data_1KSZ # _model_server_result.job_id a8bjvzWnx0l2QZO1HaO7dw _model_server_result.datetime_utc '2024-11-18 04:22:13' _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 1ksz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":440}' # _entry.id 1KSZ # _exptl.entry_id 1KSZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 445.259 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2-DEAZO-6-THIOPHOSPHATE GUANOSINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 1KSZ _cell.length_a 81.63 _cell.length_b 81.63 _cell.length_c 159.22 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KSZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _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 1,2 # 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' 6_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 106.146667 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 OD1 ASP 13 A ASP 13 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc2 A O GLY 40 A GLY 40 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc3 C O1B GDP . A GDP 432 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc4 C O2A GDP . A GDP 432 1_555 B MG MG . A MG 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc5 B MG MG . A MG 435 1_555 D O HDA . A HDA 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc6 B MG MG . A MG 435 1_555 E O3P PGS . A PGS 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? # _chem_comp.formula 'C10 H15 N4 O10 P2 S 1' _chem_comp.formula_weight 445.259 _chem_comp.id PGS _chem_comp.mon_nstd_flag . _chem_comp.name "2-DEAZO-6-THIOPHOSPHATE GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A PGS doub 294 n n PA O2A PGS sing 295 n n PA O3A PGS sing 296 n n PA O5' PGS sing 297 n n O2A HOA2 PGS sing 298 n n O3A HOA3 PGS sing 299 n n O5' C5' PGS sing 300 n n C5' C4' PGS sing 301 n n C5' "H5'1" PGS sing 302 n n C5' "H5'2" PGS sing 303 n n C4' O4' PGS sing 304 n n C4' C3' PGS sing 305 n n C4' H4' PGS sing 306 n n O4' C1' PGS sing 307 n n C3' O3' PGS sing 308 n n C3' C2' PGS sing 309 n n C3' H3' PGS sing 310 n n O3' HO3' PGS sing 311 n n C2' O2' PGS sing 312 n n C2' C1' PGS sing 313 n n C2' H2' PGS sing 314 n n O2' HO2' PGS sing 315 n n C1' N9 PGS sing 316 n n C1' H1' PGS sing 317 n n N9 C8 PGS sing 318 n y N9 C4 PGS sing 319 n y C8 N7 PGS doub 320 n y C8 H8 PGS sing 321 n n N7 C5 PGS sing 322 n y C5 C6 PGS sing 323 n y C5 C4 PGS doub 324 n y C6 S6 PGS sing 325 n n C6 N1 PGS doub 326 n y S6 P PGS sing 327 n n P O1P PGS doub 328 n n P O2P PGS sing 329 n n P O3P PGS sing 330 n n O2P HOP2 PGS sing 331 n n O3P HOP3 PGS sing 332 n n N1 C2 PGS sing 333 n y N1 HN1 PGS sing 334 n n C2 N3 PGS doub 335 n y C2 H2 PGS sing 336 n n N3 C4 PGS sing 337 n y # _atom_sites.entry_id 1KSZ _atom_sites.fract_transf_matrix[1][1] 0.01225 _atom_sites.fract_transf_matrix[1][2] 0.007073 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014146 _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] 0.006281 _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 1 435 435 MG MG . C 3 GDP A 1 432 432 GDP GDP . D 4 HDA A 1 437 437 HDA HDA . E 5 PGS A 1 440 440 PGS PGS . F 6 HOH A 1 500 500 HOH HOH . F 6 HOH A 2 501 501 HOH HOH . F 6 HOH A 3 502 502 HOH HOH . F 6 HOH A 4 503 503 HOH HOH . F 6 HOH A 5 504 504 HOH HOH . F 6 HOH A 6 505 505 HOH HOH . F 6 HOH A 7 506 506 HOH HOH . F 6 HOH A 8 507 507 HOH HOH . F 6 HOH A 9 508 508 HOH HOH . F 6 HOH A 10 509 509 HOH HOH . F 6 HOH A 11 510 510 HOH HOH . F 6 HOH A 12 511 511 HOH HOH . F 6 HOH A 13 512 512 HOH HOH . F 6 HOH A 14 513 513 HOH HOH . F 6 HOH A 15 514 514 HOH HOH . F 6 HOH A 16 515 515 HOH HOH . F 6 HOH A 17 516 516 HOH HOH . F 6 HOH A 18 517 517 HOH HOH . F 6 HOH A 19 518 518 HOH HOH . F 6 HOH A 20 519 519 HOH HOH . F 6 HOH A 21 520 520 HOH HOH . F 6 HOH A 22 521 521 HOH HOH . F 6 HOH A 23 522 522 HOH HOH . F 6 HOH A 24 523 523 HOH HOH . F 6 HOH A 25 524 524 HOH HOH . F 6 HOH A 26 525 525 HOH HOH . F 6 HOH A 27 526 526 HOH HOH . F 6 HOH A 28 527 527 HOH HOH . F 6 HOH A 29 528 528 HOH HOH . F 6 HOH A 30 529 529 HOH HOH . F 6 HOH A 31 530 530 HOH HOH . F 6 HOH A 32 531 531 HOH HOH . F 6 HOH A 33 532 532 HOH HOH . F 6 HOH A 34 533 533 HOH HOH . F 6 HOH A 35 534 534 HOH HOH . F 6 HOH A 36 535 535 HOH HOH . F 6 HOH A 37 536 536 HOH HOH . F 6 HOH A 38 537 537 HOH HOH . F 6 HOH A 39 538 538 HOH HOH . F 6 HOH A 40 539 539 HOH HOH . F 6 HOH A 41 540 540 HOH HOH . F 6 HOH A 42 541 541 HOH HOH . F 6 HOH A 43 542 542 HOH HOH . F 6 HOH A 44 543 543 HOH HOH . F 6 HOH A 45 544 544 HOH HOH . F 6 HOH A 46 545 545 HOH HOH . F 6 HOH A 47 546 546 HOH HOH . F 6 HOH A 48 547 547 HOH HOH . F 6 HOH A 49 548 548 HOH HOH . F 6 HOH A 50 549 549 HOH HOH . F 6 HOH A 51 550 550 HOH HOH . F 6 HOH A 52 551 551 HOH HOH . F 6 HOH A 53 552 552 HOH HOH . F 6 HOH A 54 553 553 HOH HOH . F 6 HOH A 55 554 554 HOH HOH . F 6 HOH A 56 555 555 HOH HOH . F 6 HOH A 57 556 556 HOH HOH . F 6 HOH A 58 557 557 HOH HOH . F 6 HOH A 59 558 558 HOH HOH . F 6 HOH A 60 559 559 HOH HOH . F 6 HOH A 61 560 560 HOH HOH . F 6 HOH A 62 561 561 HOH HOH . F 6 HOH A 63 562 562 HOH HOH . F 6 HOH A 64 563 563 HOH HOH . F 6 HOH A 65 564 564 HOH HOH . F 6 HOH A 66 565 565 HOH HOH . F 6 HOH A 67 566 566 HOH HOH . F 6 HOH A 68 567 567 HOH HOH . F 6 HOH A 69 568 568 HOH HOH . F 6 HOH A 70 569 569 HOH HOH . F 6 HOH A 71 570 570 HOH HOH . F 6 HOH A 72 571 571 HOH HOH . F 6 HOH A 73 572 572 HOH HOH . F 6 HOH A 74 573 573 HOH HOH . F 6 HOH A 75 574 574 HOH HOH . F 6 HOH A 76 575 575 HOH HOH . F 6 HOH A 77 576 576 HOH HOH . F 6 HOH A 78 577 577 HOH HOH . F 6 HOH A 79 578 578 HOH HOH . F 6 HOH A 80 579 579 HOH HOH . F 6 HOH A 81 580 580 HOH HOH . F 6 HOH A 82 581 581 HOH HOH . F 6 HOH A 83 582 582 HOH HOH . F 6 HOH A 84 583 583 HOH HOH . F 6 HOH A 85 584 584 HOH HOH . F 6 HOH A 86 585 585 HOH HOH . F 6 HOH A 87 586 586 HOH HOH . F 6 HOH A 88 587 587 HOH HOH . F 6 HOH A 89 588 588 HOH HOH . F 6 HOH A 90 589 589 HOH HOH . F 6 HOH A 91 590 590 HOH HOH . F 6 HOH A 92 591 591 HOH HOH . F 6 HOH A 93 592 592 HOH HOH . F 6 HOH A 94 593 593 HOH HOH . F 6 HOH A 95 594 594 HOH HOH . F 6 HOH A 96 595 595 HOH HOH . F 6 HOH A 97 596 596 HOH HOH . F 6 HOH A 98 597 597 HOH HOH . F 6 HOH A 99 598 598 HOH HOH . F 6 HOH A 100 599 599 HOH HOH . F 6 HOH A 101 600 600 HOH HOH . F 6 HOH A 102 601 601 HOH HOH . F 6 HOH A 103 602 602 HOH HOH . F 6 HOH A 104 603 603 HOH HOH . F 6 HOH A 105 604 604 HOH HOH . F 6 HOH A 106 605 605 HOH HOH . F 6 HOH A 107 606 606 HOH HOH . F 6 HOH A 108 607 607 HOH HOH . F 6 HOH A 109 608 608 HOH HOH . F 6 HOH A 110 609 609 HOH HOH . F 6 HOH A 111 610 610 HOH HOH . F 6 HOH A 112 611 611 HOH HOH . F 6 HOH A 113 612 612 HOH HOH . F 6 HOH A 114 613 613 HOH HOH . F 6 HOH A 115 614 614 HOH HOH . F 6 HOH A 116 615 615 HOH HOH . F 6 HOH A 117 616 616 HOH HOH . F 6 HOH A 118 617 617 HOH HOH . F 6 HOH A 119 618 618 HOH HOH . F 6 HOH A 120 619 619 HOH HOH . F 6 HOH A 121 620 620 HOH HOH . F 6 HOH A 122 621 621 HOH HOH . F 6 HOH A 123 622 622 HOH HOH . F 6 HOH A 124 623 623 HOH HOH . F 6 HOH A 125 624 624 HOH HOH . F 6 HOH A 126 625 625 HOH HOH . F 6 HOH A 127 626 626 HOH HOH . F 6 HOH A 128 627 627 HOH HOH . F 6 HOH A 129 628 628 HOH HOH . F 6 HOH A 130 629 629 HOH HOH . F 6 HOH A 131 630 630 HOH HOH . F 6 HOH A 132 631 631 HOH HOH . F 6 HOH A 133 632 632 HOH HOH . F 6 HOH A 134 633 633 HOH HOH . F 6 HOH A 135 634 634 HOH HOH . F 6 HOH A 136 635 635 HOH HOH . F 6 HOH A 137 636 636 HOH HOH . F 6 HOH A 138 637 637 HOH HOH . F 6 HOH A 139 638 638 HOH HOH . F 6 HOH A 140 639 639 HOH HOH . F 6 HOH A 141 640 640 HOH HOH . F 6 HOH A 142 641 641 HOH HOH . F 6 HOH A 143 642 642 HOH HOH . F 6 HOH A 144 643 643 HOH HOH . F 6 HOH A 145 644 644 HOH HOH . F 6 HOH A 146 645 645 HOH HOH . F 6 HOH A 147 646 646 HOH HOH . F 6 HOH A 148 647 647 HOH HOH . F 6 HOH A 149 648 648 HOH HOH . F 6 HOH A 150 649 649 HOH HOH . F 6 HOH A 151 650 650 HOH HOH . F 6 HOH A 152 651 651 HOH HOH . F 6 HOH A 153 652 652 HOH HOH . F 6 HOH A 154 653 653 HOH HOH . F 6 HOH A 155 654 654 HOH HOH . F 6 HOH A 156 655 655 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 PA PGS . . . E 5 -16.353 54.748 50.03 1 20.86 ? PA PGS 440 A 1 HETATM 2 O O1A PGS . . . E 5 -16.366 55.621 48.856 1 21.13 ? O1A PGS 440 A 1 HETATM 3 O O2A PGS . . . E 5 -17.675 54.733 50.663 1 20.9 ? O2A PGS 440 A 1 HETATM 4 O O3A PGS . . . E 5 -15.946 53.403 49.654 1 21.14 ? O3A PGS 440 A 1 HETATM 5 O O5' PGS . . . E 5 -15.303 55.308 51.056 1 21.12 ? O5' PGS 440 A 1 HETATM 6 C C5' PGS . . . E 5 -15.477 55.136 52.349 1 21.59 ? C5' PGS 440 A 1 HETATM 7 C C4' PGS . . . E 5 -14.207 54.911 52.821 1 21.98 ? C4' PGS 440 A 1 HETATM 8 O O4' PGS . . . E 5 -13.83 53.826 51.987 1 22.11 ? O4' PGS 440 A 1 HETATM 9 C C3' PGS . . . E 5 -13.313 56.132 52.747 1 22.23 ? C3' PGS 440 A 1 HETATM 10 O O3' PGS . . . E 5 -12.428 56.111 53.87 1 22.45 ? O3' PGS 440 A 1 HETATM 11 C C2' PGS . . . E 5 -12.436 55.553 51.66 1 22.46 ? C2' PGS 440 A 1 HETATM 12 O O2' PGS . . . E 5 -11.061 55.939 51.698 1 22.64 ? O2' PGS 440 A 1 HETATM 13 C C1' PGS . . . E 5 -12.47 54.039 51.826 1 22.61 ? C1' PGS 440 A 1 HETATM 14 N N9 PGS . . . E 5 -12.108 53.508 50.591 1 22.97 ? N9 PGS 440 A 1 HETATM 15 C C8 PGS . . . E 5 -12.928 53.017 49.57 1 23.04 ? C8 PGS 440 A 1 HETATM 16 N N7 PGS . . . E 5 -12.287 52.335 48.677 1 23.18 ? N7 PGS 440 A 1 HETATM 17 C C5 PGS . . . E 5 -10.952 52.372 49.107 1 23.36 ? C5 PGS 440 A 1 HETATM 18 C C6 PGS . . . E 5 -9.822 51.795 48.501 1 23.58 ? C6 PGS 440 A 1 HETATM 19 S S6 PGS . . . E 5 -9.722 50.988 46.878 1 24.32 ? S6 PGS 440 A 1 HETATM 20 P P PGS . . . E 5 -8.83 49.391 46.61 1 24.13 ? P PGS 440 A 1 HETATM 21 O O1P PGS . . . E 5 -9.89 48.405 46.228 1 23.91 ? O1P PGS 440 A 1 HETATM 22 O O2P PGS . . . E 5 -8.144 49.013 47.893 1 23.87 ? O2P PGS 440 A 1 HETATM 23 O O3P PGS . . . E 5 -7.841 49.515 45.518 1 24.2 ? O3P PGS 440 A 1 HETATM 24 N N1 PGS . . . E 5 -8.673 52.014 49.241 1 23.39 ? N1 PGS 440 A 1 HETATM 25 C C2 PGS . . . E 5 -8.631 52.759 50.393 1 23.35 ? C2 PGS 440 A 1 HETATM 26 N N3 PGS . . . E 5 -9.704 53.321 50.957 1 23.26 ? N3 PGS 440 A 1 HETATM 27 C C4 PGS . . . E 5 -10.828 53.075 50.261 1 23.17 ? C4 PGS 440 A 1 HETATM 28 H "H5'1" PGS . . . E 5 -16.084 54.252 52.552 1 0 ? "H5'1" PGS 440 A 1 HETATM 29 H "H5'2" PGS . . . E 5 -15.877 55.969 52.906 1 0 ? "H5'2" PGS 440 A 1 HETATM 30 H H4' PGS . . . E 5 -14.261 54.576 53.857 1 0 ? H4' PGS 440 A 1 HETATM 31 H H3' PGS . . . E 5 -13.758 57.104 52.585 1 0 ? H3' PGS 440 A 1 HETATM 32 H HO3' PGS . . . E 5 -12.95 56.029 54.678 1 0 ? HO3' PGS 440 A 1 HETATM 33 H H2' PGS . . . E 5 -12.871 55.857 50.711 1 0 ? H2' PGS 440 A 1 HETATM 34 H HO2' PGS . . . E 5 -10.574 55.156 51.418 1 0 ? HO2' PGS 440 A 1 HETATM 35 H H1' PGS . . . E 5 -11.858 53.695 52.663 1 0 ? H1' PGS 440 A 1 HETATM 36 H H8 PGS . . . E 5 -14.006 53.158 49.542 1 0 ? H8 PGS 440 A 1 HETATM 37 H HN1 PGS . . . E 5 -7.793 51.621 48.932 1 0 ? HN1 PGS 440 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 37 #