 80.9 ? N9 GCP 1002 A 1 HETATM 23 C C8 GCP . . . D 3 -25.246 -51.112 23.049 1 76.45 ? C8 GCP 1002 A 1 HETATM 24 N N7 GCP . . . D 3 -26.408 -50.533 22.762 1 77.53 ? N7 GCP 1002 A 1 HETATM 25 C C5 GCP . . . D 3 -27.38 -51.408 23.01 1 80.36 ? C5 GCP 1002 A 1 HETATM 26 C C6 GCP . . . D 3 -28.702 -51.309 22.884 1 78.8 ? C6 GCP 1002 A 1 HETATM 27 O O6 GCP . . . D 3 -29.218 -50.27 22.476 1 76.14 ? O6 GCP 1002 A 1 HETATM 28 N N1 GCP . . . D 3 -29.511 -52.397 23.219 1 86.79 ? N1 GCP 1002 A 1 HETATM 29 C C2 GCP . . . D 3 -28.895 -53.561 23.678 1 91.6 ? C2 GCP 1002 A 1 HETATM 30 N N2 GCP . . . D 3 -29.626 -54.622 24.009 1 99.6 ? N2 GCP 1002 A 1 HETATM 31 N N3 GCP . . . D 3 -27.561 -53.6 23.783 1 96.03 ? N3 GCP 1002 A 1 HETATM 32 C C4 GCP . . . D 3 -26.816 -52.534 23.452 1 84.05 ? C4 GCP 1002 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #