data_7ODN # _model_server_result.job_id lA6qs5uKfy0cjYX2Mp6rKg _model_server_result.datetime_utc '2024-11-26 12:18:45' _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 7odn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 7ODN # _exptl.entry_id 7ODN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 97.23 _cell.angle_gamma 90 _cell.entry_id 7ODN _cell.length_a 73.441 _cell.length_b 91.39 _cell.length_c 82.671 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ODN _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 4 _struct_asym.id D _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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc3 E MG MG . A MG 502 1_555 Q O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc4 E MG MG . A MG 502 1_555 Q O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc5 E MG MG . A MG 502 1_555 Q O HOH . A HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc6 E MG MG . A MG 502 1_555 Q O HOH . A HOH 638 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? # _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 187 n n PG O2G GTP sing 188 n n PG O3G GTP sing 189 n n PG O3B GTP sing 190 n n O2G HOG2 GTP sing 191 n n O3G HOG3 GTP sing 192 n n O3B PB GTP sing 193 n n PB O1B GTP doub 194 n n PB O2B GTP sing 195 n n PB O3A GTP sing 196 n n O2B HOB2 GTP sing 197 n n O3A PA GTP sing 198 n n PA O1A GTP doub 199 n n PA O2A GTP sing 200 n n PA O5' GTP sing 201 n n O2A HOA2 GTP sing 202 n n O5' C5' GTP sing 203 n n C5' C4' GTP sing 204 n n C5' H5' GTP sing 205 n n C5' "H5''" GTP sing 206 n n C4' O4' GTP sing 207 n n C4' C3' GTP sing 208 n n C4' H4' GTP sing 209 n n O4' C1' GTP sing 210 n n C3' O3' GTP sing 211 n n C3' C2' GTP sing 212 n n C3' H3' GTP sing 213 n n O3' HO3' GTP sing 214 n n C2' O2' GTP sing 215 n n C2' C1' GTP sing 216 n n C2' H2' GTP sing 217 n n O2' HO2' GTP sing 218 n n C1' N9 GTP sing 219 n n C1' H1' GTP sing 220 n n N9 C8 GTP sing 221 n y N9 C4 GTP sing 222 n y C8 N7 GTP doub 223 n y C8 H8 GTP sing 224 n n N7 C5 GTP sing 225 n y C5 C6 GTP sing 226 n n C5 C4 GTP doub 227 n y C6 O6 GTP doub 228 n n C6 N1 GTP sing 229 n n N1 C2 GTP sing 230 n n N1 HN1 GTP sing 231 n n C2 N2 GTP sing 232 n n C2 N3 GTP doub 233 n n N2 HN21 GTP sing 234 n n N2 HN22 GTP sing 235 n n N3 C4 GTP sing 236 n n # _atom_sites.entry_id 7ODN _atom_sites.fract_transf_matrix[1][1] 0.013616 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001728 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010942 _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] 0.012193 _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 D 4 GTP A 1 501 500 GTP GTP . E 5 MG A 1 502 501 MG MG . F 6 SO4 A 1 503 502 SO4 SO4 . G 7 CL A 1 504 503 CL CL . H 6 SO4 A 1 505 501 SO4 SO4 . I 8 GDP B 1 501 500 GDP GDP . J 9 V95 B 1 502 502 V95 MBZ . K 6 SO4 B 1 503 503 SO4 SO4 . L 6 SO4 B 1 504 504 SO4 SO4 . M 7 CL B 1 505 506 CL CL . N 10 GOL F 1 201 505 GOL GOL . O 6 SO4 F 1 202 500 SO4 SO4 . P 10 GOL F 1 203 501 GOL GOL . Q 11 HOH A 1 601 4 HOH HOH . Q 11 HOH A 2 602 97 HOH HOH . Q 11 HOH A 3 603 7 HOH HOH . Q 11 HOH A 4 604 9 HOH HOH . Q 11 HOH A 5 605 99 HOH HOH . Q 11 HOH A 6 606 15 HOH HOH . Q 11 HOH A 7 607 6 HOH HOH . Q 11 HOH A 8 608 81 HOH HOH . Q 11 HOH A 9 609 20 HOH HOH . Q 11 HOH A 10 610 1 HOH HOH . Q 11 HOH A 11 611 76 HOH HOH . Q 11 HOH A 12 612 102 HOH HOH . Q 11 HOH A 13 613 31 HOH HOH . Q 11 HOH A 14 614 14 HOH HOH . Q 11 HOH A 15 615 38 HOH HOH . Q 11 HOH A 16 616 27 HOH HOH . Q 11 HOH A 17 617 12 HOH HOH . Q 11 HOH A 18 618 60 HOH HOH . Q 11 HOH A 19 619 69 HOH HOH . Q 11 HOH A 20 620 18 HOH HOH . Q 11 HOH A 21 621 70 HOH HOH . Q 11 HOH A 22 622 101 HOH HOH . Q 11 HOH A 23 623 79 HOH HOH . Q 11 HOH A 24 624 62 HOH HOH . Q 11 HOH A 25 625 41 HOH HOH . Q 11 HOH A 26 626 35 HOH HOH . Q 11 HOH A 27 627 80 HOH HOH . Q 11 HOH A 28 628 13 HOH HOH . Q 11 HOH A 29 629 55 HOH HOH . Q 11 HOH A 30 630 40 HOH HOH . Q 11 HOH A 31 631 58 HOH HOH . Q 11 HOH A 32 632 71 HOH HOH . Q 11 HOH A 33 633 21 HOH HOH . Q 11 HOH A 34 634 3 HOH HOH . Q 11 HOH A 35 635 75 HOH HOH . Q 11 HOH A 36 636 34 HOH HOH . Q 11 HOH A 37 637 106 HOH HOH . Q 11 HOH A 38 638 8 HOH HOH . Q 11 HOH A 39 639 19 HOH HOH . Q 11 HOH A 40 640 37 HOH HOH . Q 11 HOH A 41 641 25 HOH HOH . Q 11 HOH A 42 642 49 HOH HOH . Q 11 HOH A 43 643 28 HOH HOH . Q 11 HOH A 44 644 63 HOH HOH . Q 11 HOH A 45 645 64 HOH HOH . Q 11 HOH A 46 646 65 HOH HOH . Q 11 HOH A 47 647 30 HOH HOH . Q 11 HOH A 48 648 94 HOH HOH . Q 11 HOH A 49 649 107 HOH HOH . Q 11 HOH A 50 650 59 HOH HOH . Q 11 HOH A 51 651 44 HOH HOH . Q 11 HOH A 52 652 24 HOH HOH . Q 11 HOH A 53 653 50 HOH HOH . Q 11 HOH A 54 654 68 HOH HOH . Q 11 HOH A 55 655 84 HOH HOH . Q 11 HOH A 56 656 89 HOH HOH . R 11 HOH B 1 601 56 HOH HOH . R 11 HOH B 2 602 2 HOH HOH . R 11 HOH B 3 603 98 HOH HOH . R 11 HOH B 4 604 96 HOH HOH . R 11 HOH B 5 605 91 HOH HOH . R 11 HOH B 6 606 32 HOH HOH . R 11 HOH B 7 607 78 HOH HOH . R 11 HOH B 8 608 22 HOH HOH . R 11 HOH B 9 609 100 HOH HOH . R 11 HOH B 10 610 72 HOH HOH . R 11 HOH B 11 611 51 HOH HOH . R 11 HOH B 12 612 93 HOH HOH . R 11 HOH B 13 613 16 HOH HOH . R 11 HOH B 14 614 104 HOH HOH . R 11 HOH B 15 615 85 HOH HOH . R 11 HOH B 16 616 23 HOH HOH . R 11 HOH B 17 617 46 HOH HOH . R 11 HOH B 18 618 74 HOH HOH . R 11 HOH B 19 619 108 HOH HOH . R 11 HOH B 20 620 95 HOH HOH . R 11 HOH B 21 621 109 HOH HOH . R 11 HOH B 22 622 73 HOH HOH . R 11 HOH B 23 623 86 HOH HOH . R 11 HOH B 24 624 90 HOH HOH . R 11 HOH B 25 625 83 HOH HOH . S 11 HOH F 1 301 105 HOH HOH . S 11 HOH F 2 302 10 HOH HOH . S 11 HOH F 3 303 29 HOH HOH . S 11 HOH F 4 304 26 HOH HOH . S 11 HOH F 5 305 43 HOH HOH . S 11 HOH F 6 306 61 HOH HOH . S 11 HOH F 7 307 42 HOH HOH . S 11 HOH F 8 308 36 HOH HOH . S 11 HOH F 9 309 48 HOH HOH . S 11 HOH F 10 310 67 HOH HOH . S 11 HOH F 11 311 11 HOH HOH . S 11 HOH F 12 312 66 HOH HOH . S 11 HOH F 13 313 33 HOH HOH . S 11 HOH F 14 314 17 HOH HOH . S 11 HOH F 15 315 39 HOH HOH . S 11 HOH F 16 316 103 HOH HOH . S 11 HOH F 17 317 5 HOH HOH . S 11 HOH F 18 318 88 HOH HOH . S 11 HOH F 19 319 47 HOH HOH . S 11 HOH F 20 320 52 HOH HOH . S 11 HOH F 21 321 92 HOH HOH . S 11 HOH F 22 322 45 HOH HOH . S 11 HOH F 23 323 54 HOH HOH . S 11 HOH F 24 324 77 HOH HOH . S 11 HOH F 25 325 53 HOH HOH . S 11 HOH F 26 326 82 HOH HOH . S 11 HOH F 27 327 57 HOH HOH . S 11 HOH F 28 328 87 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 . . . D 4 29.465 20.259 23.369 1 33.9 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . D 4 29.389 18.758 23.241 1 31.65 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . D 4 30.146 20.615 24.657 1 32.93 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . D 4 28.114 20.914 23.283 1 32.99 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . D 4 30.352 20.897 22.179 1 36.41 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . D 4 30.847 20.073 20.883 1 31.81 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . D 4 31.628 21.051 20.04 1 34.05 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . D 4 31.67 18.881 21.315 1 32.92 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . D 4 29.478 19.668 20.139 1 32.68 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . D 4 29.36 19.13 18.63 1 32.61 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . D 4 30.551 19.441 17.757 1 32.86 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . D 4 29.056 17.658 18.657 1 33.16 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . D 4 28.099 19.978 18.115 1 32.61 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . D 4 27.026 19.361 17.454 1 32.06 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . D 4 27.007 19.726 15.983 1 33.88 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . D 4 28.188 19.271 15.337 1 35.84 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . D 4 25.861 19.051 15.272 1 33.96 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . D 4 25.397 19.915 14.279 1 34.99 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . D 4 26.466 17.837 14.62 1 36.14 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . D 4 25.743 17.493 13.477 1 38.95 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . D 4 27.882 18.315 14.332 1 34.64 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . D 4 28.877 17.25 14.403 1 34.03 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . D 4 29.261 16.571 15.508 1 34.97 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . D 4 30.212 15.686 15.166 1 33.92 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . D 4 30.459 15.79 13.858 1 35.95 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . D 4 31.334 15.138 13.014 1 34.86 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . D 4 32.085 14.261 13.424 1 34.28 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . D 4 31.35 15.479 11.698 1 35.51 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . D 4 30.517 16.454 11.248 1 33.59 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . D 4 30.534 16.786 9.975 1 32.51 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . D 4 29.664 17.098 12.089 1 34.68 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . D 4 29.63 16.774 13.377 1 36.14 ? C4 GTP 501 A 1 HETATM 33 H H4' GTP . . . D 4 26.922 20.812 15.933 1 33.88 ? H4' GTP 501 A 1 HETATM 34 H H3' GTP . . . D 4 25.037 18.796 15.938 1 33.96 ? H3' GTP 501 A 1 HETATM 35 H H2' GTP . . . D 4 26.453 16.923 15.215 1 36.14 ? H2' GTP 501 A 1 HETATM 36 H HO2' GTP . . . D 4 26.347 17.461 12.705 1 38.95 ? HO2' GTP 501 A 1 HETATM 37 H H1' GTP . . . D 4 27.903 18.71 13.316 1 34.64 ? H1' GTP 501 A 1 HETATM 38 H H8 GTP . . . D 4 28.863 16.717 16.512 1 34.97 ? H8 GTP 501 A 1 HETATM 39 H HN1 GTP . . . D 4 31.995 14.996 11.04 1 35.51 ? HN1 GTP 501 A 1 HETATM 40 H HN21 GTP . . . D 4 29.916 17.514 9.632 1 32.51 ? HN21 GTP 501 A 1 HETATM 41 H HN22 GTP . . . D 4 31.166 16.314 9.336 1 32.51 ? HN22 GTP 501 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 41 #