data_1U90 # _model_server_result.job_id y0ZegatutQuFbCOf-wIk-Q _model_server_result.datetime_utc '2024-11-15 05:22:58' _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 1u90 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 1U90 # _exptl.entry_id 1U90 _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 2 _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 1U90 _cell.length_a 52.59 _cell.length_b 61.535 _cell.length_c 112.946 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1U90 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 OG SER 18 A SER 28 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc2 D O3B GDP . A GDP 201 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc3 C MG MG . A MG 301 1_555 G O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc4 C MG MG . A MG 301 1_555 G O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc5 C MG MG . A MG 301 1_555 G O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 C MG MG . A MG 301 1_555 G O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc7 B OG SER 18 B SER 28 1_555 E MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc8 F O3B GDP . B GDP 202 1_555 E MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc9 E MG MG . B MG 302 1_555 H O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc10 E MG MG . B MG 302 1_555 H O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc11 E MG MG . B MG 302 1_555 H O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc12 E MG MG . B MG 302 1_555 H O HOH . B HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 1U90 _atom_sites.fract_transf_matrix[1][1] 0.019015 _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] 0.016251 _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] 0.008854 _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 MG A 1 301 301 MG MG2 . D 3 GDP A 1 201 201 GDP GDP . E 2 MG B 1 302 302 MG MG2 . F 3 GDP B 1 202 202 GDP GDP . G 4 HOH A 1 401 401 HOH HOH . G 4 HOH A 2 402 402 HOH HOH . G 4 HOH A 3 403 403 HOH HOH . G 4 HOH A 4 404 404 HOH HOH . G 4 HOH A 5 405 405 HOH HOH . G 4 HOH A 6 406 406 HOH HOH . G 4 HOH A 7 407 407 HOH HOH . G 4 HOH A 8 408 408 HOH HOH . G 4 HOH A 9 409 409 HOH HOH . G 4 HOH A 10 410 410 HOH HOH . G 4 HOH A 11 411 411 HOH HOH . G 4 HOH A 12 412 412 HOH HOH . G 4 HOH A 13 413 413 HOH HOH . G 4 HOH A 14 414 414 HOH HOH . G 4 HOH A 15 415 415 HOH HOH . G 4 HOH A 16 416 416 HOH HOH . G 4 HOH A 17 417 417 HOH HOH . G 4 HOH A 18 418 418 HOH HOH . G 4 HOH A 19 419 419 HOH HOH . G 4 HOH A 20 420 420 HOH HOH . G 4 HOH A 21 421 421 HOH HOH . G 4 HOH A 22 422 422 HOH HOH . G 4 HOH A 23 423 423 HOH HOH . G 4 HOH A 24 424 424 HOH HOH . G 4 HOH A 25 425 425 HOH HOH . G 4 HOH A 26 426 426 HOH HOH . G 4 HOH A 27 427 427 HOH HOH . G 4 HOH A 28 428 428 HOH HOH . G 4 HOH A 29 429 429 HOH HOH . G 4 HOH A 30 430 430 HOH HOH . G 4 HOH A 31 431 431 HOH HOH . G 4 HOH A 32 432 432 HOH HOH . G 4 HOH A 33 433 433 HOH HOH . G 4 HOH A 34 434 434 HOH HOH . G 4 HOH A 35 435 435 HOH HOH . G 4 HOH A 36 436 436 HOH HOH . G 4 HOH A 37 437 437 HOH HOH . G 4 HOH A 38 438 438 HOH HOH . G 4 HOH A 39 439 439 HOH HOH . G 4 HOH A 40 440 440 HOH HOH . G 4 HOH A 41 441 441 HOH HOH . G 4 HOH A 42 442 442 HOH HOH . G 4 HOH A 43 443 443 HOH HOH . G 4 HOH A 44 444 444 HOH HOH . G 4 HOH A 45 445 445 HOH HOH . G 4 HOH A 46 446 446 HOH HOH . G 4 HOH A 47 447 447 HOH HOH . G 4 HOH A 48 448 448 HOH HOH . G 4 HOH A 49 449 449 HOH HOH . G 4 HOH A 50 450 450 HOH HOH . G 4 HOH A 51 451 451 HOH HOH . G 4 HOH A 52 452 452 HOH HOH . G 4 HOH A 53 453 453 HOH HOH . G 4 HOH A 54 454 454 HOH HOH . G 4 HOH A 55 455 455 HOH HOH . G 4 HOH A 56 456 456 HOH HOH . G 4 HOH A 57 457 457 HOH HOH . G 4 HOH A 58 458 458 HOH HOH . G 4 HOH A 59 459 459 HOH HOH . G 4 HOH A 60 460 460 HOH HOH . G 4 HOH A 61 461 461 HOH HOH . G 4 HOH A 62 462 462 HOH HOH . G 4 HOH A 63 463 463 HOH HOH . G 4 HOH A 64 464 464 HOH HOH . G 4 HOH A 65 465 465 HOH HOH . G 4 HOH A 66 466 466 HOH HOH . G 4 HOH A 67 467 467 HOH HOH . G 4 HOH A 68 468 468 HOH HOH . G 4 HOH A 69 469 469 HOH HOH . G 4 HOH A 70 470 470 HOH HOH . G 4 HOH A 71 625 625 HOH HOH . G 4 HOH A 72 631 631 HOH HOH . G 4 HOH A 73 645 645 HOH HOH . G 4 HOH A 74 674 674 HOH HOH . G 4 HOH A 75 684 684 HOH HOH . H 4 HOH B 1 601 601 HOH HOH . H 4 HOH B 2 602 602 HOH HOH . H 4 HOH B 3 603 603 HOH HOH . H 4 HOH B 4 604 604 HOH HOH . H 4 HOH B 5 605 605 HOH HOH . H 4 HOH B 6 606 606 HOH HOH . H 4 HOH B 7 607 607 HOH HOH . H 4 HOH B 8 608 608 HOH HOH . H 4 HOH B 9 609 609 HOH HOH . H 4 HOH B 10 610 610 HOH HOH . H 4 HOH B 11 611 611 HOH HOH . H 4 HOH B 12 612 612 HOH HOH . H 4 HOH B 13 613 613 HOH HOH . H 4 HOH B 14 614 614 HOH HOH . H 4 HOH B 15 615 615 HOH HOH . H 4 HOH B 16 616 616 HOH HOH . H 4 HOH B 17 617 617 HOH HOH . H 4 HOH B 18 618 618 HOH HOH . H 4 HOH B 19 619 619 HOH HOH . H 4 HOH B 20 620 620 HOH HOH . H 4 HOH B 21 621 621 HOH HOH . H 4 HOH B 22 622 622 HOH HOH . H 4 HOH B 23 623 623 HOH HOH . H 4 HOH B 24 624 624 HOH HOH . H 4 HOH B 25 626 626 HOH HOH . H 4 HOH B 26 627 627 HOH HOH . H 4 HOH B 27 628 628 HOH HOH . H 4 HOH B 28 629 629 HOH HOH . H 4 HOH B 29 630 630 HOH HOH . H 4 HOH B 30 632 632 HOH HOH . H 4 HOH B 31 633 633 HOH HOH . H 4 HOH B 32 634 634 HOH HOH . H 4 HOH B 33 635 635 HOH HOH . H 4 HOH B 34 636 636 HOH HOH . H 4 HOH B 35 637 637 HOH HOH . H 4 HOH B 36 638 638 HOH HOH . H 4 HOH B 37 639 639 HOH HOH . H 4 HOH B 38 640 640 HOH HOH . H 4 HOH B 39 641 641 HOH HOH . H 4 HOH B 40 642 642 HOH HOH . H 4 HOH B 41 643 643 HOH HOH . H 4 HOH B 42 644 644 HOH HOH . H 4 HOH B 43 646 646 HOH HOH . H 4 HOH B 44 647 647 HOH HOH . H 4 HOH B 45 648 648 HOH HOH . H 4 HOH B 46 649 649 HOH HOH . H 4 HOH B 47 650 650 HOH HOH . H 4 HOH B 48 651 651 HOH HOH . H 4 HOH B 49 652 652 HOH HOH . H 4 HOH B 50 653 653 HOH HOH . H 4 HOH B 51 654 654 HOH HOH . H 4 HOH B 52 655 655 HOH HOH . H 4 HOH B 53 656 656 HOH HOH . H 4 HOH B 54 657 657 HOH HOH . H 4 HOH B 55 658 658 HOH HOH . H 4 HOH B 56 659 659 HOH HOH . H 4 HOH B 57 660 660 HOH HOH . H 4 HOH B 58 661 661 HOH HOH . H 4 HOH B 59 662 662 HOH HOH . H 4 HOH B 60 663 663 HOH HOH . H 4 HOH B 61 664 664 HOH HOH . H 4 HOH B 62 665 665 HOH HOH . H 4 HOH B 63 666 666 HOH HOH . H 4 HOH B 64 667 667 HOH HOH . H 4 HOH B 65 668 668 HOH HOH . H 4 HOH B 66 669 669 HOH HOH . H 4 HOH B 67 670 670 HOH HOH . H 4 HOH B 68 671 671 HOH HOH . H 4 HOH B 69 672 672 HOH HOH . H 4 HOH B 70 673 673 HOH HOH . H 4 HOH B 71 675 675 HOH HOH . H 4 HOH B 72 676 676 HOH HOH . H 4 HOH B 73 677 677 HOH HOH . H 4 HOH B 74 678 678 HOH HOH . H 4 HOH B 75 679 679 HOH HOH . H 4 HOH B 76 680 680 HOH HOH . H 4 HOH B 77 681 681 HOH HOH . H 4 HOH B 78 682 682 HOH HOH . H 4 HOH B 79 683 683 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 3 23.956 -4.253 7.649 1 15.14 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 3 23.559 -2.844 7.343 1 14.63 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 3 24.995 -4.827 6.693 1 16.08 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 3 22.748 -5.198 7.797 1 13.75 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 3 24.682 -4.185 9.133 1 17.74 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 3 24.584 -5.162 10.34 1 19.54 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 3 24.863 -6.554 9.921 1 20.41 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 3 23.268 -4.963 11.062 1 20.79 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 3 25.751 -4.61 11.299 1 22.27 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 3 27.13 -4.666 10.881 1 25.42 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 3 28.024 -4.758 12.094 1 25.72 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 3 27.93 -3.484 12.801 1 25.15 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 3 27.657 -5.885 13.093 1 27.31 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 3 28.957 -6.397 13.559 1 29.34 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 3 26.92 -5.153 14.201 1 27.13 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 3 26.98 -5.827 15.43 1 27.17 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 3 27.543 -3.731 14.137 1 25.77 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 3 26.505 -2.635 14.571 1 23.84 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 3 25.285 -2.405 13.984 1 21.2 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 3 24.656 -1.399 14.601 1 20.82 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 3 25.515 -0.982 15.614 1 20.37 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 3 25.367 0.045 16.584 1 20.66 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 3 24.385 0.797 16.702 1 21.02 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 3 26.478 0.165 17.457 1 22.8 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 3 27.601 -0.654 17.364 1 23.84 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 3 28.601 -0.459 18.241 1 28.03 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 3 27.735 -1.628 16.443 1 22.53 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 3 26.662 -1.734 15.61 1 22.91 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 28 #