data_1KY3 # _model_server_result.job_id 5wvSw12sw0HHpEo1c_BOxw _model_server_result.datetime_utc '2024-11-16 18:34:43' _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 1ky3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 1KY3 # _exptl.entry_id 1KY3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 1KY3 _cell.length_a 49.535 _cell.length_b 55.43 _cell.length_c 60.177 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KY3 _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 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,D _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 3 _struct_asym.id C _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 22 A THR 22 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc2 C O3B GDP . A GDP 400 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc3 B MG MG . A MG 401 1_555 D O HOH . A HOH 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc4 B MG MG . A MG 401 1_555 D O HOH . A HOH 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc5 B MG MG . A MG 401 1_555 D O HOH . A HOH 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc6 B MG MG . A MG 401 1_555 D O HOH . A HOH 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _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 1KY3 _atom_sites.fract_transf_matrix[1][1] 0.020188 _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] 0.018041 _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] 0.016618 _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 MG A 1 401 401 MG MG . C 3 GDP A 1 400 400 GDP GDP . D 4 HOH A 1 500 500 HOH HOH . D 4 HOH A 2 501 501 HOH HOH . D 4 HOH A 3 502 502 HOH HOH . D 4 HOH A 4 503 503 HOH HOH . D 4 HOH A 5 504 504 HOH HOH . D 4 HOH A 6 505 505 HOH HOH . D 4 HOH A 7 506 506 HOH HOH . D 4 HOH A 8 507 507 HOH HOH . D 4 HOH A 9 508 508 HOH HOH . D 4 HOH A 10 509 509 HOH HOH . D 4 HOH A 11 510 510 HOH HOH . D 4 HOH A 12 511 511 HOH HOH . D 4 HOH A 13 512 512 HOH HOH . D 4 HOH A 14 513 513 HOH HOH . D 4 HOH A 15 514 514 HOH HOH . D 4 HOH A 16 515 515 HOH HOH . D 4 HOH A 17 516 516 HOH HOH . D 4 HOH A 18 517 517 HOH HOH . D 4 HOH A 19 518 518 HOH HOH . D 4 HOH A 20 519 519 HOH HOH . D 4 HOH A 21 520 520 HOH HOH . D 4 HOH A 22 521 521 HOH HOH . D 4 HOH A 23 522 522 HOH HOH . D 4 HOH A 24 523 523 HOH HOH . D 4 HOH A 25 524 524 HOH HOH . D 4 HOH A 26 525 525 HOH HOH . D 4 HOH A 27 526 526 HOH HOH . D 4 HOH A 28 527 527 HOH HOH . D 4 HOH A 29 528 528 HOH HOH . D 4 HOH A 30 529 529 HOH HOH . D 4 HOH A 31 530 530 HOH HOH . D 4 HOH A 32 531 531 HOH HOH . D 4 HOH A 33 532 532 HOH HOH . D 4 HOH A 34 533 533 HOH HOH . D 4 HOH A 35 534 534 HOH HOH . D 4 HOH A 36 535 535 HOH HOH . D 4 HOH A 37 536 536 HOH HOH . D 4 HOH A 38 537 537 HOH HOH . D 4 HOH A 39 538 538 HOH HOH . D 4 HOH A 40 539 539 HOH HOH . D 4 HOH A 41 540 540 HOH HOH . D 4 HOH A 42 541 541 HOH HOH . D 4 HOH A 43 542 542 HOH HOH . D 4 HOH A 44 543 543 HOH HOH . D 4 HOH A 45 544 544 HOH HOH . D 4 HOH A 46 545 545 HOH HOH . D 4 HOH A 47 546 546 HOH HOH . D 4 HOH A 48 547 547 HOH HOH . D 4 HOH A 49 548 548 HOH HOH . D 4 HOH A 50 549 549 HOH HOH . D 4 HOH A 51 550 550 HOH HOH . D 4 HOH A 52 551 551 HOH HOH . D 4 HOH A 53 552 552 HOH HOH . D 4 HOH A 54 553 553 HOH HOH . D 4 HOH A 55 554 554 HOH HOH . D 4 HOH A 56 555 555 HOH HOH . D 4 HOH A 57 556 556 HOH HOH . D 4 HOH A 58 557 557 HOH HOH . D 4 HOH A 59 558 558 HOH HOH . D 4 HOH A 60 559 559 HOH HOH . D 4 HOH A 61 560 560 HOH HOH . D 4 HOH A 62 561 561 HOH HOH . D 4 HOH A 63 562 562 HOH HOH . D 4 HOH A 64 563 563 HOH HOH . D 4 HOH A 65 564 564 HOH HOH . D 4 HOH A 66 565 565 HOH HOH . D 4 HOH A 67 566 566 HOH HOH . D 4 HOH A 68 567 567 HOH HOH . D 4 HOH A 69 568 568 HOH HOH . D 4 HOH A 70 569 569 HOH HOH . D 4 HOH A 71 570 570 HOH HOH . D 4 HOH A 72 571 571 HOH HOH . D 4 HOH A 73 572 572 HOH HOH . D 4 HOH A 74 573 573 HOH HOH . D 4 HOH A 75 574 574 HOH HOH . D 4 HOH A 76 575 575 HOH HOH . D 4 HOH A 77 576 576 HOH HOH . D 4 HOH A 78 577 577 HOH HOH . D 4 HOH A 79 578 578 HOH HOH . D 4 HOH A 80 579 579 HOH HOH . D 4 HOH A 81 580 580 HOH HOH . D 4 HOH A 82 581 581 HOH HOH . D 4 HOH A 83 582 582 HOH HOH . D 4 HOH A 84 583 583 HOH HOH . D 4 HOH A 85 584 584 HOH HOH . D 4 HOH A 86 585 585 HOH HOH . D 4 HOH A 87 586 586 HOH HOH . D 4 HOH A 88 587 587 HOH HOH . D 4 HOH A 89 588 588 HOH HOH . D 4 HOH A 90 589 589 HOH HOH . D 4 HOH A 91 590 590 HOH HOH . D 4 HOH A 92 591 591 HOH HOH . D 4 HOH A 93 592 592 HOH HOH . D 4 HOH A 94 593 593 HOH HOH . D 4 HOH A 95 594 594 HOH HOH . D 4 HOH A 96 595 595 HOH HOH . D 4 HOH A 97 596 596 HOH HOH . D 4 HOH A 98 597 597 HOH HOH . D 4 HOH A 99 598 598 HOH HOH . D 4 HOH A 100 599 599 HOH HOH . D 4 HOH A 101 600 600 HOH HOH . D 4 HOH A 102 601 601 HOH HOH . D 4 HOH A 103 602 602 HOH HOH . D 4 HOH A 104 603 603 HOH HOH . D 4 HOH A 105 604 604 HOH HOH . D 4 HOH A 106 605 605 HOH HOH . D 4 HOH A 107 606 606 HOH HOH . D 4 HOH A 108 607 607 HOH HOH . D 4 HOH A 109 608 608 HOH HOH . D 4 HOH A 110 609 609 HOH HOH . D 4 HOH A 111 610 610 HOH HOH . D 4 HOH A 112 611 611 HOH HOH . D 4 HOH A 113 612 612 HOH HOH . D 4 HOH A 114 613 613 HOH HOH . D 4 HOH A 115 614 614 HOH HOH . D 4 HOH A 116 615 615 HOH HOH . D 4 HOH A 117 616 616 HOH HOH . D 4 HOH A 118 617 617 HOH HOH . D 4 HOH A 119 618 618 HOH HOH . D 4 HOH A 120 619 619 HOH HOH . D 4 HOH A 121 620 620 HOH HOH . D 4 HOH A 122 621 621 HOH HOH . D 4 HOH A 123 622 622 HOH HOH . D 4 HOH A 124 623 623 HOH HOH . D 4 HOH A 125 624 624 HOH HOH . D 4 HOH A 126 625 625 HOH HOH . D 4 HOH A 127 626 626 HOH HOH . D 4 HOH A 128 627 627 HOH HOH . D 4 HOH A 129 628 628 HOH HOH . D 4 HOH A 130 629 629 HOH HOH . D 4 HOH A 131 630 630 HOH HOH . D 4 HOH A 132 631 631 HOH HOH . D 4 HOH A 133 632 632 HOH HOH . D 4 HOH A 134 633 633 HOH HOH . D 4 HOH A 135 634 634 HOH HOH . D 4 HOH A 136 635 635 HOH HOH . D 4 HOH A 137 636 636 HOH HOH . D 4 HOH A 138 637 637 HOH HOH . D 4 HOH A 139 638 638 HOH HOH . D 4 HOH A 140 639 639 HOH HOH . D 4 HOH A 141 640 640 HOH HOH . D 4 HOH A 142 641 641 HOH HOH . D 4 HOH A 143 642 642 HOH HOH . D 4 HOH A 144 643 643 HOH HOH . D 4 HOH A 145 644 644 HOH HOH . D 4 HOH A 146 645 645 HOH HOH . D 4 HOH A 147 646 646 HOH HOH . D 4 HOH A 148 647 647 HOH HOH . D 4 HOH A 149 648 648 HOH HOH . D 4 HOH A 150 649 649 HOH HOH . D 4 HOH A 151 650 650 HOH HOH . D 4 HOH A 152 651 651 HOH HOH . D 4 HOH A 153 652 652 HOH HOH . D 4 HOH A 154 653 653 HOH HOH . D 4 HOH A 155 654 654 HOH HOH . D 4 HOH A 156 655 655 HOH HOH . D 4 HOH A 157 656 656 HOH HOH . D 4 HOH A 158 657 657 HOH HOH . D 4 HOH A 159 658 658 HOH HOH . D 4 HOH A 160 659 659 HOH HOH . D 4 HOH A 161 660 660 HOH HOH . D 4 HOH A 162 661 661 HOH HOH . D 4 HOH A 163 662 662 HOH HOH . D 4 HOH A 164 663 663 HOH HOH . D 4 HOH A 165 664 664 HOH HOH . D 4 HOH A 166 665 665 HOH HOH . D 4 HOH A 167 666 666 HOH HOH . D 4 HOH A 168 667 667 HOH HOH . D 4 HOH A 169 668 668 HOH HOH . D 4 HOH A 170 669 669 HOH HOH . D 4 HOH A 171 670 670 HOH HOH . D 4 HOH A 172 671 671 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 3 -1.162 -4.409 27.317 1 21.9 ? PB GDP 400 A 1 HETATM 2 O O1B GDP . . . C 3 0.296 -4.224 27.042 1 20.25 ? O1B GDP 400 A 1 HETATM 3 O O2B GDP . . . C 3 -1.849 -5.376 26.362 1 24.54 ? O2B GDP 400 A 1 HETATM 4 O O3B GDP . . . C 3 -1.949 -3.111 27.563 1 21.81 ? O3B GDP 400 A 1 HETATM 5 O O3A GDP . . . C 3 -1.199 -5.204 28.784 1 20.76 ? O3A GDP 400 A 1 HETATM 6 P PA GDP . . . C 3 -2.21 -5.076 29.977 1 21.49 ? PA GDP 400 A 1 HETATM 7 O O1A GDP . . . C 3 -3.607 -5.283 29.524 1 25.21 ? O1A GDP 400 A 1 HETATM 8 O O2A GDP . . . C 3 -1.929 -3.875 30.85 1 22.25 ? O2A GDP 400 A 1 HETATM 9 O O5' GDP . . . C 3 -1.779 -6.345 30.863 1 21.51 ? O5' GDP 400 A 1 HETATM 10 C C5' GDP . . . C 3 -1.732 -7.652 30.286 1 21.12 ? C5' GDP 400 A 1 HETATM 11 C C4' GDP . . . C 3 -1.903 -8.642 31.395 1 24.2 ? C4' GDP 400 A 1 HETATM 12 O O4' GDP . . . C 3 -0.663 -8.618 32.175 1 23.68 ? O4' GDP 400 A 1 HETATM 13 C C3' GDP . . . C 3 -3.087 -8.34 32.334 1 27.1 ? C3' GDP 400 A 1 HETATM 14 O O3' GDP . . . C 3 -3.563 -9.659 32.765 1 34.15 ? O3' GDP 400 A 1 HETATM 15 C C2' GDP . . . C 3 -2.372 -7.685 33.509 1 27.04 ? C2' GDP 400 A 1 HETATM 16 O O2' GDP . . . C 3 -3.132 -7.739 34.685 1 28.02 ? O2' GDP 400 A 1 HETATM 17 C C1' GDP . . . C 3 -0.999 -8.395 33.513 1 24.74 ? C1' GDP 400 A 1 HETATM 18 N N9 GDP . . . C 3 0.089 -7.444 34.125 1 21.68 ? N9 GDP 400 A 1 HETATM 19 C C8 GDP . . . C 3 0.262 -6.132 33.802 1 20.81 ? C8 GDP 400 A 1 HETATM 20 N N7 GDP . . . C 3 1.275 -5.614 34.505 1 22.32 ? N7 GDP 400 A 1 HETATM 21 C C5 GDP . . . C 3 1.748 -6.659 35.304 1 21.63 ? C5 GDP 400 A 1 HETATM 22 C C6 GDP . . . C 3 2.799 -6.671 36.232 1 20.24 ? C6 GDP 400 A 1 HETATM 23 O O6 GDP . . . C 3 3.531 -5.711 36.525 1 20.11 ? O6 GDP 400 A 1 HETATM 24 N N1 GDP . . . C 3 2.971 -7.914 36.835 1 19.68 ? N1 GDP 400 A 1 HETATM 25 C C2 GDP . . . C 3 2.187 -9.002 36.538 1 20.36 ? C2 GDP 400 A 1 HETATM 26 N N2 GDP . . . C 3 2.447 -10.153 37.185 1 24.63 ? N2 GDP 400 A 1 HETATM 27 N N3 GDP . . . C 3 1.189 -8.987 35.653 1 22.17 ? N3 GDP 400 A 1 HETATM 28 C C4 GDP . . . C 3 1.032 -7.787 35.08 1 20.39 ? C4 GDP 400 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #