data_3W5J # _model_server_result.job_id HQWDspI3qw81P6XfdcxDIg _model_server_result.datetime_utc '2024-11-05 00:53:43' _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 3w5j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 3W5J # _exptl.entry_id 3W5J _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 3W5J _cell.length_a 45.76 _cell.length_b 84.04 _cell.length_c 95.45 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3W5J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 # _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 2 _struct_asym.id C _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 3W5J _atom_sites.fract_transf_matrix[1][1] 0.021853 _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] 0.011899 _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] 0.010477 _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 GDP A 1 301 1 GDP GDP . D 3 GOL A 1 302 1 GOL GOL . E 4 SO4 B 1 301 1 SO4 SO4 . F 5 HOH A 1 401 3 HOH HOH . F 5 HOH A 2 402 6 HOH HOH . F 5 HOH A 3 403 7 HOH HOH . F 5 HOH A 4 404 8 HOH HOH . F 5 HOH A 5 405 10 HOH HOH . F 5 HOH A 6 406 14 HOH HOH . F 5 HOH A 7 407 15 HOH HOH . F 5 HOH A 8 408 16 HOH HOH . F 5 HOH A 9 409 17 HOH HOH . F 5 HOH A 10 410 21 HOH HOH . F 5 HOH A 11 411 22 HOH HOH . F 5 HOH A 12 412 30 HOH HOH . F 5 HOH A 13 413 31 HOH HOH . F 5 HOH A 14 414 35 HOH HOH . F 5 HOH A 15 415 37 HOH HOH . F 5 HOH A 16 416 41 HOH HOH . F 5 HOH A 17 417 45 HOH HOH . F 5 HOH A 18 418 46 HOH HOH . F 5 HOH A 19 419 47 HOH HOH . F 5 HOH A 20 420 49 HOH HOH . F 5 HOH A 21 421 50 HOH HOH . F 5 HOH A 22 422 52 HOH HOH . F 5 HOH A 23 423 57 HOH HOH . F 5 HOH A 24 424 58 HOH HOH . F 5 HOH A 25 425 59 HOH HOH . F 5 HOH A 26 426 60 HOH HOH . F 5 HOH A 27 427 64 HOH HOH . F 5 HOH A 28 428 65 HOH HOH . F 5 HOH A 29 429 69 HOH HOH . F 5 HOH A 30 430 74 HOH HOH . F 5 HOH A 31 431 75 HOH HOH . F 5 HOH A 32 432 76 HOH HOH . F 5 HOH A 33 433 78 HOH HOH . F 5 HOH A 34 434 79 HOH HOH . F 5 HOH A 35 435 80 HOH HOH . F 5 HOH A 36 436 81 HOH HOH . F 5 HOH A 37 437 88 HOH HOH . F 5 HOH A 38 438 89 HOH HOH . F 5 HOH A 39 439 91 HOH HOH . F 5 HOH A 40 440 93 HOH HOH . F 5 HOH A 41 441 96 HOH HOH . F 5 HOH A 42 442 97 HOH HOH . F 5 HOH A 43 443 104 HOH HOH . F 5 HOH A 44 444 105 HOH HOH . F 5 HOH A 45 445 106 HOH HOH . F 5 HOH A 46 446 109 HOH HOH . F 5 HOH A 47 447 113 HOH HOH . F 5 HOH A 48 448 117 HOH HOH . F 5 HOH A 49 449 119 HOH HOH . F 5 HOH A 50 450 121 HOH HOH . F 5 HOH A 51 451 123 HOH HOH . F 5 HOH A 52 452 127 HOH HOH . F 5 HOH A 53 453 134 HOH HOH . F 5 HOH A 54 454 137 HOH HOH . F 5 HOH A 55 455 138 HOH HOH . F 5 HOH A 56 456 141 HOH HOH . F 5 HOH A 57 457 143 HOH HOH . F 5 HOH A 58 458 149 HOH HOH . F 5 HOH A 59 459 160 HOH HOH . F 5 HOH A 60 460 161 HOH HOH . F 5 HOH A 61 461 162 HOH HOH . F 5 HOH A 62 462 164 HOH HOH . F 5 HOH A 63 463 174 HOH HOH . F 5 HOH A 64 464 176 HOH HOH . F 5 HOH A 65 465 178 HOH HOH . F 5 HOH A 66 466 179 HOH HOH . F 5 HOH A 67 467 182 HOH HOH . F 5 HOH A 68 468 188 HOH HOH . F 5 HOH A 69 469 192 HOH HOH . F 5 HOH A 70 470 195 HOH HOH . F 5 HOH A 71 471 197 HOH HOH . F 5 HOH A 72 472 199 HOH HOH . F 5 HOH A 73 473 200 HOH HOH . F 5 HOH A 74 474 209 HOH HOH . F 5 HOH A 75 475 212 HOH HOH . F 5 HOH A 76 476 215 HOH HOH . F 5 HOH A 77 477 217 HOH HOH . F 5 HOH A 78 478 218 HOH HOH . F 5 HOH A 79 479 222 HOH HOH . F 5 HOH A 80 480 224 HOH HOH . F 5 HOH A 81 481 225 HOH HOH . F 5 HOH A 82 482 234 HOH HOH . F 5 HOH A 83 483 235 HOH HOH . F 5 HOH A 84 484 237 HOH HOH . F 5 HOH A 85 485 242 HOH HOH . F 5 HOH A 86 486 246 HOH HOH . F 5 HOH A 87 487 247 HOH HOH . F 5 HOH A 88 488 249 HOH HOH . F 5 HOH A 89 489 259 HOH HOH . F 5 HOH A 90 490 262 HOH HOH . F 5 HOH A 91 491 271 HOH HOH . F 5 HOH A 92 492 274 HOH HOH . F 5 HOH A 93 493 275 HOH HOH . F 5 HOH A 94 494 276 HOH HOH . F 5 HOH A 95 495 281 HOH HOH . F 5 HOH A 96 496 294 HOH HOH . F 5 HOH A 97 497 298 HOH HOH . F 5 HOH A 98 498 327 HOH HOH . F 5 HOH A 99 499 334 HOH HOH . F 5 HOH A 100 500 352 HOH HOH . F 5 HOH A 101 501 361 HOH HOH . F 5 HOH A 102 502 384 HOH HOH . F 5 HOH A 103 503 394 HOH HOH . F 5 HOH A 104 504 426 HOH HOH . F 5 HOH A 105 505 430 HOH HOH . F 5 HOH A 106 506 486 HOH HOH . F 5 HOH A 107 507 596 HOH HOH . F 5 HOH A 108 508 597 HOH HOH . F 5 HOH A 109 509 598 HOH HOH . F 5 HOH A 110 510 599 HOH HOH . F 5 HOH A 111 511 601 HOH HOH . F 5 HOH A 112 512 602 HOH HOH . F 5 HOH A 113 513 603 HOH HOH . F 5 HOH A 114 514 605 HOH HOH . F 5 HOH A 115 515 607 HOH HOH . F 5 HOH A 116 516 609 HOH HOH . F 5 HOH A 117 517 612 HOH HOH . F 5 HOH A 118 518 613 HOH HOH . F 5 HOH A 119 519 618 HOH HOH . F 5 HOH A 120 520 619 HOH HOH . F 5 HOH A 121 521 620 HOH HOH . F 5 HOH A 122 522 622 HOH HOH . F 5 HOH A 123 523 623 HOH HOH . F 5 HOH A 124 524 624 HOH HOH . F 5 HOH A 125 525 625 HOH HOH . F 5 HOH A 126 526 626 HOH HOH . G 5 HOH B 1 401 5 HOH HOH . G 5 HOH B 2 402 13 HOH HOH . G 5 HOH B 3 403 18 HOH HOH . G 5 HOH B 4 404 20 HOH HOH . G 5 HOH B 5 405 23 HOH HOH . G 5 HOH B 6 406 25 HOH HOH . G 5 HOH B 7 407 28 HOH HOH . G 5 HOH B 8 408 29 HOH HOH . G 5 HOH B 9 409 39 HOH HOH . G 5 HOH B 10 410 40 HOH HOH . G 5 HOH B 11 411 51 HOH HOH . G 5 HOH B 12 412 55 HOH HOH . G 5 HOH B 13 413 62 HOH HOH . G 5 HOH B 14 414 63 HOH HOH . G 5 HOH B 15 415 67 HOH HOH . G 5 HOH B 16 416 68 HOH HOH . G 5 HOH B 17 417 71 HOH HOH . G 5 HOH B 18 418 72 HOH HOH . G 5 HOH B 19 419 73 HOH HOH . G 5 HOH B 20 420 83 HOH HOH . G 5 HOH B 21 421 84 HOH HOH . G 5 HOH B 22 422 85 HOH HOH . G 5 HOH B 23 423 86 HOH HOH . G 5 HOH B 24 424 87 HOH HOH . G 5 HOH B 25 425 95 HOH HOH . G 5 HOH B 26 426 102 HOH HOH . G 5 HOH B 27 427 108 HOH HOH . G 5 HOH B 28 428 111 HOH HOH . G 5 HOH B 29 429 112 HOH HOH . G 5 HOH B 30 430 114 HOH HOH . G 5 HOH B 31 431 115 HOH HOH . G 5 HOH B 32 432 124 HOH HOH . G 5 HOH B 33 433 135 HOH HOH . G 5 HOH B 34 434 142 HOH HOH . G 5 HOH B 35 435 144 HOH HOH . G 5 HOH B 36 436 146 HOH HOH . G 5 HOH B 37 437 151 HOH HOH . G 5 HOH B 38 438 155 HOH HOH . G 5 HOH B 39 439 159 HOH HOH . G 5 HOH B 40 440 165 HOH HOH . G 5 HOH B 41 441 166 HOH HOH . G 5 HOH B 42 442 171 HOH HOH . G 5 HOH B 43 443 173 HOH HOH . G 5 HOH B 44 444 175 HOH HOH . G 5 HOH B 45 445 184 HOH HOH . G 5 HOH B 46 446 189 HOH HOH . G 5 HOH B 47 447 193 HOH HOH . G 5 HOH B 48 448 204 HOH HOH . G 5 HOH B 49 449 208 HOH HOH . G 5 HOH B 50 450 211 HOH HOH . G 5 HOH B 51 451 213 HOH HOH . G 5 HOH B 52 452 220 HOH HOH . G 5 HOH B 53 453 227 HOH HOH . G 5 HOH B 54 454 230 HOH HOH . G 5 HOH B 55 455 236 HOH HOH . G 5 HOH B 56 456 239 HOH HOH . G 5 HOH B 57 457 240 HOH HOH . G 5 HOH B 58 458 241 HOH HOH . G 5 HOH B 59 459 245 HOH HOH . G 5 HOH B 60 460 251 HOH HOH . G 5 HOH B 61 461 253 HOH HOH . G 5 HOH B 62 462 254 HOH HOH . G 5 HOH B 63 463 255 HOH HOH . G 5 HOH B 64 464 258 HOH HOH . G 5 HOH B 65 465 263 HOH HOH . G 5 HOH B 66 466 266 HOH HOH . G 5 HOH B 67 467 267 HOH HOH . G 5 HOH B 68 468 268 HOH HOH . G 5 HOH B 69 469 270 HOH HOH . G 5 HOH B 70 470 272 HOH HOH . G 5 HOH B 71 471 277 HOH HOH . G 5 HOH B 72 472 279 HOH HOH . G 5 HOH B 73 473 282 HOH HOH . G 5 HOH B 74 474 292 HOH HOH . G 5 HOH B 75 475 306 HOH HOH . G 5 HOH B 76 476 308 HOH HOH . G 5 HOH B 77 477 312 HOH HOH . G 5 HOH B 78 478 318 HOH HOH . G 5 HOH B 79 479 333 HOH HOH . G 5 HOH B 80 480 339 HOH HOH . G 5 HOH B 81 481 354 HOH HOH . G 5 HOH B 82 482 392 HOH HOH . G 5 HOH B 83 483 396 HOH HOH . G 5 HOH B 84 484 408 HOH HOH . G 5 HOH B 85 485 409 HOH HOH . G 5 HOH B 86 486 424 HOH HOH . G 5 HOH B 87 487 432 HOH HOH . G 5 HOH B 88 488 445 HOH HOH . G 5 HOH B 89 489 452 HOH HOH . G 5 HOH B 90 490 526 HOH HOH . G 5 HOH B 91 491 558 HOH HOH . G 5 HOH B 92 492 561 HOH HOH . G 5 HOH B 93 493 600 HOH HOH . G 5 HOH B 94 494 604 HOH HOH . G 5 HOH B 95 495 606 HOH HOH . G 5 HOH B 96 496 608 HOH HOH . G 5 HOH B 97 497 610 HOH HOH . G 5 HOH B 98 498 611 HOH HOH . G 5 HOH B 99 499 614 HOH HOH . G 5 HOH B 100 500 615 HOH HOH . G 5 HOH B 101 501 616 HOH HOH . G 5 HOH B 102 502 617 HOH HOH . G 5 HOH B 103 503 621 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 . . . C 2 -6.922 -23.726 5.722 1 13.75 ? PB GDP 301 A 1 HETATM 2 O O1B GDP . . . C 2 -8.165 -24.272 5.081 1 15.7 ? O1B GDP 301 A 1 HETATM 3 O O2B GDP . . . C 2 -7.211 -22.539 6.565 1 10.86 ? O2B GDP 301 A 1 HETATM 4 O O3B GDP . . . C 2 -5.898 -23.224 4.666 1 15.98 ? O3B GDP 301 A 1 HETATM 5 O O3A GDP . . . C 2 -6.367 -24.809 6.729 1 15.76 ? O3A GDP 301 A 1 HETATM 6 P PA GDP . . . C 2 -6.544 -26.423 6.571 1 21.21 ? PA GDP 301 A 1 HETATM 7 O O1A GDP . . . C 2 -5.969 -26.873 5.248 1 20.92 ? O1A GDP 301 A 1 HETATM 8 O O2A GDP . . . C 2 -7.955 -26.95 6.802 1 19.05 ? O2A GDP 301 A 1 HETATM 9 O O5' GDP . . . C 2 -5.503 -26.936 7.706 1 23.42 ? O5' GDP 301 A 1 HETATM 10 C C5' GDP . . . C 2 -4.143 -26.483 7.688 1 26.48 ? C5' GDP 301 A 1 HETATM 11 C C4' GDP . . . C 2 -3.292 -27.313 8.654 1 30.37 ? C4' GDP 301 A 1 HETATM 12 O O4' GDP . . . C 2 -3.812 -27.224 9.995 1 30.38 ? O4' GDP 301 A 1 HETATM 13 C C3' GDP . . . C 2 -3.285 -28.802 8.316 1 31.69 ? C3' GDP 301 A 1 HETATM 14 O O3' GDP . . . C 2 -2.059 -29.402 8.76 1 32.02 ? O3' GDP 301 A 1 HETATM 15 C C2' GDP . . . C 2 -4.432 -29.338 9.14 1 32.92 ? C2' GDP 301 A 1 HETATM 16 O O2' GDP . . . C 2 -4.401 -30.762 9.28 1 33.98 ? O2' GDP 301 A 1 HETATM 17 C C1' GDP . . . C 2 -4.213 -28.534 10.422 1 32.78 ? C1' GDP 301 A 1 HETATM 18 N N9 GDP . . . C 2 -5.429 -28.455 11.279 1 35.24 ? N9 GDP 301 A 1 HETATM 19 C C8 GDP . . . C 2 -6.687 -28.131 10.895 1 35.35 ? C8 GDP 301 A 1 HETATM 20 N N7 GDP . . . C 2 -7.53 -28.165 11.967 1 35.38 ? N7 GDP 301 A 1 HETATM 21 C C5 GDP . . . C 2 -6.811 -28.514 13.055 1 36.32 ? C5 GDP 301 A 1 HETATM 22 C C6 GDP . . . C 2 -7.07 -28.749 14.505 1 37.67 ? C6 GDP 301 A 1 HETATM 23 O O6 GDP . . . C 2 -8.218 -28.614 14.989 1 39.07 ? O6 GDP 301 A 1 HETATM 24 N N1 GDP . . . C 2 -6.033 -29.098 15.29 1 36.78 ? N1 GDP 301 A 1 HETATM 25 C C2 GDP . . . C 2 -4.786 -29.262 14.804 1 36.59 ? C2 GDP 301 A 1 HETATM 26 N N2 GDP . . . C 2 -3.796 -29.619 15.658 1 36.5 ? N2 GDP 301 A 1 HETATM 27 N N3 GDP . . . C 2 -4.474 -29.075 13.488 1 35.49 ? N3 GDP 301 A 1 HETATM 28 C C4 GDP . . . C 2 -5.424 -28.703 12.592 1 35.67 ? C4 GDP 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #