data_4M1T # _model_server_result.job_id yiX5XMBHwhxpebKOOpn3hw _model_server_result.datetime_utc '2024-11-25 18:07:28' _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":"D","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 . . . D 2 28.326 26.746 -17.444 1 18.14 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 2 28.521 27.277 -18.852 1 20.72 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 2 29.376 25.7 -17.142 1 20.93 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 2 26.928 26.22 -17.261 1 16.19 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 2 28.403 27.987 -16.419 1 21.4 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 2 29.639 28.394 -15.46 1 20.34 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 2 30.861 28.704 -16.306 1 28.07 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 2 29.938 27.358 -14.419 1 20.83 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 2 29.073 29.723 -14.786 1 18.64 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 2 28.814 30.893 -15.559 1 22.92 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 2 28.908 32.116 -14.657 1 29.81 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 2 27.936 32.048 -13.61 1 22.42 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 2 30.255 32.173 -13.96 1 27.61 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 2 30.604 33.555 -13.822 1 28.26 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 2 29.996 31.604 -12.586 1 21.66 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 2 30.865 32.185 -11.608 1 27.73 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 2 28.58 32.064 -12.337 1 21.55 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 2 27.829 31.158 -11.468 1 20.34 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 2 27.656 29.837 -11.642 1 16.77 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 2 26.882 29.335 -10.657 1 16.6 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 2 26.522 30.363 -9.858 1 16.1 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 2 25.706 30.541 -8.653 1 15.77 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 2 25.104 29.582 -8.11 1 15.95 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 2 25.62 31.789 -8.174 1 18.71 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 2 26.229 32.852 -8.725 1 19.69 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 2 26.079 34.074 -8.158 1 22.1 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 2 26.981 32.768 -9.82 1 17.89 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 2 27.153 31.564 -10.411 1 16.61 ? C4 GDP 201 A 1 HETATM 29 H H8 GDP . . . D 2 28.102 29.253 -12.437 1 20.12 ? H8 GDP 201 A 1 HETATM 30 H HN1 GDP . . . D 2 25.05 31.943 -7.317 1 22.45 ? HN1 GDP 201 A 1 HETATM 31 H HN21 GDP . . . D 2 25.514 34.179 -7.328 1 26.52 ? HN21 GDP 201 A 1 HETATM 32 H HN22 GDP . . . D 2 26.529 34.879 -8.568 1 26.52 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #