data_1DS6 # _model_server_result.job_id d25zjf5T8kWzzl-MfOYQ4g _model_server_result.datetime_utc '2024-12-20 04:57:14' _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 1ds6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":194}' # _entry.id 1DS6 # _exptl.entry_id 1DS6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 1DS6 _cell.length_a 53.026 _cell.length_b 61.922 _cell.length_c 141.068 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DS6 _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 D _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 OG1 THR 17 A THR 17 1_555 C MG MG . A MG 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc2 A O THR 35 A THR 35 1_555 C MG MG . A MG 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc3 C MG MG . A MG 193 1_555 D O2B GDP . A GDP 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc4 C MG MG . A MG 193 1_555 E O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc5 C MG MG . A MG 193 1_555 E O HOH . A HOH 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc6 C MG MG . A MG 193 1_555 E O HOH . A HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 1DS6 _atom_sites.fract_transf_matrix[1][1] 0.018859 _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] 0.016149 _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] 0.007089 _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 3 MG A 1 193 192 MG MG . D 4 GDP A 1 194 191 GDP GDP . E 5 HOH A 1 501 501 HOH HOH . E 5 HOH A 2 502 502 HOH HOH . E 5 HOH A 3 503 503 HOH HOH . E 5 HOH A 4 504 504 HOH HOH . E 5 HOH A 5 506 506 HOH HOH . E 5 HOH A 6 509 509 HOH HOH . E 5 HOH A 7 511 511 HOH HOH . E 5 HOH A 8 512 512 HOH HOH . E 5 HOH A 9 514 514 HOH HOH . E 5 HOH A 10 515 515 HOH HOH . E 5 HOH A 11 516 516 HOH HOH . E 5 HOH A 12 517 517 HOH HOH . E 5 HOH A 13 518 518 HOH HOH . E 5 HOH A 14 520 520 HOH HOH . E 5 HOH A 15 522 522 HOH HOH . E 5 HOH A 16 526 526 HOH HOH . E 5 HOH A 17 528 528 HOH HOH . E 5 HOH A 18 529 529 HOH HOH . E 5 HOH A 19 531 531 HOH HOH . E 5 HOH A 20 533 533 HOH HOH . E 5 HOH A 21 536 536 HOH HOH . E 5 HOH A 22 539 539 HOH HOH . E 5 HOH A 23 540 540 HOH HOH . E 5 HOH A 24 541 541 HOH HOH . E 5 HOH A 25 546 546 HOH HOH . E 5 HOH A 26 547 547 HOH HOH . E 5 HOH A 27 549 549 HOH HOH . E 5 HOH A 28 550 550 HOH HOH . E 5 HOH A 29 551 551 HOH HOH . E 5 HOH A 30 552 552 HOH HOH . E 5 HOH A 31 554 554 HOH HOH . E 5 HOH A 32 556 556 HOH HOH . E 5 HOH A 33 557 557 HOH HOH . E 5 HOH A 34 559 559 HOH HOH . E 5 HOH A 35 561 561 HOH HOH . E 5 HOH A 36 562 562 HOH HOH . E 5 HOH A 37 564 564 HOH HOH . E 5 HOH A 38 567 567 HOH HOH . E 5 HOH A 39 568 568 HOH HOH . E 5 HOH A 40 570 570 HOH HOH . E 5 HOH A 41 571 571 HOH HOH . E 5 HOH A 42 572 572 HOH HOH . E 5 HOH A 43 573 573 HOH HOH . E 5 HOH A 44 575 575 HOH HOH . E 5 HOH A 45 576 576 HOH HOH . E 5 HOH A 46 578 578 HOH HOH . E 5 HOH A 47 579 579 HOH HOH . E 5 HOH A 48 583 583 HOH HOH . E 5 HOH A 49 584 584 HOH HOH . E 5 HOH A 50 585 585 HOH HOH . E 5 HOH A 51 589 589 HOH HOH . E 5 HOH A 52 591 591 HOH HOH . E 5 HOH A 53 592 592 HOH HOH . E 5 HOH A 54 593 593 HOH HOH . E 5 HOH A 55 594 594 HOH HOH . E 5 HOH A 56 596 596 HOH HOH . E 5 HOH A 57 599 599 HOH HOH . E 5 HOH A 58 600 600 HOH HOH . E 5 HOH A 59 602 602 HOH HOH . E 5 HOH A 60 605 605 HOH HOH . E 5 HOH A 61 606 606 HOH HOH . E 5 HOH A 62 607 607 HOH HOH . E 5 HOH A 63 616 616 HOH HOH . E 5 HOH A 64 617 617 HOH HOH . E 5 HOH A 65 619 619 HOH HOH . E 5 HOH A 66 621 621 HOH HOH . E 5 HOH A 67 622 622 HOH HOH . E 5 HOH A 68 623 623 HOH HOH . E 5 HOH A 69 625 625 HOH HOH . E 5 HOH A 70 626 626 HOH HOH . E 5 HOH A 71 627 627 HOH HOH . E 5 HOH A 72 628 628 HOH HOH . F 5 HOH B 1 505 505 HOH HOH . F 5 HOH B 2 507 507 HOH HOH . F 5 HOH B 3 508 508 HOH HOH . F 5 HOH B 4 510 510 HOH HOH . F 5 HOH B 5 513 513 HOH HOH . F 5 HOH B 6 519 519 HOH HOH . F 5 HOH B 7 521 521 HOH HOH . F 5 HOH B 8 523 523 HOH HOH . F 5 HOH B 9 524 524 HOH HOH . F 5 HOH B 10 525 525 HOH HOH . F 5 HOH B 11 527 527 HOH HOH . F 5 HOH B 12 530 530 HOH HOH . F 5 HOH B 13 532 532 HOH HOH . F 5 HOH B 14 534 534 HOH HOH . F 5 HOH B 15 535 535 HOH HOH . F 5 HOH B 16 537 537 HOH HOH . F 5 HOH B 17 538 538 HOH HOH . F 5 HOH B 18 542 542 HOH HOH . F 5 HOH B 19 543 543 HOH HOH . F 5 HOH B 20 544 544 HOH HOH . F 5 HOH B 21 545 545 HOH HOH . F 5 HOH B 22 548 548 HOH HOH . F 5 HOH B 23 553 553 HOH HOH . F 5 HOH B 24 555 555 HOH HOH . F 5 HOH B 25 558 558 HOH HOH . F 5 HOH B 26 560 560 HOH HOH . F 5 HOH B 27 563 563 HOH HOH . F 5 HOH B 28 565 565 HOH HOH . F 5 HOH B 29 566 566 HOH HOH . F 5 HOH B 30 569 569 HOH HOH . F 5 HOH B 31 574 574 HOH HOH . F 5 HOH B 32 577 577 HOH HOH . F 5 HOH B 33 580 580 HOH HOH . F 5 HOH B 34 581 581 HOH HOH . F 5 HOH B 35 582 582 HOH HOH . F 5 HOH B 36 586 586 HOH HOH . F 5 HOH B 37 587 587 HOH HOH . F 5 HOH B 38 588 588 HOH HOH . F 5 HOH B 39 590 590 HOH HOH . F 5 HOH B 40 595 595 HOH HOH . F 5 HOH B 41 597 597 HOH HOH . F 5 HOH B 42 598 598 HOH HOH . F 5 HOH B 43 601 601 HOH HOH . F 5 HOH B 44 603 603 HOH HOH . F 5 HOH B 45 604 604 HOH HOH . F 5 HOH B 46 608 608 HOH HOH . F 5 HOH B 47 609 609 HOH HOH . F 5 HOH B 48 610 610 HOH HOH . F 5 HOH B 49 611 611 HOH HOH . F 5 HOH B 50 612 612 HOH HOH . F 5 HOH B 51 613 613 HOH HOH . F 5 HOH B 52 614 614 HOH HOH . F 5 HOH B 53 615 615 HOH HOH . F 5 HOH B 54 618 618 HOH HOH . F 5 HOH B 55 620 620 HOH HOH . F 5 HOH B 56 624 624 HOH HOH . F 5 HOH B 57 629 629 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 4 34.035 5.899 19.388 1 14.78 ? PB GDP 194 A 1 HETATM 2 O O1B GDP . . . D 4 33.135 5.729 18.218 1 12.84 ? O1B GDP 194 A 1 HETATM 3 O O2B GDP . . . D 4 33.49 5.659 20.646 1 16.71 ? O2B GDP 194 A 1 HETATM 4 O O3B GDP . . . D 4 35.423 5.067 19.149 1 12.47 ? O3B GDP 194 A 1 HETATM 5 O O3A GDP . . . D 4 34.493 7.405 19.437 1 15.32 ? O3A GDP 194 A 1 HETATM 6 P PA GDP . . . D 4 34.468 8.508 20.687 1 13.42 ? PA GDP 194 A 1 HETATM 7 O O1A GDP . . . D 4 33.072 8.734 21.173 1 17.27 ? O1A GDP 194 A 1 HETATM 8 O O2A GDP . . . D 4 35.423 7.949 21.698 1 15.37 ? O2A GDP 194 A 1 HETATM 9 O O5' GDP . . . D 4 35.006 9.787 19.974 1 16.5 ? O5' GDP 194 A 1 HETATM 10 C C5' GDP . . . D 4 36.034 9.775 18.926 1 16.6 ? C5' GDP 194 A 1 HETATM 11 C C4' GDP . . . D 4 36.63 11.094 18.67 1 19.53 ? C4' GDP 194 A 1 HETATM 12 O O4' GDP . . . D 4 35.59 11.974 18.016 1 20.42 ? O4' GDP 194 A 1 HETATM 13 C C3' GDP . . . D 4 36.955 11.923 19.97 1 20.39 ? C3' GDP 194 A 1 HETATM 14 O O3' GDP . . . D 4 38.164 12.698 19.648 1 22.07 ? O3' GDP 194 A 1 HETATM 15 C C2' GDP . . . D 4 35.762 12.897 20.226 1 18.79 ? C2' GDP 194 A 1 HETATM 16 O O2' GDP . . . D 4 35.977 14.12 20.953 1 23.68 ? O2' GDP 194 A 1 HETATM 17 C C1' GDP . . . D 4 35.258 13.213 18.801 1 18.07 ? C1' GDP 194 A 1 HETATM 18 N N9 GDP . . . D 4 33.798 13.422 18.705 1 17.2 ? N9 GDP 194 A 1 HETATM 19 C C8 GDP . . . D 4 32.895 12.352 19.229 1 16.64 ? C8 GDP 194 A 1 HETATM 20 N N7 GDP . . . D 4 31.728 13.065 18.88 1 14.45 ? N7 GDP 194 A 1 HETATM 21 C C5 GDP . . . D 4 31.798 14.262 18.299 1 15.57 ? C5 GDP 194 A 1 HETATM 22 C C6 GDP . . . D 4 31.066 15.334 17.771 1 14.54 ? C6 GDP 194 A 1 HETATM 23 O O6 GDP . . . D 4 29.732 15.218 17.82 1 16.02 ? O6 GDP 194 A 1 HETATM 24 N N1 GDP . . . D 4 31.607 16.435 17.236 1 14.07 ? N1 GDP 194 A 1 HETATM 25 C C2 GDP . . . D 4 33.085 16.531 17.197 1 15.27 ? C2 GDP 194 A 1 HETATM 26 N N2 GDP . . . D 4 33.409 17.682 16.636 1 15.75 ? N2 GDP 194 A 1 HETATM 27 N N3 GDP . . . D 4 33.79 15.598 17.652 1 16.67 ? N3 GDP 194 A 1 HETATM 28 C C4 GDP . . . D 4 33.208 14.521 18.176 1 16.71 ? C4 GDP 194 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #