data_4M1T # _model_server_result.job_id YyNIHsZWu3u6DeXcHlx2Ig _model_server_result.datetime_utc '2024-11-22 12:37:57' _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 4m1t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":201}' # _entry.id 4M1T # _exptl.entry_id 4M1T _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 110.63 _cell.angle_gamma 90 _cell.entry_id 4M1T _cell.length_a 68.166 _cell.length_b 83.48 _cell.length_c 85.747 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M1T _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 C16 _struct_conn.ptnr2_label_comp_id 21M _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id 21M _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 1.831 _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 128 n n PB O2B GDP sing 129 n n PB O3B GDP sing 130 n n PB O3A GDP sing 131 n n O2B HOB2 GDP sing 132 n n O3B HOB3 GDP sing 133 n n O3A PA GDP sing 134 n n PA O1A GDP doub 135 n n PA O2A GDP sing 136 n n PA O5' GDP sing 137 n n O2A HOA2 GDP sing 138 n n O5' C5' GDP sing 139 n n C5' C4' GDP sing 140 n n C5' H5' GDP sing 141 n n C5' "H5''" GDP sing 142 n n C4' O4' GDP sing 143 n n C4' C3' GDP sing 144 n n C4' H4' GDP sing 145 n n O4' C1' GDP sing 146 n n C3' O3' GDP sing 147 n n C3' C2' GDP sing 148 n n C3' H3' GDP sing 149 n n O3' HO3' GDP sing 150 n n C2' O2' GDP sing 151 n n C2' C1' GDP sing 152 n n C2' H2' GDP sing 153 n n O2' HO2' GDP sing 154 n n C1' N9 GDP sing 155 n n C1' H1' GDP sing 156 n n N9 C8 GDP sing 157 n y N9 C4 GDP sing 158 n y C8 N7 GDP doub 159 n y C8 H8 GDP sing 160 n n N7 C5 GDP sing 161 n y C5 C6 GDP sing 162 n n C5 C4 GDP doub 163 n y C6 O6 GDP doub 164 n n C6 N1 GDP sing 165 n n N1 C2 GDP sing 166 n n N1 HN1 GDP sing 167 n n C2 N2 GDP sing 168 n n C2 N3 GDP doub 169 n n N2 HN21 GDP sing 170 n n N2 HN22 GDP sing 171 n n N3 C4 GDP sing 172 n n # _atom_sites.entry_id 4M1T _atom_sites.fract_transf_matrix[1][1] 0.01467 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005523 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011979 _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] 0.012461 _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 21M B 1 201 210 21M 31A . 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 3 HOH HOH . H 4 HOH A 4 304 5 HOH HOH . H 4 HOH A 5 305 8 HOH HOH . H 4 HOH A 6 306 9 HOH HOH . H 4 HOH A 7 307 11 HOH HOH . H 4 HOH A 8 308 14 HOH HOH . H 4 HOH A 9 309 15 HOH HOH . H 4 HOH A 10 310 20 HOH HOH . H 4 HOH A 11 311 24 HOH HOH . H 4 HOH A 12 312 25 HOH HOH . H 4 HOH A 13 313 33 HOH HOH . H 4 HOH A 14 314 34 HOH HOH . H 4 HOH A 15 315 37 HOH HOH . H 4 HOH A 16 316 38 HOH HOH . H 4 HOH A 17 317 39 HOH HOH . H 4 HOH A 18 318 40 HOH HOH . H 4 HOH A 19 319 41 HOH HOH . H 4 HOH A 20 320 45 HOH HOH . H 4 HOH A 21 321 50 HOH HOH . H 4 HOH A 22 322 52 HOH HOH . H 4 HOH A 23 323 55 HOH HOH . H 4 HOH A 24 324 57 HOH HOH . H 4 HOH A 25 325 58 HOH HOH . H 4 HOH A 26 326 60 HOH HOH . H 4 HOH A 27 327 64 HOH HOH . H 4 HOH A 28 328 68 HOH HOH . H 4 HOH A 29 329 70 HOH HOH . H 4 HOH A 30 330 71 HOH HOH . H 4 HOH A 31 331 72 HOH HOH . H 4 HOH A 32 332 73 HOH HOH . H 4 HOH A 33 333 74 HOH HOH . H 4 HOH A 34 334 77 HOH HOH . H 4 HOH A 35 335 78 HOH HOH . H 4 HOH A 36 336 81 HOH HOH . H 4 HOH A 37 337 82 HOH HOH . H 4 HOH A 38 338 88 HOH HOH . H 4 HOH A 39 339 92 HOH HOH . H 4 HOH A 40 340 93 HOH HOH . H 4 HOH A 41 341 98 HOH HOH . H 4 HOH A 42 342 100 HOH HOH . H 4 HOH A 43 343 101 HOH HOH . H 4 HOH A 44 344 106 HOH HOH . H 4 HOH A 45 345 107 HOH HOH . H 4 HOH A 46 346 108 HOH HOH . H 4 HOH A 47 347 110 HOH HOH . H 4 HOH A 48 348 113 HOH HOH . H 4 HOH A 49 349 116 HOH HOH . H 4 HOH A 50 350 118 HOH HOH . H 4 HOH A 51 351 120 HOH HOH . H 4 HOH A 52 352 121 HOH HOH . H 4 HOH A 53 353 124 HOH HOH . H 4 HOH A 54 354 126 HOH HOH . H 4 HOH A 55 355 127 HOH HOH . H 4 HOH A 56 356 128 HOH HOH . H 4 HOH A 57 357 129 HOH HOH . H 4 HOH A 58 358 132 HOH HOH . H 4 HOH A 59 359 133 HOH HOH . H 4 HOH A 60 360 134 HOH HOH . H 4 HOH A 61 361 138 HOH HOH . H 4 HOH A 62 362 139 HOH HOH . H 4 HOH A 63 363 140 HOH HOH . H 4 HOH A 64 364 142 HOH HOH . H 4 HOH A 65 365 143 HOH HOH . H 4 HOH A 66 366 147 HOH HOH . H 4 HOH A 67 367 154 HOH HOH . H 4 HOH A 68 368 156 HOH HOH . H 4 HOH A 69 369 159 HOH HOH . H 4 HOH A 70 370 162 HOH HOH . H 4 HOH A 71 371 163 HOH HOH . I 4 HOH B 1 301 6 HOH HOH . I 4 HOH B 2 302 10 HOH HOH . I 4 HOH B 3 303 12 HOH HOH . I 4 HOH B 4 304 13 HOH HOH . I 4 HOH B 5 305 16 HOH HOH . I 4 HOH B 6 306 19 HOH HOH . I 4 HOH B 7 307 21 HOH HOH . I 4 HOH B 8 308 26 HOH HOH . I 4 HOH B 9 309 27 HOH HOH . I 4 HOH B 10 310 30 HOH HOH . I 4 HOH B 11 311 31 HOH HOH . I 4 HOH B 12 312 35 HOH HOH . I 4 HOH B 13 313 36 HOH HOH . I 4 HOH B 14 314 42 HOH HOH . I 4 HOH B 15 315 43 HOH HOH . I 4 HOH B 16 316 46 HOH HOH . I 4 HOH B 17 317 49 HOH HOH . I 4 HOH B 18 318 54 HOH HOH . I 4 HOH B 19 319 56 HOH HOH . I 4 HOH B 20 320 59 HOH HOH . I 4 HOH B 21 321 61 HOH HOH . I 4 HOH B 22 322 67 HOH HOH . I 4 HOH B 23 323 69 HOH HOH . I 4 HOH B 24 324 75 HOH HOH . I 4 HOH B 25 325 80 HOH HOH . I 4 HOH B 26 326 84 HOH HOH . I 4 HOH B 27 327 86 HOH HOH . I 4 HOH B 28 328 87 HOH HOH . I 4 HOH B 29 329 89 HOH HOH . I 4 HOH B 30 330 91 HOH HOH . I 4 HOH B 31 331 103 HOH HOH . I 4 HOH B 32 332 111 HOH HOH . I 4 HOH B 33 333 112 HOH HOH . I 4 HOH B 34 334 114 HOH HOH . I 4 HOH B 35 335 115 HOH HOH . I 4 HOH B 36 336 122 HOH HOH . I 4 HOH B 37 337 125 HOH HOH . I 4 HOH B 38 338 135 HOH HOH . I 4 HOH B 39 339 136 HOH HOH . I 4 HOH B 40 340 137 HOH HOH . I 4 HOH B 41 341 148 HOH HOH . I 4 HOH B 42 342 149 HOH HOH . I 4 HOH B 43 343 150 HOH HOH . I 4 HOH B 44 344 152 HOH HOH . I 4 HOH B 45 345 155 HOH HOH . I 4 HOH B 46 346 157 HOH HOH . I 4 HOH B 47 347 158 HOH HOH . I 4 HOH B 48 348 160 HOH HOH . I 4 HOH B 49 349 161 HOH HOH . J 4 HOH C 1 301 4 HOH HOH . J 4 HOH C 2 302 7 HOH HOH . J 4 HOH C 3 303 17 HOH HOH . J 4 HOH C 4 304 18 HOH HOH . J 4 HOH C 5 305 22 HOH HOH . J 4 HOH C 6 306 23 HOH HOH . J 4 HOH C 7 307 28 HOH HOH . J 4 HOH C 8 308 29 HOH HOH . J 4 HOH C 9 309 32 HOH HOH . J 4 HOH C 10 310 44 HOH HOH . J 4 HOH C 11 311 47 HOH HOH . J 4 HOH C 12 312 48 HOH HOH . J 4 HOH C 13 313 51 HOH HOH . J 4 HOH C 14 314 53 HOH HOH . J 4 HOH C 15 315 62 HOH HOH . J 4 HOH C 16 316 63 HOH HOH . J 4 HOH C 17 317 65 HOH HOH . J 4 HOH C 18 318 66 HOH HOH . J 4 HOH C 19 319 76 HOH HOH . J 4 HOH C 20 320 79 HOH HOH . J 4 HOH C 21 321 83 HOH HOH . J 4 HOH C 22 322 85 HOH HOH . J 4 HOH C 23 323 90 HOH HOH . J 4 HOH C 24 324 94 HOH HOH . J 4 HOH C 25 325 95 HOH HOH . J 4 HOH C 26 326 96 HOH HOH . J 4 HOH C 27 327 97 HOH HOH . J 4 HOH C 28 328 99 HOH HOH . J 4 HOH C 29 329 102 HOH HOH . J 4 HOH C 30 330 104 HOH HOH . J 4 HOH C 31 331 105 HOH HOH . J 4 HOH C 32 332 109 HOH HOH . J 4 HOH C 33 333 117 HOH HOH . J 4 HOH C 34 334 119 HOH HOH . J 4 HOH C 35 335 123 HOH HOH . J 4 HOH C 36 336 130 HOH HOH . J 4 HOH C 37 337 131 HOH HOH . J 4 HOH C 38 338 141 HOH HOH . J 4 HOH C 39 339 144 HOH HOH . J 4 HOH C 40 340 145 HOH HOH . J 4 HOH C 41 341 146 HOH HOH . J 4 HOH C 42 342 151 HOH HOH . J 4 HOH C 43 343 153 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 . . . G 2 -9.002 28.962 37.877 1 26.56 ? PB GDP 201 C 1 HETATM 2 O O1B GDP . . . G 2 -8.206 30.032 37.154 1 25.43 ? O1B GDP 201 C 1 HETATM 3 O O2B GDP . . . G 2 -10.451 29.414 37.906 1 28.6 ? O2B GDP 201 C 1 HETATM 4 O O3B GDP . . . G 2 -8.465 28.722 39.279 1 24.44 ? O3B GDP 201 C 1 HETATM 5 O O3A GDP . . . G 2 -8.916 27.647 36.976 1 21.06 ? O3A GDP 201 C 1 HETATM 6 P PA GDP . . . G 2 -8.753 26.136 37.501 1 28.85 ? PA GDP 201 C 1 HETATM 7 O O1A GDP . . . G 2 -7.414 25.878 38.154 1 32.27 ? O1A GDP 201 C 1 HETATM 8 O O2A GDP . . . G 2 -9.911 25.77 38.403 1 40.91 ? O2A GDP 201 C 1 HETATM 9 O O5' GDP . . . G 2 -8.833 25.32 36.133 1 22.93 ? O5' GDP 201 C 1 HETATM 10 C C5' GDP . . . G 2 -10.076 25.319 35.421 1 34.26 ? C5' GDP 201 C 1 HETATM 11 C C4' GDP . . . G 2 -10.193 24.08 34.542 1 35.3 ? C4' GDP 201 C 1 HETATM 12 O O4' GDP . . . G 2 -9.146 24.097 33.571 1 30.88 ? O4' GDP 201 C 1 HETATM 13 C C3' GDP . . . G 2 -10.041 22.79 35.335 1 30.14 ? C3' GDP 201 C 1 HETATM 14 O O3' GDP . . . G 2 -10.873 21.788 34.74 1 29.58 ? O3' GDP 201 C 1 HETATM 15 C C2' GDP . . . G 2 -8.602 22.394 35.11 1 40.52 ? C2' GDP 201 C 1 HETATM 16 O O2' GDP . . . G 2 -8.399 20.98 35.141 1 42.3 ? O2' GDP 201 C 1 HETATM 17 C C1' GDP . . . G 2 -8.345 22.922 33.716 1 34.92 ? C1' GDP 201 C 1 HETATM 18 N N9 GDP . . . G 2 -6.925 23.274 33.56 1 26.92 ? N9 GDP 201 C 1 HETATM 19 C C8 GDP . . . G 2 -6.189 24.088 34.339 1 28.03 ? C8 GDP 201 C 1 HETATM 20 N N7 GDP . . . G 2 -4.926 24.176 33.854 1 22.15 ? N7 GDP 201 C 1 HETATM 21 C C5 GDP . . . G 2 -4.848 23.419 32.742 1 18.76 ? C5 GDP 201 C 1 HETATM 22 C C6 GDP . . . G 2 -3.832 23.056 31.731 1 23.91 ? C6 GDP 201 C 1 HETATM 23 O O6 GDP . . . G 2 -2.663 23.494 31.774 1 25.38 ? O6 GDP 201 C 1 HETATM 24 N N1 GDP . . . G 2 -4.21 22.24 30.751 1 21.76 ? N1 GDP 201 C 1 HETATM 25 C C2 GDP . . . G 2 -5.45 21.737 30.646 1 24.56 ? C2 GDP 201 C 1 HETATM 26 N N2 GDP . . . G 2 -5.747 20.913 29.616 1 27.46 ? N2 GDP 201 C 1 HETATM 27 N N3 GDP . . . G 2 -6.421 22.024 31.522 1 20.77 ? N3 GDP 201 C 1 HETATM 28 C C4 GDP . . . G 2 -6.184 22.838 32.562 1 20.87 ? C4 GDP 201 C 1 HETATM 29 H H8 GDP . . . G 2 -6.549 24.59 35.229 1 33.63 ? H8 GDP 201 C 1 HETATM 30 H HN1 GDP . . . G 2 -3.507 21.973 30.033 1 26.11 ? HN1 GDP 201 C 1 HETATM 31 H HN21 GDP . . . G 2 -5.037 20.678 28.937 1 32.95 ? HN21 GDP 201 C 1 HETATM 32 H HN22 GDP . . . G 2 -6.678 20.532 29.527 1 32.95 ? HN22 GDP 201 C 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #