data_1SVI # _model_server_result.job_id 82h4oiL7t2tghC5Ry-EDBQ _model_server_result.datetime_utc '2024-10-11 06:16:57' _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 1svi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 1SVI # _exptl.entry_id 1SVI _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 94.05 _cell.angle_gamma 90 _cell.entry_id 1SVI _cell.length_a 46.179 _cell.length_b 68.305 _cell.length_c 61.999 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SVI _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 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 1SVI _atom_sites.fract_transf_matrix[1][1] 0.021655 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001534 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01464 _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] 0.01617 _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 1 401 401 GDP GDP . C 3 HOH A 1 402 1 HOH HOH . C 3 HOH A 2 403 2 HOH HOH . C 3 HOH A 3 404 3 HOH HOH . C 3 HOH A 4 405 4 HOH HOH . C 3 HOH A 5 406 5 HOH HOH . C 3 HOH A 6 407 6 HOH HOH . C 3 HOH A 7 408 7 HOH HOH . C 3 HOH A 8 409 8 HOH HOH . C 3 HOH A 9 410 9 HOH HOH . C 3 HOH A 10 411 10 HOH HOH . C 3 HOH A 11 412 11 HOH HOH . C 3 HOH A 12 413 12 HOH HOH . C 3 HOH A 13 414 13 HOH HOH . C 3 HOH A 14 415 14 HOH HOH . C 3 HOH A 15 416 15 HOH HOH . C 3 HOH A 16 417 16 HOH HOH . C 3 HOH A 17 418 17 HOH HOH . C 3 HOH A 18 419 18 HOH HOH . C 3 HOH A 19 420 19 HOH HOH . C 3 HOH A 20 421 20 HOH HOH . C 3 HOH A 21 422 21 HOH HOH . C 3 HOH A 22 423 22 HOH HOH . C 3 HOH A 23 424 23 HOH HOH . C 3 HOH A 24 425 24 HOH HOH . C 3 HOH A 25 426 25 HOH HOH . C 3 HOH A 26 427 26 HOH HOH . C 3 HOH A 27 428 27 HOH HOH . C 3 HOH A 28 429 28 HOH HOH . C 3 HOH A 29 430 29 HOH HOH . C 3 HOH A 30 431 30 HOH HOH . C 3 HOH A 31 432 31 HOH HOH . C 3 HOH A 32 433 32 HOH HOH . C 3 HOH A 33 434 33 HOH HOH . C 3 HOH A 34 435 34 HOH HOH . C 3 HOH A 35 436 35 HOH HOH . C 3 HOH A 36 437 36 HOH HOH . C 3 HOH A 37 438 37 HOH HOH . C 3 HOH A 38 439 38 HOH HOH . C 3 HOH A 39 440 39 HOH HOH . C 3 HOH A 40 441 40 HOH HOH . C 3 HOH A 41 442 41 HOH HOH . C 3 HOH A 42 443 42 HOH HOH . C 3 HOH A 43 444 43 HOH HOH . C 3 HOH A 44 445 44 HOH HOH . C 3 HOH A 45 446 45 HOH HOH . C 3 HOH A 46 447 46 HOH HOH . C 3 HOH A 47 448 47 HOH HOH . C 3 HOH A 48 449 48 HOH HOH . C 3 HOH A 49 450 49 HOH HOH . C 3 HOH A 50 451 50 HOH HOH . C 3 HOH A 51 452 51 HOH HOH . C 3 HOH A 52 453 52 HOH HOH . C 3 HOH A 53 454 53 HOH HOH . C 3 HOH A 54 455 54 HOH HOH . C 3 HOH A 55 456 55 HOH HOH . C 3 HOH A 56 457 56 HOH HOH . C 3 HOH A 57 458 57 HOH HOH . C 3 HOH A 58 459 58 HOH HOH . C 3 HOH A 59 460 59 HOH HOH . C 3 HOH A 60 461 60 HOH HOH . C 3 HOH A 61 462 61 HOH HOH . C 3 HOH A 62 463 62 HOH HOH . C 3 HOH A 63 464 63 HOH HOH . C 3 HOH A 64 465 64 HOH HOH . C 3 HOH A 65 466 65 HOH HOH . C 3 HOH A 66 467 66 HOH HOH . C 3 HOH A 67 468 67 HOH HOH . C 3 HOH A 68 469 68 HOH HOH . C 3 HOH A 69 470 69 HOH HOH . C 3 HOH A 70 471 70 HOH HOH . C 3 HOH A 71 472 71 HOH HOH . C 3 HOH A 72 473 72 HOH HOH . C 3 HOH A 73 474 73 HOH HOH . C 3 HOH A 74 475 74 HOH HOH . C 3 HOH A 75 476 75 HOH HOH . C 3 HOH A 76 477 76 HOH HOH . C 3 HOH A 77 478 77 HOH HOH . C 3 HOH A 78 479 78 HOH HOH . C 3 HOH A 79 480 79 HOH HOH . C 3 HOH A 80 481 80 HOH HOH . C 3 HOH A 81 482 81 HOH HOH . C 3 HOH A 82 483 82 HOH HOH . C 3 HOH A 83 484 83 HOH HOH . C 3 HOH A 84 485 84 HOH HOH . C 3 HOH A 85 486 85 HOH HOH . C 3 HOH A 86 487 86 HOH HOH . C 3 HOH A 87 488 87 HOH HOH . C 3 HOH A 88 489 88 HOH HOH . C 3 HOH A 89 490 89 HOH HOH . C 3 HOH A 90 491 90 HOH HOH . C 3 HOH A 91 492 91 HOH HOH . C 3 HOH A 92 493 92 HOH HOH . C 3 HOH A 93 494 93 HOH HOH . C 3 HOH A 94 495 94 HOH HOH . C 3 HOH A 95 496 95 HOH HOH . C 3 HOH A 96 497 96 HOH HOH . C 3 HOH A 97 498 97 HOH HOH . C 3 HOH A 98 499 98 HOH HOH . C 3 HOH A 99 500 99 HOH HOH . C 3 HOH A 100 501 100 HOH HOH . C 3 HOH A 101 502 101 HOH HOH . C 3 HOH A 102 503 102 HOH HOH . C 3 HOH A 103 504 103 HOH HOH . C 3 HOH A 104 505 104 HOH HOH . C 3 HOH A 105 506 105 HOH HOH . C 3 HOH A 106 507 106 HOH HOH . C 3 HOH A 107 508 107 HOH HOH . C 3 HOH A 108 509 108 HOH HOH . C 3 HOH A 109 510 109 HOH HOH . C 3 HOH A 110 511 110 HOH HOH . C 3 HOH A 111 512 111 HOH HOH . C 3 HOH A 112 513 112 HOH HOH . C 3 HOH A 113 514 113 HOH HOH . C 3 HOH A 114 515 114 HOH HOH . C 3 HOH A 115 516 115 HOH HOH . C 3 HOH A 116 517 116 HOH HOH . C 3 HOH A 117 518 117 HOH HOH . C 3 HOH A 118 519 118 HOH HOH . C 3 HOH A 119 520 119 HOH HOH . C 3 HOH A 120 521 120 HOH HOH . C 3 HOH A 121 522 121 HOH HOH . C 3 HOH A 122 523 122 HOH HOH . C 3 HOH A 123 524 123 HOH HOH . C 3 HOH A 124 525 124 HOH HOH . C 3 HOH A 125 526 125 HOH HOH . C 3 HOH A 126 527 126 HOH HOH . C 3 HOH A 127 528 127 HOH HOH . C 3 HOH A 128 529 128 HOH HOH . C 3 HOH A 129 530 129 HOH HOH . C 3 HOH A 130 531 130 HOH HOH . C 3 HOH A 131 532 131 HOH HOH . C 3 HOH A 132 533 132 HOH HOH . C 3 HOH A 133 534 133 HOH HOH . C 3 HOH A 134 535 134 HOH HOH . C 3 HOH A 135 536 135 HOH HOH . C 3 HOH A 136 537 136 HOH HOH . C 3 HOH A 137 538 137 HOH HOH . C 3 HOH A 138 539 138 HOH HOH . C 3 HOH A 139 540 139 HOH HOH . C 3 HOH A 140 541 140 HOH HOH . C 3 HOH A 141 542 141 HOH HOH . C 3 HOH A 142 543 142 HOH HOH . C 3 HOH A 143 544 143 HOH HOH . C 3 HOH A 144 545 144 HOH HOH . C 3 HOH A 145 546 145 HOH HOH . C 3 HOH A 146 547 146 HOH HOH . C 3 HOH A 147 548 147 HOH HOH . C 3 HOH A 148 549 148 HOH HOH . C 3 HOH A 149 550 149 HOH HOH . C 3 HOH A 150 551 150 HOH HOH . C 3 HOH A 151 552 151 HOH HOH . C 3 HOH A 152 553 152 HOH HOH . C 3 HOH A 153 554 153 HOH HOH . C 3 HOH A 154 555 154 HOH HOH . C 3 HOH A 155 556 155 HOH HOH . C 3 HOH A 156 557 156 HOH HOH . C 3 HOH A 157 558 157 HOH HOH . C 3 HOH A 158 559 158 HOH HOH . C 3 HOH A 159 560 159 HOH HOH . C 3 HOH A 160 561 160 HOH HOH . C 3 HOH A 161 562 161 HOH HOH . C 3 HOH A 162 563 162 HOH HOH . C 3 HOH A 163 564 163 HOH HOH . C 3 HOH A 164 565 164 HOH HOH . C 3 HOH A 165 566 165 HOH HOH . C 3 HOH A 166 567 166 HOH HOH . C 3 HOH A 167 568 167 HOH HOH . C 3 HOH A 168 569 168 HOH HOH . C 3 HOH A 169 570 169 HOH HOH . C 3 HOH A 170 571 170 HOH HOH . C 3 HOH A 171 572 171 HOH HOH . C 3 HOH A 172 573 172 HOH HOH . C 3 HOH A 173 574 173 HOH HOH . C 3 HOH A 174 575 174 HOH HOH . C 3 HOH A 175 576 175 HOH HOH . C 3 HOH A 176 577 176 HOH HOH . C 3 HOH A 177 578 177 HOH HOH . C 3 HOH A 178 579 178 HOH HOH . C 3 HOH A 179 580 179 HOH HOH . C 3 HOH A 180 581 180 HOH HOH . C 3 HOH A 181 582 181 HOH HOH . C 3 HOH A 182 583 182 HOH HOH . C 3 HOH A 183 584 183 HOH HOH . C 3 HOH A 184 585 184 HOH HOH . C 3 HOH A 185 586 185 HOH HOH . C 3 HOH A 186 587 186 HOH HOH . C 3 HOH A 187 588 187 HOH HOH . C 3 HOH A 188 589 188 HOH HOH . C 3 HOH A 189 590 189 HOH HOH . C 3 HOH A 190 591 190 HOH HOH . C 3 HOH A 191 592 191 HOH HOH . C 3 HOH A 192 593 192 HOH HOH . C 3 HOH A 193 594 193 HOH HOH . C 3 HOH A 194 595 194 HOH HOH . C 3 HOH A 195 596 195 HOH HOH . C 3 HOH A 196 597 196 HOH HOH . C 3 HOH A 197 598 197 HOH HOH . C 3 HOH A 198 599 198 HOH HOH . C 3 HOH A 199 600 199 HOH HOH . C 3 HOH A 200 601 200 HOH HOH . C 3 HOH A 201 602 201 HOH HOH . C 3 HOH A 202 603 202 HOH HOH . C 3 HOH A 203 604 203 HOH HOH . C 3 HOH A 204 605 204 HOH HOH . C 3 HOH A 205 606 205 HOH HOH . C 3 HOH A 206 607 206 HOH HOH . C 3 HOH A 207 608 207 HOH HOH . C 3 HOH A 208 609 208 HOH HOH . C 3 HOH A 209 610 209 HOH HOH . C 3 HOH A 210 611 210 HOH HOH . C 3 HOH A 211 612 211 HOH HOH . C 3 HOH A 212 613 212 HOH HOH . C 3 HOH A 213 614 213 HOH HOH . C 3 HOH A 214 615 214 HOH HOH . C 3 HOH A 215 616 215 HOH HOH . C 3 HOH A 216 617 216 HOH HOH . C 3 HOH A 217 618 217 HOH HOH . C 3 HOH A 218 619 218 HOH HOH . C 3 HOH A 219 620 219 HOH HOH . C 3 HOH A 220 621 220 HOH HOH . C 3 HOH A 221 622 221 HOH HOH . C 3 HOH A 222 623 222 HOH HOH . C 3 HOH A 223 624 223 HOH HOH . C 3 HOH A 224 625 224 HOH HOH . C 3 HOH A 225 626 225 HOH HOH . C 3 HOH A 226 627 226 HOH HOH . C 3 HOH A 227 628 227 HOH HOH . C 3 HOH A 228 629 228 HOH HOH . C 3 HOH A 229 630 229 HOH HOH . C 3 HOH A 230 631 230 HOH HOH . C 3 HOH A 231 632 231 HOH HOH . C 3 HOH A 232 633 232 HOH HOH . C 3 HOH A 233 634 233 HOH HOH . C 3 HOH A 234 635 234 HOH HOH . C 3 HOH A 235 636 235 HOH HOH . C 3 HOH A 236 637 236 HOH HOH . C 3 HOH A 237 638 237 HOH HOH . C 3 HOH A 238 639 238 HOH HOH . C 3 HOH A 239 640 239 HOH HOH . C 3 HOH A 240 641 240 HOH HOH . C 3 HOH A 241 642 241 HOH HOH . C 3 HOH A 242 643 242 HOH HOH . C 3 HOH A 243 644 243 HOH HOH . C 3 HOH A 244 645 244 HOH HOH . C 3 HOH A 245 646 245 HOH HOH . C 3 HOH A 246 647 246 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 18.931 41.317 44.457 1 16.42 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 17.943 40.622 43.612 1 15.7 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 18.541 41.147 45.922 1 13.6 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 20.33 40.794 44.174 1 15.72 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 18.923 42.841 43.892 1 16.59 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 18.679 44.209 44.695 1 16.1 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 17.405 44.196 45.444 1 15.46 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 19.888 44.468 45.594 1 16.48 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 18.637 45.234 43.471 1 16.07 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 19.729 45.328 42.58 1 15.62 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 19.841 46.742 42.024 1 14.75 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 18.654 47.095 41.336 1 14.43 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 19.996 47.743 43.154 1 15.67 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 20.815 48.819 42.722 1 16.09 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 18.587 48.244 43.394 1 14.86 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 18.633 49.581 43.858 1 15.19 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 17.967 48.14 42.001 1 13.78 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 16.505 47.902 42.002 1 13.62 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 15.818 46.871 42.586 1 11.71 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 14.494 47.042 42.337 1 11.37 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 14.324 48.156 41.595 1 11.84 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 13.194 48.798 41.077 1 11.69 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 12.076 48.283 41.112 1 11.15 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 13.362 49.955 40.358 1 11.49 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 14.625 50.482 40.149 1 13.24 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 14.772 51.558 39.376 1 13.65 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 15.734 49.852 40.672 1 12.33 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 15.584 48.706 41.379 1 12.07 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #