data_3UT5 # _model_server_result.job_id GkZhU9npvJHQ4xj2tHnwsw _model_server_result.datetime_utc '2024-11-17 02:31:43' _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 3ut5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":501}' # _entry.id 3UT5 # _exptl.entry_id 3UT5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _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 3UT5 _cell.length_a 64.81 _cell.length_b 128.87 _cell.length_c 254.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UT5 _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 8 K N N ? 8 P 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 covale ? covale1 F C 0EA 1 F 0EA 1 1_555 F N VAL 2 F VAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 sing covale ? covale2 F O1 0EA 1 F 0EA 1 1_555 F C3 0E5 3 F 0E5 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.536 sing covale ? covale3 F C VAL 2 F VAL 2 1_555 F N 0E5 3 F 0E5 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 sing covale ? covale4 F C 0E5 3 F 0E5 3 1_555 F N GLY 4 F GLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 sing metalc ? metalc1 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc2 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc3 H MG MG . A MG 502 1_555 T O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc4 H MG MG . A MG 502 1_555 T O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc5 H MG MG . A MG 502 1_555 T O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc6 H MG MG . A MG 502 1_555 U O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc7 N O2G GTP . C GTP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc8 N O1B GTP . C GTP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc9 O MG MG . C MG 601 1_555 V O HOH . C HOH 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc10 O MG MG . C MG 601 1_555 V O HOH . C HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc11 O MG MG . C MG 601 1_555 V O HOH . C HOH 725 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc12 O MG MG . C MG 601 1_555 W O HOH . D HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? # _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 134 n n PB O2B GDP sing 135 n n PB O3B GDP sing 136 n n PB O3A GDP sing 137 n n O2B HOB2 GDP sing 138 n n O3B HOB3 GDP sing 139 n n O3A PA GDP sing 140 n n PA O1A GDP doub 141 n n PA O2A GDP sing 142 n n PA O5' GDP sing 143 n n O2A HOA2 GDP sing 144 n n O5' C5' GDP sing 145 n n C5' C4' GDP sing 146 n n C5' H5' GDP sing 147 n n C5' "H5''" GDP sing 148 n n C4' O4' GDP sing 149 n n C4' C3' GDP sing 150 n n C4' H4' GDP sing 151 n n O4' C1' GDP sing 152 n n C3' O3' GDP sing 153 n n C3' C2' GDP sing 154 n n C3' H3' GDP sing 155 n n O3' HO3' GDP sing 156 n n C2' O2' GDP sing 157 n n C2' C1' GDP sing 158 n n C2' H2' GDP sing 159 n n O2' HO2' GDP sing 160 n n C1' N9 GDP sing 161 n n C1' H1' GDP sing 162 n n N9 C8 GDP sing 163 n y N9 C4 GDP sing 164 n y C8 N7 GDP doub 165 n y C8 H8 GDP sing 166 n n N7 C5 GDP sing 167 n y C5 C6 GDP sing 168 n n C5 C4 GDP doub 169 n y C6 O6 GDP doub 170 n n C6 N1 GDP sing 171 n n N1 C2 GDP sing 172 n n N1 HN1 GDP sing 173 n n C2 N2 GDP sing 174 n n C2 N3 GDP doub 175 n n N2 HN21 GDP sing 176 n n N2 HN22 GDP sing 177 n n N3 C4 GDP sing 178 n n # _atom_sites.entry_id 3UT5 _atom_sites.fract_transf_matrix[1][1] 0.01543 _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] 0.00776 _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] 0.003924 _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 G 5 GTP A 1 501 600 GTP GTP . H 6 MG A 1 502 601 MG MG . I 7 SO4 A 1 503 452 SO4 SO4 . J 7 SO4 A 1 504 453 SO4 SO4 . K 8 GDP B 1 501 600 GDP GDP . L 9 LOC B 1 502 700 LOC LOC . M 7 SO4 B 1 503 456 SO4 SO4 . N 5 GTP C 1 600 600 GTP GTP . O 6 MG C 1 601 601 MG MG . P 8 GDP D 1 501 600 GDP GDP . Q 9 LOC D 1 502 700 LOC LOC . R 7 SO4 D 1 503 456 SO4 SO4 . S 7 SO4 D 1 504 457 SO4 SO4 . T 10 HOH A 1 601 454 HOH HOH . T 10 HOH A 2 602 455 HOH HOH . T 10 HOH A 3 603 456 HOH HOH . T 10 HOH A 4 604 457 HOH HOH . T 10 HOH A 5 605 458 HOH HOH . T 10 HOH A 6 606 459 HOH HOH . T 10 HOH A 7 607 460 HOH HOH . T 10 HOH A 8 608 461 HOH HOH . T 10 HOH A 9 609 462 HOH HOH . T 10 HOH A 10 610 463 HOH HOH . T 10 HOH A 11 611 464 HOH HOH . T 10 HOH A 12 612 465 HOH HOH . T 10 HOH A 13 613 466 HOH HOH . T 10 HOH A 14 614 467 HOH HOH . T 10 HOH A 15 615 469 HOH HOH . T 10 HOH A 16 616 470 HOH HOH . T 10 HOH A 17 617 471 HOH HOH . T 10 HOH A 18 618 472 HOH HOH . T 10 HOH A 19 619 473 HOH HOH . T 10 HOH A 20 620 474 HOH HOH . T 10 HOH A 21 621 475 HOH HOH . T 10 HOH A 22 622 476 HOH HOH . T 10 HOH A 23 623 477 HOH HOH . T 10 HOH A 24 624 478 HOH HOH . T 10 HOH A 25 625 479 HOH HOH . T 10 HOH A 26 626 463 HOH HOH . T 10 HOH A 27 627 483 HOH HOH . U 10 HOH B 1 601 468 HOH HOH . U 10 HOH B 2 602 458 HOH HOH . U 10 HOH B 3 603 459 HOH HOH . U 10 HOH B 4 604 461 HOH HOH . U 10 HOH B 5 605 462 HOH HOH . U 10 HOH B 6 606 464 HOH HOH . U 10 HOH B 7 607 465 HOH HOH . U 10 HOH B 8 608 466 HOH HOH . U 10 HOH B 9 609 467 HOH HOH . U 10 HOH B 10 610 468 HOH HOH . U 10 HOH B 11 611 469 HOH HOH . U 10 HOH B 12 612 470 HOH HOH . U 10 HOH B 13 613 471 HOH HOH . U 10 HOH B 14 614 472 HOH HOH . U 10 HOH B 15 615 473 HOH HOH . U 10 HOH B 16 616 474 HOH HOH . U 10 HOH B 17 617 475 HOH HOH . U 10 HOH B 18 618 476 HOH HOH . U 10 HOH B 19 619 477 HOH HOH . U 10 HOH B 20 620 478 HOH HOH . U 10 HOH B 21 621 479 HOH HOH . U 10 HOH B 22 622 480 HOH HOH . U 10 HOH B 23 623 481 HOH HOH . U 10 HOH B 24 624 482 HOH HOH . U 10 HOH B 25 625 484 HOH HOH . U 10 HOH B 26 626 485 HOH HOH . U 10 HOH B 27 627 486 HOH HOH . U 10 HOH B 28 628 487 HOH HOH . V 10 HOH C 1 701 460 HOH HOH . V 10 HOH C 2 702 452 HOH HOH . V 10 HOH C 3 703 453 HOH HOH . V 10 HOH C 4 704 455 HOH HOH . V 10 HOH C 5 705 456 HOH HOH . V 10 HOH C 6 706 457 HOH HOH . V 10 HOH C 7 707 458 HOH HOH . V 10 HOH C 8 708 459 HOH HOH . V 10 HOH C 9 709 460 HOH HOH . V 10 HOH C 10 710 461 HOH HOH . V 10 HOH C 11 711 462 HOH HOH . V 10 HOH C 12 712 463 HOH HOH . V 10 HOH C 13 713 464 HOH HOH . V 10 HOH C 14 714 465 HOH HOH . V 10 HOH C 15 715 466 HOH HOH . V 10 HOH C 16 716 467 HOH HOH . V 10 HOH C 17 717 468 HOH HOH . V 10 HOH C 18 718 469 HOH HOH . V 10 HOH C 19 719 470 HOH HOH . V 10 HOH C 20 720 471 HOH HOH . V 10 HOH C 21 721 472 HOH HOH . V 10 HOH C 22 722 473 HOH HOH . V 10 HOH C 23 723 474 HOH HOH . V 10 HOH C 24 724 475 HOH HOH . V 10 HOH C 25 725 476 HOH HOH . V 10 HOH C 26 726 477 HOH HOH . V 10 HOH C 27 727 478 HOH HOH . V 10 HOH C 28 728 479 HOH HOH . V 10 HOH C 29 729 480 HOH HOH . V 10 HOH C 30 730 481 HOH HOH . V 10 HOH C 31 731 482 HOH HOH . V 10 HOH C 32 732 483 HOH HOH . V 10 HOH C 33 733 484 HOH HOH . V 10 HOH C 34 734 485 HOH HOH . V 10 HOH C 35 735 486 HOH HOH . V 10 HOH C 36 736 487 HOH HOH . V 10 HOH C 37 737 488 HOH HOH . V 10 HOH C 38 738 489 HOH HOH . V 10 HOH C 39 739 490 HOH HOH . V 10 HOH C 40 740 491 HOH HOH . V 10 HOH C 41 741 492 HOH HOH . V 10 HOH C 42 742 493 HOH HOH . V 10 HOH C 43 743 494 HOH HOH . W 10 HOH D 1 601 454 HOH HOH . W 10 HOH D 2 602 458 HOH HOH . W 10 HOH D 3 603 459 HOH HOH . W 10 HOH D 4 604 460 HOH HOH . W 10 HOH D 5 605 461 HOH HOH . W 10 HOH D 6 606 462 HOH HOH . W 10 HOH D 7 607 463 HOH HOH . W 10 HOH D 8 608 464 HOH HOH . W 10 HOH D 9 609 465 HOH HOH . W 10 HOH D 10 610 466 HOH HOH . W 10 HOH D 11 611 467 HOH HOH . W 10 HOH D 12 612 468 HOH HOH . W 10 HOH D 13 613 469 HOH HOH . W 10 HOH D 14 614 470 HOH HOH . W 10 HOH D 15 615 471 HOH HOH . W 10 HOH D 16 616 472 HOH HOH . W 10 HOH D 17 617 473 HOH HOH . W 10 HOH D 18 618 474 HOH HOH . W 10 HOH D 19 619 475 HOH HOH . W 10 HOH D 20 620 476 HOH HOH . W 10 HOH D 21 621 477 HOH HOH . W 10 HOH D 22 622 478 HOH HOH . W 10 HOH D 23 623 479 HOH HOH . W 10 HOH D 24 624 480 HOH HOH . W 10 HOH D 25 625 481 HOH HOH . W 10 HOH D 26 626 482 HOH HOH . W 10 HOH D 27 627 483 HOH HOH . W 10 HOH D 28 628 484 HOH HOH . W 10 HOH D 29 629 485 HOH HOH . W 10 HOH D 30 630 486 HOH HOH . W 10 HOH D 31 631 487 HOH HOH . W 10 HOH D 32 632 488 HOH HOH . W 10 HOH D 33 633 489 HOH HOH . W 10 HOH D 34 634 490 HOH HOH . W 10 HOH D 35 635 491 HOH HOH . W 10 HOH D 36 636 492 HOH HOH . X 10 HOH E 1 201 146 HOH HOH . X 10 HOH E 2 202 147 HOH HOH . X 10 HOH E 3 203 148 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 . . . P 8 -42.122 156.148 117.695 1 69.97 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . P 8 -41.422 157.127 116.834 1 73.1 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . P 8 -41.677 154.638 117.27 1 69.76 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . P 8 -43.711 156.242 117.558 1 73.08 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . P 8 -41.82 156.484 119.282 1 69.53 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . P 8 -40.332 156.306 119.902 1 67.39 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . P 8 -39.336 155.793 118.91 1 67.95 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . P 8 -39.73 157.649 120.534 1 70.95 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . P 8 -40.597 155.196 121.049 1 66.51 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . P 8 -40.625 155.725 122.394 1 66.37 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . P 8 -39.821 154.73 123.206 1 65.34 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . P 8 -38.462 154.708 122.682 1 64.51 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . P 8 -39.682 155.102 124.683 1 66.66 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . P 8 -39.584 153.902 125.48 1 69.07 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . P 8 -38.384 155.939 124.716 1 67.47 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . P 8 -37.751 155.914 126.019 1 69.55 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . P 8 -37.536 155.223 123.641 1 64.55 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . P 8 -36.663 156.092 122.883 1 64.4 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . P 8 -36.976 157.163 122.082 1 65.82 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . P 8 -35.897 157.674 121.541 1 66.65 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . P 8 -34.837 156.961 121.968 1 64.32 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . P 8 -33.409 157.012 121.754 1 65.71 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . P 8 -32.81 157.816 121.045 1 66.98 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . P 8 -32.694 156.053 122.409 1 64.14 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . P 8 -33.242 155.076 123.237 1 62.72 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . P 8 -32.416 154.2 123.833 1 63.75 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . P 8 -34.536 155.007 123.445 1 62.68 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . P 8 -35.344 155.916 122.834 1 63.45 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #