data_3UT5 # _model_server_result.job_id 1FivMG5Xv-GuvMDRQDm_sQ _model_server_result.datetime_utc '2024-11-17 02:27:24' _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":"N","auth_seq_id":600}' # _entry.id 3UT5 # _exptl.entry_id 3UT5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 ? 5 G N N ? 5 N 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 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _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 PG O1G GTP doub 225 n n PG O2G GTP sing 226 n n PG O3G GTP sing 227 n n PG O3B GTP sing 228 n n O2G HOG2 GTP sing 229 n n O3G HOG3 GTP sing 230 n n O3B PB GTP sing 231 n n PB O1B GTP doub 232 n n PB O2B GTP sing 233 n n PB O3A GTP sing 234 n n O2B HOB2 GTP sing 235 n n O3A PA GTP sing 236 n n PA O1A GTP doub 237 n n PA O2A GTP sing 238 n n PA O5' GTP sing 239 n n O2A HOA2 GTP sing 240 n n O5' C5' GTP sing 241 n n C5' C4' GTP sing 242 n n C5' H5' GTP sing 243 n n C5' "H5''" GTP sing 244 n n C4' O4' GTP sing 245 n n C4' C3' GTP sing 246 n n C4' H4' GTP sing 247 n n O4' C1' GTP sing 248 n n C3' O3' GTP sing 249 n n C3' C2' GTP sing 250 n n C3' H3' GTP sing 251 n n O3' HO3' GTP sing 252 n n C2' O2' GTP sing 253 n n C2' C1' GTP sing 254 n n C2' H2' GTP sing 255 n n O2' HO2' GTP sing 256 n n C1' N9 GTP sing 257 n n C1' H1' GTP sing 258 n n N9 C8 GTP sing 259 n y N9 C4 GTP sing 260 n y C8 N7 GTP doub 261 n y C8 H8 GTP sing 262 n n N7 C5 GTP sing 263 n y C5 C6 GTP sing 264 n n C5 C4 GTP doub 265 n y C6 O6 GTP doub 266 n n C6 N1 GTP sing 267 n n N1 C2 GTP sing 268 n n N1 HN1 GTP sing 269 n n C2 N2 GTP sing 270 n n C2 N3 GTP doub 271 n n N2 HN21 GTP sing 272 n n N2 HN22 GTP sing 273 n n N3 C4 GTP sing 274 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 PG GTP . . . N 5 -21.33 124.789 105.973 1 58.42 ? PG GTP 600 C 1 HETATM 2 O O1G GTP . . . N 5 -22.268 125.053 104.865 1 60.81 ? O1G GTP 600 C 1 HETATM 3 O O2G GTP . . . N 5 -20.266 125.948 106.238 1 59.48 ? O2G GTP 600 C 1 HETATM 4 O O3G GTP . . . N 5 -22.135 124.64 107.348 1 58.43 ? O3G GTP 600 C 1 HETATM 5 O O3B GTP . . . N 5 -20.545 123.368 105.565 1 57.7 ? O3B GTP 600 C 1 HETATM 6 P PB GTP . . . N 5 -18.917 123.19 105.703 1 58.21 ? PB GTP 600 C 1 HETATM 7 O O1B GTP . . . N 5 -18.138 124.048 104.786 1 58 ? O1B GTP 600 C 1 HETATM 8 O O2B GTP . . . N 5 -18.709 121.645 105.327 1 58.02 ? O2B GTP 600 C 1 HETATM 9 O O3A GTP . . . N 5 -18.52 123.515 107.284 1 57.92 ? O3A GTP 600 C 1 HETATM 10 P PA GTP . . . N 5 -17.022 123.092 107.813 1 58.8 ? PA GTP 600 C 1 HETATM 11 O O1A GTP . . . N 5 -16.276 122.128 106.875 1 58.96 ? O1A GTP 600 C 1 HETATM 12 O O2A GTP . . . N 5 -16.12 124.402 108.042 1 59.15 ? O2A GTP 600 C 1 HETATM 13 O O5' GTP . . . N 5 -17.376 122.349 109.181 1 58.22 ? O5' GTP 600 C 1 HETATM 14 C C5' GTP . . . N 5 -16.684 122.806 110.322 1 59.03 ? C5' GTP 600 C 1 HETATM 15 C C4' GTP . . . N 5 -16.256 121.582 111.11 1 59.18 ? C4' GTP 600 C 1 HETATM 16 O O4' GTP . . . N 5 -15.138 121.097 110.359 1 58.18 ? O4' GTP 600 C 1 HETATM 17 C C3' GTP . . . N 5 -15.662 121.894 112.5 1 60.24 ? C3' GTP 600 C 1 HETATM 18 O O3' GTP . . . N 5 -15.559 120.721 113.322 1 62.53 ? O3' GTP 600 C 1 HETATM 19 C C2' GTP . . . N 5 -14.285 122.471 112.149 1 60.79 ? C2' GTP 600 C 1 HETATM 20 O O2' GTP . . . N 5 -13.357 122.303 113.224 1 64.15 ? O2' GTP 600 C 1 HETATM 21 C C1' GTP . . . N 5 -13.91 121.543 110.989 1 59.66 ? C1' GTP 600 C 1 HETATM 22 N N9 GTP . . . N 5 -13.088 122.187 109.989 1 60.85 ? N9 GTP 600 C 1 HETATM 23 C C8 GTP . . . N 5 -13.433 123.215 109.136 1 61.01 ? C8 GTP 600 C 1 HETATM 24 N N7 GTP . . . N 5 -12.429 123.504 108.384 1 62.91 ? N7 GTP 600 C 1 HETATM 25 C C5 GTP . . . N 5 -11.373 122.678 108.722 1 63.27 ? C5 GTP 600 C 1 HETATM 26 C C6 GTP . . . N 5 -10.032 122.465 108.246 1 65.53 ? C6 GTP 600 C 1 HETATM 27 O O6 GTP . . . N 5 -9.582 123.134 107.361 1 68.36 ? O6 GTP 600 C 1 HETATM 28 N N1 GTP . . . N 5 -9.243 121.515 108.838 1 66.29 ? N1 GTP 600 C 1 HETATM 29 C C2 GTP . . . N 5 -9.744 120.724 109.865 1 64.71 ? C2 GTP 600 C 1 HETATM 30 N N2 GTP . . . N 5 -8.935 119.76 110.426 1 66.27 ? N2 GTP 600 C 1 HETATM 31 N N3 GTP . . . N 5 -11.005 120.886 110.316 1 62.27 ? N3 GTP 600 C 1 HETATM 32 C C4 GTP . . . N 5 -11.821 121.818 109.756 1 61.12 ? C4 GTP 600 C 1 # _model_server_stats.io_time_ms 107 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #