data_4M1O # _model_server_result.job_id X9FOvAPilrUTsHYxynL-ew _model_server_result.datetime_utc '2024-11-27 05:21:22' _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 4m1o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":202}' # _entry.id 4M1O # _exptl.entry_id 4M1O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.95 _cell.angle_gamma 90 _cell.entry_id 4M1O _cell.length_a 68.333 _cell.length_b 84.163 _cell.length_c 86.432 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M1O _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,H 1 1 B,E,F,I 2 1 C,G,J 3 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 ? 2 D N N ? 2 F N N ? 2 G N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 13 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 12 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id C28 _struct_conn.ptnr2_label_comp_id 21J _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id 21J _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 1_555 _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 1.828 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 138 n n PB O2B GDP sing 139 n n PB O3B GDP sing 140 n n PB O3A GDP sing 141 n n O2B HOB2 GDP sing 142 n n O3B HOB3 GDP sing 143 n n O3A PA GDP sing 144 n n PA O1A GDP doub 145 n n PA O2A GDP sing 146 n n PA O5' GDP sing 147 n n O2A HOA2 GDP sing 148 n n O5' C5' GDP sing 149 n n C5' C4' GDP sing 150 n n C5' H5' GDP sing 151 n n C5' "H5''" GDP sing 152 n n C4' O4' GDP sing 153 n n C4' C3' GDP sing 154 n n C4' H4' GDP sing 155 n n O4' C1' GDP sing 156 n n C3' O3' GDP sing 157 n n C3' C2' GDP sing 158 n n C3' H3' GDP sing 159 n n O3' HO3' GDP sing 160 n n C2' O2' GDP sing 161 n n C2' C1' GDP sing 162 n n C2' H2' GDP sing 163 n n O2' HO2' GDP sing 164 n n C1' N9 GDP sing 165 n n C1' H1' GDP sing 166 n n N9 C8 GDP sing 167 n y N9 C4 GDP sing 168 n y C8 N7 GDP doub 169 n y C8 H8 GDP sing 170 n n N7 C5 GDP sing 171 n y C5 C6 GDP sing 172 n n C5 C4 GDP doub 173 n y C6 O6 GDP doub 174 n n C6 N1 GDP sing 175 n n N1 C2 GDP sing 176 n n N1 HN1 GDP sing 177 n n C2 N2 GDP sing 178 n n C2 N3 GDP doub 179 n n N2 HN21 GDP sing 180 n n N2 HN22 GDP sing 181 n n N3 C4 GDP sing 182 n n # _atom_sites.entry_id 4M1O _atom_sites.fract_transf_matrix[1][1] 0.014634 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005603 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011882 _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] 0.012389 _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 D 2 GDP A 1 201 220 GDP GDP . E 3 21J B 1 201 210 21J 21J . F 2 GDP B 1 202 220 GDP GDP . G 2 GDP C 1 201 220 GDP GDP . H 4 HOH A 1 301 1 HOH HOH . H 4 HOH A 2 302 2 HOH HOH . H 4 HOH A 3 303 5 HOH HOH . H 4 HOH A 4 304 7 HOH HOH . H 4 HOH A 5 305 8 HOH HOH . H 4 HOH A 6 306 14 HOH HOH . H 4 HOH A 7 307 16 HOH HOH . H 4 HOH A 8 308 17 HOH HOH . H 4 HOH A 9 309 19 HOH HOH . H 4 HOH A 10 310 22 HOH HOH . H 4 HOH A 11 311 23 HOH HOH . H 4 HOH A 12 312 27 HOH HOH . H 4 HOH A 13 313 29 HOH HOH . H 4 HOH A 14 314 34 HOH HOH . H 4 HOH A 15 315 35 HOH HOH . H 4 HOH A 16 316 36 HOH HOH . H 4 HOH A 17 317 38 HOH HOH . H 4 HOH A 18 318 41 HOH HOH . H 4 HOH A 19 319 42 HOH HOH . H 4 HOH A 20 320 45 HOH HOH . H 4 HOH A 21 321 48 HOH HOH . H 4 HOH A 22 322 50 HOH HOH . H 4 HOH A 23 323 52 HOH HOH . H 4 HOH A 24 324 54 HOH HOH . H 4 HOH A 25 325 60 HOH HOH . H 4 HOH A 26 326 61 HOH HOH . H 4 HOH A 27 327 62 HOH HOH . H 4 HOH A 28 328 64 HOH HOH . H 4 HOH A 29 329 67 HOH HOH . H 4 HOH A 30 330 70 HOH HOH . H 4 HOH A 31 331 71 HOH HOH . H 4 HOH A 32 332 73 HOH HOH . H 4 HOH A 33 333 76 HOH HOH . H 4 HOH A 34 334 78 HOH HOH . H 4 HOH A 35 335 82 HOH HOH . H 4 HOH A 36 336 85 HOH HOH . H 4 HOH A 37 337 87 HOH HOH . H 4 HOH A 38 338 91 HOH HOH . H 4 HOH A 39 339 93 HOH HOH . H 4 HOH A 40 340 95 HOH HOH . H 4 HOH A 41 341 97 HOH HOH . H 4 HOH A 42 342 98 HOH HOH . H 4 HOH A 43 343 100 HOH HOH . H 4 HOH A 44 344 103 HOH HOH . H 4 HOH A 45 345 110 HOH HOH . H 4 HOH A 46 346 111 HOH HOH . H 4 HOH A 47 347 112 HOH HOH . H 4 HOH A 48 348 119 HOH HOH . H 4 HOH A 49 349 120 HOH HOH . H 4 HOH A 50 350 121 HOH HOH . H 4 HOH A 51 351 127 HOH HOH . H 4 HOH A 52 352 133 HOH HOH . H 4 HOH A 53 353 136 HOH HOH . H 4 HOH A 54 354 137 HOH HOH . H 4 HOH A 55 355 141 HOH HOH . H 4 HOH A 56 356 147 HOH HOH . H 4 HOH A 57 357 151 HOH HOH . H 4 HOH A 58 358 152 HOH HOH . H 4 HOH A 59 359 156 HOH HOH . H 4 HOH A 60 360 163 HOH HOH . H 4 HOH A 61 361 169 HOH HOH . H 4 HOH A 62 362 171 HOH HOH . H 4 HOH A 63 363 172 HOH HOH . H 4 HOH A 64 364 173 HOH HOH . H 4 HOH A 65 365 175 HOH HOH . H 4 HOH A 66 366 182 HOH HOH . I 4 HOH B 1 301 4 HOH HOH . I 4 HOH B 2 302 6 HOH HOH . I 4 HOH B 3 303 9 HOH HOH . I 4 HOH B 4 304 11 HOH HOH . I 4 HOH B 5 305 12 HOH HOH . I 4 HOH B 6 306 18 HOH HOH . I 4 HOH B 7 307 21 HOH HOH . I 4 HOH B 8 308 24 HOH HOH . I 4 HOH B 9 309 25 HOH HOH . I 4 HOH B 10 310 26 HOH HOH . I 4 HOH B 11 311 28 HOH HOH . I 4 HOH B 12 312 32 HOH HOH . I 4 HOH B 13 313 33 HOH HOH . I 4 HOH B 14 314 39 HOH HOH . I 4 HOH B 15 315 43 HOH HOH . I 4 HOH B 16 316 44 HOH HOH . I 4 HOH B 17 317 46 HOH HOH . I 4 HOH B 18 318 47 HOH HOH . I 4 HOH B 19 319 49 HOH HOH . I 4 HOH B 20 320 53 HOH HOH . I 4 HOH B 21 321 55 HOH HOH . I 4 HOH B 22 322 58 HOH HOH . I 4 HOH B 23 323 59 HOH HOH . I 4 HOH B 24 324 63 HOH HOH . I 4 HOH B 25 325 66 HOH HOH . I 4 HOH B 26 326 69 HOH HOH . I 4 HOH B 27 327 75 HOH HOH . I 4 HOH B 28 328 79 HOH HOH . I 4 HOH B 29 329 84 HOH HOH . I 4 HOH B 30 330 99 HOH HOH . I 4 HOH B 31 331 102 HOH HOH . I 4 HOH B 32 332 105 HOH HOH . I 4 HOH B 33 333 106 HOH HOH . I 4 HOH B 34 334 113 HOH HOH . I 4 HOH B 35 335 114 HOH HOH . I 4 HOH B 36 336 122 HOH HOH . I 4 HOH B 37 337 123 HOH HOH . I 4 HOH B 38 338 124 HOH HOH . I 4 HOH B 39 339 126 HOH HOH . I 4 HOH B 40 340 128 HOH HOH . I 4 HOH B 41 341 129 HOH HOH . I 4 HOH B 42 342 130 HOH HOH . I 4 HOH B 43 343 131 HOH HOH . I 4 HOH B 44 344 132 HOH HOH . I 4 HOH B 45 345 134 HOH HOH . I 4 HOH B 46 346 139 HOH HOH . I 4 HOH B 47 347 142 HOH HOH . I 4 HOH B 48 348 148 HOH HOH . I 4 HOH B 49 349 149 HOH HOH . I 4 HOH B 50 350 150 HOH HOH . I 4 HOH B 51 351 153 HOH HOH . I 4 HOH B 52 352 154 HOH HOH . I 4 HOH B 53 353 155 HOH HOH . I 4 HOH B 54 354 157 HOH HOH . I 4 HOH B 55 355 158 HOH HOH . I 4 HOH B 56 356 159 HOH HOH . I 4 HOH B 57 357 160 HOH HOH . I 4 HOH B 58 358 164 HOH HOH . I 4 HOH B 59 359 165 HOH HOH . I 4 HOH B 60 360 166 HOH HOH . I 4 HOH B 61 361 167 HOH HOH . I 4 HOH B 62 362 174 HOH HOH . I 4 HOH B 63 363 176 HOH HOH . I 4 HOH B 64 364 177 HOH HOH . I 4 HOH B 65 365 181 HOH HOH . J 4 HOH C 1 301 3 HOH HOH . J 4 HOH C 2 302 10 HOH HOH . J 4 HOH C 3 303 13 HOH HOH . J 4 HOH C 4 304 15 HOH HOH . J 4 HOH C 5 305 20 HOH HOH . J 4 HOH C 6 306 30 HOH HOH . J 4 HOH C 7 307 31 HOH HOH . J 4 HOH C 8 308 37 HOH HOH . J 4 HOH C 9 309 40 HOH HOH . J 4 HOH C 10 310 51 HOH HOH . J 4 HOH C 11 311 56 HOH HOH . J 4 HOH C 12 312 57 HOH HOH . J 4 HOH C 13 313 65 HOH HOH . J 4 HOH C 14 314 68 HOH HOH . J 4 HOH C 15 315 72 HOH HOH . J 4 HOH C 16 316 74 HOH HOH . J 4 HOH C 17 317 77 HOH HOH . J 4 HOH C 18 318 80 HOH HOH . J 4 HOH C 19 319 81 HOH HOH . J 4 HOH C 20 320 83 HOH HOH . J 4 HOH C 21 321 86 HOH HOH . J 4 HOH C 22 322 88 HOH HOH . J 4 HOH C 23 323 89 HOH HOH . J 4 HOH C 24 324 90 HOH HOH . J 4 HOH C 25 325 92 HOH HOH . J 4 HOH C 26 326 94 HOH HOH . J 4 HOH C 27 327 96 HOH HOH . J 4 HOH C 28 328 101 HOH HOH . J 4 HOH C 29 329 104 HOH HOH . J 4 HOH C 30 330 107 HOH HOH . J 4 HOH C 31 331 108 HOH HOH . J 4 HOH C 32 332 109 HOH HOH . J 4 HOH C 33 333 115 HOH HOH . J 4 HOH C 34 334 116 HOH HOH . J 4 HOH C 35 335 117 HOH HOH . J 4 HOH C 36 336 118 HOH HOH . J 4 HOH C 37 337 125 HOH HOH . J 4 HOH C 38 338 135 HOH HOH . J 4 HOH C 39 339 138 HOH HOH . J 4 HOH C 40 340 140 HOH HOH . J 4 HOH C 41 341 143 HOH HOH . J 4 HOH C 42 342 144 HOH HOH . J 4 HOH C 43 343 145 HOH HOH . J 4 HOH C 44 344 146 HOH HOH . J 4 HOH C 45 345 161 HOH HOH . J 4 HOH C 46 346 162 HOH HOH . J 4 HOH C 47 347 168 HOH HOH . J 4 HOH C 48 348 170 HOH HOH . J 4 HOH C 49 349 178 HOH HOH . J 4 HOH C 50 350 179 HOH HOH . J 4 HOH C 51 351 180 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 PB GDP . . . F 2 14.681 10.319 25.994 1 26.24 ? PB GDP 202 B 1 HETATM 2 O O1B GDP . . . F 2 14.094 11.696 25.921 1 27.25 ? O1B GDP 202 B 1 HETATM 3 O O2B GDP . . . F 2 13.917 9.373 26.9 1 29.5 ? O2B GDP 202 B 1 HETATM 4 O O3B GDP . . . F 2 14.841 9.659 24.631 1 27.37 ? O3B GDP 202 B 1 HETATM 5 O O3A GDP . . . F 2 16.177 10.346 26.586 1 27.66 ? O3A GDP 202 B 1 HETATM 6 P PA GDP . . . F 2 16.928 11.517 27.411 1 28.89 ? PA GDP 202 B 1 HETATM 7 O O1A GDP . . . F 2 16.228 11.683 28.749 1 36.9 ? O1A GDP 202 B 1 HETATM 8 O O2A GDP . . . F 2 17.019 12.814 26.652 1 28.89 ? O2A GDP 202 B 1 HETATM 9 O O5' GDP . . . F 2 18.38 10.918 27.613 1 27.18 ? O5' GDP 202 B 1 HETATM 10 C C5' GDP . . . F 2 18.5 9.684 28.305 1 29.16 ? C5' GDP 202 B 1 HETATM 11 C C4' GDP . . . F 2 19.889 9.593 28.905 1 28.66 ? C4' GDP 202 B 1 HETATM 12 O O4' GDP . . . F 2 20.864 9.534 27.868 1 28.71 ? O4' GDP 202 B 1 HETATM 13 C C3' GDP . . . F 2 20.234 10.82 29.726 1 27.45 ? C3' GDP 202 B 1 HETATM 14 O O3' GDP . . . F 2 20.997 10.355 30.844 1 33 ? O3' GDP 202 B 1 HETATM 15 C C2' GDP . . . F 2 21.063 11.683 28.808 1 28.9 ? C2' GDP 202 B 1 HETATM 16 O O2' GDP . . . F 2 22.045 12.479 29.477 1 34.64 ? O2' GDP 202 B 1 HETATM 17 C C1' GDP . . . F 2 21.754 10.638 27.969 1 28.18 ? C1' GDP 202 B 1 HETATM 18 N N9 GDP . . . F 2 22.065 11.113 26.62 1 27.2 ? N9 GDP 202 B 1 HETATM 19 C C8 GDP . . . F 2 21.197 11.636 25.717 1 23.62 ? C8 GDP 202 B 1 HETATM 20 N N7 GDP . . . F 2 21.845 11.917 24.569 1 22.05 ? N7 GDP 202 B 1 HETATM 21 C C5 GDP . . . F 2 23.138 11.571 24.744 1 24.69 ? C5 GDP 202 B 1 HETATM 22 C C6 GDP . . . F 2 24.348 11.567 23.931 1 22.67 ? C6 GDP 202 B 1 HETATM 23 O O6 GDP . . . F 2 24.327 12.019 22.774 1 25.87 ? O6 GDP 202 B 1 HETATM 24 N N1 GDP . . . F 2 25.478 11.106 24.528 1 22.58 ? N1 GDP 202 B 1 HETATM 25 C C2 GDP . . . F 2 25.51 10.605 25.77 1 23.86 ? C2 GDP 202 B 1 HETATM 26 N N2 GDP . . . F 2 26.68 10.148 26.279 1 30.03 ? N2 GDP 202 B 1 HETATM 27 N N3 GDP . . . F 2 24.446 10.56 26.563 1 24.17 ? N3 GDP 202 B 1 HETATM 28 C C4 GDP . . . F 2 23.258 11.013 26.09 1 25.08 ? C4 GDP 202 B 1 HETATM 29 H H5' GDP . . . F 2 17.749 9.626 29.095 1 35 ? H5' GDP 202 B 1 HETATM 30 H "H5''" GDP . . . F 2 18.338 8.853 27.615 1 35 ? "H5''" GDP 202 B 1 HETATM 31 H H4' GDP . . . F 2 19.952 8.7 29.542 1 34.39 ? H4' GDP 202 B 1 HETATM 32 H H3' GDP . . . F 2 19.321 11.346 30.04 1 32.94 ? H3' GDP 202 B 1 HETATM 33 H HO3' GDP . . . F 2 21.252 11.108 31.395 1 39.6 ? HO3' GDP 202 B 1 HETATM 34 H H2' GDP . . . F 2 20.408 12.299 28.176 1 34.68 ? H2' GDP 202 B 1 HETATM 35 H HO2' GDP . . . F 2 21.604 13.11 30.063 1 41.57 ? HO2' GDP 202 B 1 HETATM 36 H H1' GDP . . . F 2 22.677 10.329 28.479 1 33.82 ? H1' GDP 202 B 1 HETATM 37 H H8 GDP . . . F 2 20.144 11.814 25.897 1 28.35 ? H8 GDP 202 B 1 HETATM 38 H HN1 GDP . . . F 2 26.358 11.098 23.973 1 27.1 ? HN1 GDP 202 B 1 HETATM 39 H HN21 GDP . . . F 2 26.713 9.784 27.221 1 36.04 ? HN21 GDP 202 B 1 HETATM 40 H HN22 GDP . . . F 2 27.518 10.167 25.716 1 36.04 ? HN22 GDP 202 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #