data_3MD0 # _model_server_result.job_id 4cJzepBEIXoyco2k8J6-RQ _model_server_result.datetime_utc '2024-12-03 15:37:17' _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 3md0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":335}' # _entry.id 3MD0 # _exptl.entry_id 3MD0 _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 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 90 _cell.entry_id 3MD0 _cell.length_a 65.53 _cell.length_b 187.36 _cell.length_c 66.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MD0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -33.1 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 3MD0 _atom_sites.fract_transf_matrix[1][1] 0.01526 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005337 _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] 0.015106 _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 B 2 GDP A 1 335 335 GDP GDP . C 3 UNX A 1 336 336 UNX UNX . D 3 UNX A 1 337 337 UNX UNX . E 3 UNX A 1 338 338 UNX UNX . F 3 UNX A 1 339 339 UNX UNX . G 4 HOH A 1 340 340 HOH HOH . G 4 HOH A 2 341 341 HOH HOH . G 4 HOH A 3 342 342 HOH HOH . G 4 HOH A 4 343 343 HOH HOH . G 4 HOH A 5 344 344 HOH HOH . G 4 HOH A 6 345 345 HOH HOH . G 4 HOH A 7 346 346 HOH HOH . G 4 HOH A 8 347 347 HOH HOH . G 4 HOH A 9 348 348 HOH HOH . G 4 HOH A 10 349 349 HOH HOH . G 4 HOH A 11 350 350 HOH HOH . G 4 HOH A 12 351 351 HOH HOH . G 4 HOH A 13 352 352 HOH HOH . G 4 HOH A 14 353 353 HOH HOH . G 4 HOH A 15 354 354 HOH HOH . G 4 HOH A 16 355 355 HOH HOH . G 4 HOH A 17 356 356 HOH HOH . G 4 HOH A 18 357 357 HOH HOH . G 4 HOH A 19 358 358 HOH HOH . G 4 HOH A 20 359 359 HOH HOH . G 4 HOH A 21 360 360 HOH HOH . G 4 HOH A 22 361 361 HOH HOH . G 4 HOH A 23 362 362 HOH HOH . G 4 HOH A 24 363 363 HOH HOH . G 4 HOH A 25 364 364 HOH HOH . G 4 HOH A 26 365 365 HOH HOH . G 4 HOH A 27 366 366 HOH HOH . G 4 HOH A 28 367 367 HOH HOH . G 4 HOH A 29 368 368 HOH HOH . G 4 HOH A 30 369 369 HOH HOH . G 4 HOH A 31 370 370 HOH HOH . G 4 HOH A 32 371 371 HOH HOH . G 4 HOH A 33 372 372 HOH HOH . G 4 HOH A 34 373 373 HOH HOH . G 4 HOH A 35 374 374 HOH HOH . G 4 HOH A 36 375 375 HOH HOH . G 4 HOH A 37 376 376 HOH HOH . G 4 HOH A 38 377 377 HOH HOH . G 4 HOH A 39 378 378 HOH HOH . G 4 HOH A 40 379 379 HOH HOH . G 4 HOH A 41 380 380 HOH HOH . G 4 HOH A 42 381 381 HOH HOH . G 4 HOH A 43 382 382 HOH HOH . G 4 HOH A 44 383 383 HOH HOH . G 4 HOH A 45 384 384 HOH HOH . G 4 HOH A 46 385 385 HOH HOH . G 4 HOH A 47 386 386 HOH HOH . G 4 HOH A 48 387 387 HOH HOH . G 4 HOH A 49 388 388 HOH HOH . G 4 HOH A 50 389 389 HOH HOH . G 4 HOH A 51 390 390 HOH HOH . G 4 HOH A 52 391 391 HOH HOH . G 4 HOH A 53 392 392 HOH HOH . G 4 HOH A 54 393 393 HOH HOH . G 4 HOH A 55 394 394 HOH HOH . G 4 HOH A 56 395 395 HOH HOH . G 4 HOH A 57 396 396 HOH HOH . G 4 HOH A 58 397 397 HOH HOH . G 4 HOH A 59 398 398 HOH HOH . G 4 HOH A 60 399 399 HOH HOH . G 4 HOH A 61 400 400 HOH HOH . G 4 HOH A 62 401 401 HOH HOH . G 4 HOH A 63 402 402 HOH HOH . G 4 HOH A 64 403 403 HOH HOH . G 4 HOH A 65 404 404 HOH HOH . G 4 HOH A 66 405 405 HOH HOH . G 4 HOH A 67 406 406 HOH HOH . G 4 HOH A 68 407 407 HOH HOH . G 4 HOH A 69 408 408 HOH HOH . G 4 HOH A 70 409 409 HOH HOH . G 4 HOH A 71 410 410 HOH HOH . G 4 HOH A 72 411 411 HOH HOH . G 4 HOH A 73 412 412 HOH HOH . G 4 HOH A 74 413 413 HOH HOH . G 4 HOH A 75 414 414 HOH HOH . G 4 HOH A 76 415 415 HOH HOH . G 4 HOH A 77 416 416 HOH HOH . G 4 HOH A 78 417 417 HOH HOH . G 4 HOH A 79 418 418 HOH HOH . G 4 HOH A 80 419 419 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 . . . B 2 22.831 37.257 -15.132 1 36.97 ? PB GDP 335 A 1 HETATM 2 O O1B GDP . . . B 2 23.469 36.38 -14.076 1 39.47 ? O1B GDP 335 A 1 HETATM 3 O O2B GDP . . . B 2 22.909 36.64 -16.502 1 37.78 ? O2B GDP 335 A 1 HETATM 4 O O3B GDP . . . B 2 21.351 37.473 -14.868 1 39.1 ? O3B GDP 335 A 1 HETATM 5 O O3A GDP . . . B 2 23.466 38.711 -15.047 1 40.37 ? O3A GDP 335 A 1 HETATM 6 P PA GDP . . . B 2 24.929 39.022 -14.433 1 43.9 ? PA GDP 335 A 1 HETATM 7 O O1A GDP . . . B 2 25.881 37.955 -14.934 1 44.61 ? O1A GDP 335 A 1 HETATM 8 O O2A GDP . . . B 2 24.957 39.211 -12.944 1 44.09 ? O2A GDP 335 A 1 HETATM 9 O O5' GDP . . . B 2 25.202 40.443 -15.109 1 43.85 ? O5' GDP 335 A 1 HETATM 10 C C5' GDP . . . B 2 25.4 40.446 -16.526 1 47.34 ? C5' GDP 335 A 1 HETATM 11 C C4' GDP . . . B 2 26.097 41.737 -16.909 1 50.97 ? C4' GDP 335 A 1 HETATM 12 O O4' GDP . . . B 2 25.292 42.834 -16.463 1 50.85 ? O4' GDP 335 A 1 HETATM 13 C C3' GDP . . . B 2 27.472 41.874 -16.236 1 52.65 ? C3' GDP 335 A 1 HETATM 14 O O3' GDP . . . B 2 28.369 42.565 -17.121 1 55.2 ? O3' GDP 335 A 1 HETATM 15 C C2' GDP . . . B 2 27.197 42.75 -15.04 1 52.11 ? C2' GDP 335 A 1 HETATM 16 O O2' GDP . . . B 2 28.325 43.529 -14.629 1 53.39 ? O2' GDP 335 A 1 HETATM 17 C C1' GDP . . . B 2 26.065 43.625 -15.559 1 51.67 ? C1' GDP 335 A 1 HETATM 18 N N9 GDP . . . B 2 25.248 44.067 -14.419 1 52.24 ? N9 GDP 335 A 1 HETATM 19 C C8 GDP . . . B 2 24.742 43.313 -13.42 1 52.71 ? C8 GDP 335 A 1 HETATM 20 N N7 GDP . . . B 2 24.043 44.08 -12.542 1 52.96 ? N7 GDP 335 A 1 HETATM 21 C C5 GDP . . . B 2 24.118 45.348 -12.987 1 53.52 ? C5 GDP 335 A 1 HETATM 22 C C6 GDP . . . B 2 23.617 46.665 -12.549 1 53.59 ? C6 GDP 335 A 1 HETATM 23 O O6 GDP . . . B 2 22.941 46.792 -11.514 1 55.5 ? O6 GDP 335 A 1 HETATM 24 N N1 GDP . . . B 2 23.93 47.727 -13.307 1 54.79 ? N1 GDP 335 A 1 HETATM 25 C C2 GDP . . . B 2 24.667 47.653 -14.445 1 52.09 ? C2 GDP 335 A 1 HETATM 26 N N2 GDP . . . B 2 24.9 48.794 -15.127 1 50.89 ? N2 GDP 335 A 1 HETATM 27 N N3 GDP . . . B 2 25.167 46.488 -14.912 1 51.35 ? N3 GDP 335 A 1 HETATM 28 C C4 GDP . . . B 2 24.922 45.337 -14.228 1 52.79 ? C4 GDP 335 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #