data_2ODB # _model_server_result.job_id ziJcPWPoiesWmLyo_tIxPw _model_server_result.datetime_utc '2025-08-02 08:54:45' _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 2odb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":200}' # _entry.id 2ODB # _exptl.entry_id 2ODB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE 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 2ODB _cell.length_a 162.366 _cell.length_b 162.366 _cell.length_c 45.968 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ODB _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 PISA tetrameric 4 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 1,2 A,B,C,D,E,F,G,H,I,J 3 1,3 A,B,C,D,E,F,G,H,I,J 4 1,4 # 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' 9_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -30.645333 3 'crystal symmetry operation' 12_544 x,x-y-1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 81.183 -140.613081 -7.661333 4 'crystal symmetry operation' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -22.984 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _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 OG1 THR 18 A THR 17 1_555 D MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc2 A OG1 THR 36 A THR 35 1_555 D MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc3 G O1G GCP . A GCP 200 1_555 D MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc4 G O2B GCP . A GCP 200 1_555 D MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc5 D MG MG . A MG 205 1_555 I O HOH . A HOH 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc6 D MG MG . A MG 205 1_555 I O HOH . A HOH 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? # _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 2ODB _atom_sites.fract_transf_matrix[1][1] 0.006159 _atom_sites.fract_transf_matrix[1][2] 0.003556 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007112 _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] 0.021754 _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 CL A 1 204 204 CL CL . D 4 MG A 1 205 205 MG MG . E 5 SO4 A 1 202 202 SO4 SO4 . F 5 SO4 A 1 203 203 SO4 SO4 . G 6 GCP A 1 200 200 GCP GCP . H 5 SO4 B 1 201 201 SO4 SO4 . I 7 HOH A 1 206 1 HOH HOH . I 7 HOH A 2 207 2 HOH HOH . I 7 HOH A 3 208 3 HOH HOH . I 7 HOH A 4 209 4 HOH HOH . I 7 HOH A 5 210 7 HOH HOH . I 7 HOH A 6 211 8 HOH HOH . I 7 HOH A 7 212 9 HOH HOH . I 7 HOH A 8 213 14 HOH HOH . I 7 HOH A 9 214 16 HOH HOH . I 7 HOH A 10 215 17 HOH HOH . I 7 HOH A 11 216 18 HOH HOH . I 7 HOH A 12 217 19 HOH HOH . I 7 HOH A 13 218 20 HOH HOH . I 7 HOH A 14 219 23 HOH HOH . I 7 HOH A 15 220 24 HOH HOH . I 7 HOH A 16 221 25 HOH HOH . I 7 HOH A 17 222 26 HOH HOH . I 7 HOH A 18 223 27 HOH HOH . I 7 HOH A 19 224 28 HOH HOH . I 7 HOH A 20 225 29 HOH HOH . I 7 HOH A 21 226 30 HOH HOH . I 7 HOH A 22 227 33 HOH HOH . I 7 HOH A 23 228 34 HOH HOH . I 7 HOH A 24 229 35 HOH HOH . I 7 HOH A 25 230 36 HOH HOH . I 7 HOH A 26 231 38 HOH HOH . I 7 HOH A 27 232 39 HOH HOH . I 7 HOH A 28 233 44 HOH HOH . I 7 HOH A 29 234 45 HOH HOH . I 7 HOH A 30 235 46 HOH HOH . I 7 HOH A 31 236 48 HOH HOH . J 7 HOH B 1 202 5 HOH HOH . J 7 HOH B 2 203 10 HOH HOH . J 7 HOH B 3 204 11 HOH HOH . J 7 HOH B 4 205 12 HOH HOH . J 7 HOH B 5 206 15 HOH HOH . J 7 HOH B 6 207 21 HOH HOH . J 7 HOH B 7 208 22 HOH HOH . J 7 HOH B 8 209 31 HOH HOH . J 7 HOH B 9 210 32 HOH HOH . J 7 HOH B 10 211 37 HOH HOH . J 7 HOH B 11 212 40 HOH HOH . J 7 HOH B 12 213 41 HOH HOH . J 7 HOH B 13 214 47 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 . . . G 6 6.126 -67.808 -9.643 1 43.62 ? PG GCP 200 A 1 HETATM 2 O O1G GCP . . . G 6 7.292 -68.173 -10.517 1 41.9 ? O1G GCP 200 A 1 HETATM 3 O O2G GCP . . . G 6 6.386 -67.923 -8.133 1 41.67 ? O2G GCP 200 A 1 HETATM 4 O O3G GCP . . . G 6 4.836 -68.451 -10.029 1 44.97 ? O3G GCP 200 A 1 HETATM 5 C C3B GCP . . . G 6 5.874 -66.03 -9.977 1 45.14 ? C3B GCP 200 A 1 HETATM 6 P PB GCP . . . G 6 7.351 -64.966 -9.857 1 46.66 ? PB GCP 200 A 1 HETATM 7 O O1B GCP . . . G 6 7.702 -64.703 -8.393 1 41.03 ? O1B GCP 200 A 1 HETATM 8 O O2B GCP . . . G 6 8.411 -65.622 -10.71 1 44.06 ? O2B GCP 200 A 1 HETATM 9 O O3A GCP . . . G 6 6.968 -63.545 -10.485 1 47.79 ? O3A GCP 200 A 1 HETATM 10 P PA GCP . . . G 6 7.167 -63.08 -12.011 1 51.99 ? PA GCP 200 A 1 HETATM 11 O O1A GCP . . . G 6 8.608 -62.657 -12.21 1 52.65 ? O1A GCP 200 A 1 HETATM 12 O O2A GCP . . . G 6 6.564 -64.042 -12.99 1 49.97 ? O2A GCP 200 A 1 HETATM 13 O O5' GCP . . . G 6 6.349 -61.688 -12.001 1 53.72 ? O5' GCP 200 A 1 HETATM 14 C C5' GCP . . . G 6 5.012 -61.518 -11.532 1 56.8 ? C5' GCP 200 A 1 HETATM 15 C C4' GCP . . . G 6 4.334 -60.288 -12.157 1 58.6 ? C4' GCP 200 A 1 HETATM 16 O O4' GCP . . . G 6 4.909 -59.096 -11.628 1 59.71 ? O4' GCP 200 A 1 HETATM 17 C C3' GCP . . . G 6 4.502 -60.191 -13.665 1 60.31 ? C3' GCP 200 A 1 HETATM 18 O O3' GCP . . . G 6 3.308 -59.674 -14.238 1 61.17 ? O3' GCP 200 A 1 HETATM 19 C C2' GCP . . . G 6 5.638 -59.209 -13.869 1 61.14 ? C2' GCP 200 A 1 HETATM 20 O O2' GCP . . . G 6 5.541 -58.495 -15.098 1 62.21 ? O2' GCP 200 A 1 HETATM 21 C C1' GCP . . . G 6 5.525 -58.319 -12.655 1 62.08 ? C1' GCP 200 A 1 HETATM 22 N N9 GCP . . . G 6 6.815 -57.873 -12.084 1 62.94 ? N9 GCP 200 A 1 HETATM 23 C C8 GCP . . . G 6 7.869 -58.61 -11.681 1 63.3 ? C8 GCP 200 A 1 HETATM 24 N N7 GCP . . . G 6 8.852 -57.822 -11.169 1 63.15 ? N7 GCP 200 A 1 HETATM 25 C C5 GCP . . . G 6 8.423 -56.545 -11.239 1 64.03 ? C5 GCP 200 A 1 HETATM 26 C C6 GCP . . . G 6 8.932 -55.175 -10.893 1 63.7 ? C6 GCP 200 A 1 HETATM 27 O O6 GCP . . . G 6 10.058 -54.98 -10.378 1 62.96 ? O6 GCP 200 A 1 HETATM 28 N N1 GCP . . . G 6 8.125 -54.134 -11.133 1 63.46 ? N1 GCP 200 A 1 HETATM 29 C C2 GCP . . . G 6 6.905 -54.267 -11.681 1 63.18 ? C2 GCP 200 A 1 HETATM 30 N N2 GCP . . . G 6 6.152 -53.175 -11.9 1 63.66 ? N2 GCP 200 A 1 HETATM 31 N N3 GCP . . . G 6 6.378 -55.457 -12.023 1 63.42 ? N3 GCP 200 A 1 HETATM 32 C C4 GCP . . . G 6 7.076 -56.602 -11.828 1 63.71 ? C4 GCP 200 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #