data_3O3P # _model_server_result.job_id F7y--l1gsG2jkmYeV5aIhg _model_server_result.datetime_utc '2024-11-05 00:19:58' _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 3o3p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":340}' # _entry.id 3O3P # _exptl.entry_id 3O3P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 605.341 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _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 3O3P _cell.length_a 108.37 _cell.length_b 108.37 _cell.length_c 311.96 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3O3P _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 4 _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 OD2 ASP 189 A ASP 137 1_555 F MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc2 A OD1 ASN 308 A ASN 256 1_555 F MG MG . A MG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc3 A O GLN 351 A GLN 299 1_555 E MG MG . A MG 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc4 A O ASP 354 A ASP 302 1_555 E MG MG . A MG 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc5 E MG MG . A MG 338 1_555 I O HOH . A HOH 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc6 E MG MG . A MG 338 1_555 I O HOH . A HOH 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc7 E MG MG . A MG 338 1_555 J O HOH . B HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc8 E MG MG . A MG 338 1_555 J O HOH . B HOH 373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc9 F MG MG . A MG 339 1_555 G O2B GDD . A GDD 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc10 F MG MG . A MG 339 1_555 G O2A GDD . A GDD 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? # _chem_comp.formula 'C16 H25 N5 O16 P2' _chem_comp.formula_weight 605.341 _chem_comp.id GDD _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _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 N2 C2 GDD sing 83 n n N2 H2N1 GDD sing 84 n n N2 H2N2 GDD sing 85 n n C2 N1 GDD sing 86 n n C2 N3 GDD doub 87 n n N1 C6 GDD sing 88 n n N1 H1 GDD sing 89 n n N3 C4 GDD sing 90 n n C4 C5 GDD doub 91 n y C4 N9 GDD sing 92 n y C5 C6 GDD sing 93 n n C5 N7 GDD sing 94 n y C6 O6 GDD doub 95 n n N7 C8 GDD doub 96 n y C8 N9 GDD sing 97 n y C8 H8 GDD sing 98 n n N9 C1' GDD sing 99 n n C1' C2' GDD sing 100 n n C1' O4' GDD sing 101 n n C1' H1' GDD sing 102 n n C2' O2' GDD sing 103 n n C2' C3' GDD sing 104 n n C2' H2' GDD sing 105 n n O2' HA GDD sing 106 n n C3' O3' GDD sing 107 n n C3' C4' GDD sing 108 n n C3' H3' GDD sing 109 n n O3' HB GDD sing 110 n n C4' O4' GDD sing 111 n n C4' C5' GDD sing 112 n n C4' H4' GDD sing 113 n n C5' O5' GDD sing 114 n n C5' "H5'1" GDD sing 115 n n C5' "H5'2" GDD sing 116 n n O5' PA GDD sing 117 n n PA O1A GDD doub 118 n n PA O2A GDD sing 119 n n PA O3A GDD sing 120 n n O2A HO2A GDD sing 121 n n O3A PB GDD sing 122 n n PB O2B GDD sing 123 n n PB O3B GDD doub 124 n n PB O1B GDD sing 125 n n O2B HO2B GDD sing 126 n n O1B C11 GDD sing 127 n n C11 O51 GDD sing 128 n n C11 C21 GDD sing 129 n n C11 H11 GDD sing 130 n n O51 C51 GDD sing 131 n n C51 C61 GDD sing 132 n n C51 C41 GDD sing 133 n n C51 H51 GDD sing 134 n n C61 O6A GDD sing 135 n n C61 H611 GDD sing 136 n n C61 H612 GDD sing 137 n n O6A H6A GDD sing 138 n n C21 O21 GDD sing 139 n n C21 C31 GDD sing 140 n n C21 H21 GDD sing 141 n n O21 HC GDD sing 142 n n C31 O31 GDD sing 143 n n C31 C41 GDD sing 144 n n C31 H31 GDD sing 145 n n O31 HD GDD sing 146 n n C41 O41 GDD sing 147 n n C41 H41 GDD sing 148 n n O41 HE GDD sing 149 n n # _atom_sites.entry_id 3O3P _atom_sites.fract_transf_matrix[1][1] 0.009228 _atom_sites.fract_transf_matrix[1][2] 0.005328 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010655 _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] 0.003206 _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 CL A 1 336 1 CL CL . D 2 CL A 1 337 1 CL CL . E 3 MG A 1 338 1 MG MG . F 3 MG A 1 339 1 MG MG . G 4 GDD A 1 340 1 GDD GDD . H 5 GDP B 1 336 1 GDP GDP . I 6 HOH A 1 341 1 HOH HOH . I 6 HOH A 2 342 2 HOH HOH . I 6 HOH A 3 343 3 HOH HOH . I 6 HOH A 4 344 8 HOH HOH . I 6 HOH A 5 345 9 HOH HOH . I 6 HOH A 6 346 10 HOH HOH . I 6 HOH A 7 347 11 HOH HOH . I 6 HOH A 8 348 16 HOH HOH . I 6 HOH A 9 349 18 HOH HOH . I 6 HOH A 10 350 21 HOH HOH . I 6 HOH A 11 351 24 HOH HOH . I 6 HOH A 12 352 26 HOH HOH . I 6 HOH A 13 353 31 HOH HOH . I 6 HOH A 14 354 32 HOH HOH . I 6 HOH A 15 355 33 HOH HOH . I 6 HOH A 16 356 34 HOH HOH . I 6 HOH A 17 357 36 HOH HOH . I 6 HOH A 18 358 37 HOH HOH . I 6 HOH A 19 359 39 HOH HOH . I 6 HOH A 20 360 43 HOH HOH . I 6 HOH A 21 361 44 HOH HOH . I 6 HOH A 22 362 45 HOH HOH . I 6 HOH A 23 363 47 HOH HOH . I 6 HOH A 24 364 48 HOH HOH . I 6 HOH A 25 365 52 HOH HOH . I 6 HOH A 26 366 53 HOH HOH . I 6 HOH A 27 367 55 HOH HOH . I 6 HOH A 28 368 56 HOH HOH . I 6 HOH A 29 369 57 HOH HOH . I 6 HOH A 30 370 58 HOH HOH . I 6 HOH A 31 371 59 HOH HOH . I 6 HOH A 32 372 61 HOH HOH . I 6 HOH A 33 373 62 HOH HOH . I 6 HOH A 34 374 63 HOH HOH . I 6 HOH A 35 375 65 HOH HOH . I 6 HOH A 36 376 69 HOH HOH . I 6 HOH A 37 377 70 HOH HOH . I 6 HOH A 38 378 73 HOH HOH . I 6 HOH A 39 379 76 HOH HOH . I 6 HOH A 40 380 80 HOH HOH . I 6 HOH A 41 381 82 HOH HOH . I 6 HOH A 42 382 83 HOH HOH . I 6 HOH A 43 383 84 HOH HOH . I 6 HOH A 44 384 85 HOH HOH . I 6 HOH A 45 385 86 HOH HOH . I 6 HOH A 46 386 87 HOH HOH . I 6 HOH A 47 387 88 HOH HOH . I 6 HOH A 48 388 90 HOH HOH . I 6 HOH A 49 389 92 HOH HOH . I 6 HOH A 50 390 94 HOH HOH . I 6 HOH A 51 391 96 HOH HOH . I 6 HOH A 52 392 98 HOH HOH . I 6 HOH A 53 394 100 HOH HOH . I 6 HOH A 54 395 109 HOH HOH . I 6 HOH A 55 396 114 HOH HOH . I 6 HOH A 56 397 115 HOH HOH . I 6 HOH A 57 398 116 HOH HOH . I 6 HOH A 58 399 117 HOH HOH . I 6 HOH A 59 400 118 HOH HOH . I 6 HOH A 60 401 121 HOH HOH . I 6 HOH A 61 402 122 HOH HOH . I 6 HOH A 62 403 126 HOH HOH . I 6 HOH A 63 404 128 HOH HOH . I 6 HOH A 64 405 130 HOH HOH . I 6 HOH A 65 406 131 HOH HOH . I 6 HOH A 66 407 134 HOH HOH . I 6 HOH A 67 408 137 HOH HOH . J 6 HOH B 1 337 4 HOH HOH . J 6 HOH B 2 338 5 HOH HOH . J 6 HOH B 3 339 6 HOH HOH . J 6 HOH B 4 340 7 HOH HOH . J 6 HOH B 5 341 12 HOH HOH . J 6 HOH B 6 342 13 HOH HOH . J 6 HOH B 7 343 14 HOH HOH . J 6 HOH B 8 344 15 HOH HOH . J 6 HOH B 9 345 17 HOH HOH . J 6 HOH B 10 346 19 HOH HOH . J 6 HOH B 11 347 22 HOH HOH . J 6 HOH B 12 348 23 HOH HOH . J 6 HOH B 13 349 25 HOH HOH . J 6 HOH B 14 350 27 HOH HOH . J 6 HOH B 15 351 28 HOH HOH . J 6 HOH B 16 352 29 HOH HOH . J 6 HOH B 17 353 30 HOH HOH . J 6 HOH B 18 354 38 HOH HOH . J 6 HOH B 19 355 40 HOH HOH . J 6 HOH B 20 356 41 HOH HOH . J 6 HOH B 21 357 42 HOH HOH . J 6 HOH B 22 358 46 HOH HOH . J 6 HOH B 23 359 50 HOH HOH . J 6 HOH B 24 360 51 HOH HOH . J 6 HOH B 25 361 54 HOH HOH . J 6 HOH B 26 362 60 HOH HOH . J 6 HOH B 27 363 64 HOH HOH . J 6 HOH B 28 364 66 HOH HOH . J 6 HOH B 29 365 67 HOH HOH . J 6 HOH B 30 366 68 HOH HOH . J 6 HOH B 31 367 72 HOH HOH . J 6 HOH B 32 368 74 HOH HOH . J 6 HOH B 33 369 75 HOH HOH . J 6 HOH B 34 370 77 HOH HOH . J 6 HOH B 35 371 78 HOH HOH . J 6 HOH B 36 372 79 HOH HOH . J 6 HOH B 37 373 95 HOH HOH . J 6 HOH B 38 374 97 HOH HOH . J 6 HOH B 39 375 101 HOH HOH . J 6 HOH B 40 376 102 HOH HOH . J 6 HOH B 41 377 103 HOH HOH . J 6 HOH B 42 378 104 HOH HOH . J 6 HOH B 43 379 105 HOH HOH . J 6 HOH B 44 380 106 HOH HOH . J 6 HOH B 45 381 110 HOH HOH . J 6 HOH B 46 382 111 HOH HOH . J 6 HOH B 47 383 112 HOH HOH . J 6 HOH B 48 384 113 HOH HOH . J 6 HOH B 49 385 119 HOH HOH . J 6 HOH B 50 386 120 HOH HOH . J 6 HOH B 51 387 123 HOH HOH . J 6 HOH B 52 388 124 HOH HOH . J 6 HOH B 53 389 125 HOH HOH . J 6 HOH B 54 390 127 HOH HOH . J 6 HOH B 55 391 129 HOH HOH . J 6 HOH B 56 392 132 HOH HOH . J 6 HOH B 57 393 99 HOH HOH . J 6 HOH B 58 394 135 HOH HOH . J 6 HOH B 59 395 136 HOH HOH . J 6 HOH B 60 396 138 HOH HOH . J 6 HOH B 61 397 139 HOH HOH . J 6 HOH B 62 398 140 HOH HOH . J 6 HOH B 63 399 133 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 N N2 GDD . . . G 4 47.415 -23.929 -12.81 1 29.36 ? N2 GDD 340 A 1 HETATM 2 C C2 GDD . . . G 4 46.239 -24.211 -12.034 1 37.88 ? C2 GDD 340 A 1 HETATM 3 N N1 GDD . . . G 4 45.385 -25.164 -12.415 1 44.86 ? N1 GDD 340 A 1 HETATM 4 N N3 GDD . . . G 4 46 -23.468 -10.902 1 37.69 ? N3 GDD 340 A 1 HETATM 5 C C4 GDD . . . G 4 44.877 -23.697 -10.146 1 39.13 ? C4 GDD 340 A 1 HETATM 6 C C5 GDD . . . G 4 43.981 -24.675 -10.515 1 38.14 ? C5 GDD 340 A 1 HETATM 7 C C6 GDD . . . G 4 44.26 -25.429 -11.703 1 37.97 ? C6 GDD 340 A 1 HETATM 8 O O6 GDD . . . G 4 43.5 -26.282 -12.062 1 30.98 ? O6 GDD 340 A 1 HETATM 9 N N7 GDD . . . G 4 42.98 -24.667 -9.587 1 36.9 ? N7 GDD 340 A 1 HETATM 10 C C8 GDD . . . G 4 43.27 -23.683 -8.651 1 37.86 ? C8 GDD 340 A 1 HETATM 11 N N9 GDD . . . G 4 44.394 -23.095 -8.978 1 37.01 ? N9 GDD 340 A 1 HETATM 12 C C1' GDD . . . G 4 45.06 -22.044 -8.275 1 35.38 ? C1' GDD 340 A 1 HETATM 13 C C2' GDD . . . G 4 44.2 -20.892 -7.952 1 38.4 ? C2' GDD 340 A 1 HETATM 14 O O2' GDD . . . G 4 44.189 -20.033 -9.047 1 38.67 ? O2' GDD 340 A 1 HETATM 15 C C3' GDD . . . G 4 44.83 -20.335 -6.738 1 47.02 ? C3' GDD 340 A 1 HETATM 16 O O3' GDD . . . G 4 45.844 -19.488 -7.064 1 50.43 ? O3' GDD 340 A 1 HETATM 17 C C4' GDD . . . G 4 45.371 -21.515 -6.017 1 46.99 ? C4' GDD 340 A 1 HETATM 18 O O4' GDD . . . G 4 45.608 -22.497 -6.985 1 46.64 ? O4' GDD 340 A 1 HETATM 19 C C5' GDD . . . G 4 44.439 -21.921 -4.838 1 44.07 ? C5' GDD 340 A 1 HETATM 20 O O5' GDD . . . G 4 43.45 -22.695 -5.301 1 46.61 ? O5' GDD 340 A 1 HETATM 21 P PA GDD . . . G 4 41.991 -22.494 -4.702 1 52.3 ? PA GDD 340 A 1 HETATM 22 O O1A GDD . . . G 4 40.918 -23.101 -5.641 1 48.51 ? O1A GDD 340 A 1 HETATM 23 O O2A GDD . . . G 4 41.768 -20.995 -4.519 1 53.84 ? O2A GDD 340 A 1 HETATM 24 O O3A GDD . . . G 4 41.97 -23.218 -3.314 1 171.46 ? O3A GDD 340 A 1 HETATM 25 P PB GDD . . . G 4 41.223 -22.61 -1.998 1 69.79 ? PB GDD 340 A 1 HETATM 26 O O2B GDD . . . G 4 41.855 -21.25 -1.607 1 74.01 ? O2B GDD 340 A 1 HETATM 27 O O3B GDD . . . G 4 39.717 -22.384 -2.326 1 72.05 ? O3B GDD 340 A 1 HETATM 28 O O1B GDD . . . G 4 41.337 -23.619 -0.82 1 93.02 ? O1B GDD 340 A 1 HETATM 29 C C11 GDD . . . G 4 42.532 -23.995 -0.192 1 84.7 ? C11 GDD 340 A 1 HETATM 30 O O51 GDD . . . G 4 42.584 -25.436 0.161 1 79.73 ? O51 GDD 340 A 1 HETATM 31 C C51 GDD . . . G 4 43.017 -26.28 -0.863 1 79.57 ? C51 GDD 340 A 1 HETATM 32 C C61 GDD . . . G 4 43.14 -27.736 -0.389 1 73.3 ? C61 GDD 340 A 1 HETATM 33 O O6A GDD . . . G 4 44.159 -28.371 -0.97 1 71.05 ? O6A GDD 340 A 1 HETATM 34 C C21 GDD . . . G 4 43.778 -23.497 -0.872 1 85.13 ? C21 GDD 340 A 1 HETATM 35 O O21 GDD . . . G 4 44.717 -23.299 0.176 1 78.54 ? O21 GDD 340 A 1 HETATM 36 C C31 GDD . . . G 4 44.363 -24.399 -1.839 1 88.53 ? C31 GDD 340 A 1 HETATM 37 O O31 GDD . . . G 4 45.724 -24.051 -2.079 1 84.16 ? O31 GDD 340 A 1 HETATM 38 C C41 GDD . . . G 4 44.336 -25.818 -1.507 1 86.09 ? C41 GDD 340 A 1 HETATM 39 O O41 GDD . . . G 4 44.693 -26.544 -2.684 1 78.97 ? O41 GDD 340 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #