data_7VBW # _model_server_result.job_id 8YGg3vmzzYOSxewvnG6D1g _model_server_result.datetime_utc '2024-10-10 11:26:43' _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 7vbw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7VBW # _exptl.entry_id 7VBW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 2 _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 90 _cell.angle_gamma 120 _cell.entry_id 7VBW _cell.length_a 107.574 _cell.length_b 107.574 _cell.length_c 40.436 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VBW _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 OD2 ASP 238 A ASP 236 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc2 B O3G GTP . A GTP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc3 C MG MG . A MG 502 1_555 D O HOH . A HOH 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? # _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 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 7VBW _atom_sites.fract_transf_matrix[1][1] 0.009296 _atom_sites.fract_transf_matrix[1][2] 0.005367 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010734 _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] 0.02473 _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 GTP A 1 501 401 GTP GTP . C 3 MG A 1 502 1 MG MG . D 4 HOH A 1 601 29 HOH HOH . D 4 HOH A 2 602 43 HOH HOH . D 4 HOH A 3 603 37 HOH HOH . D 4 HOH A 4 604 71 HOH HOH . D 4 HOH A 5 605 16 HOH HOH . D 4 HOH A 6 606 60 HOH HOH . D 4 HOH A 7 607 59 HOH HOH . D 4 HOH A 8 608 25 HOH HOH . D 4 HOH A 9 609 51 HOH HOH . D 4 HOH A 10 610 32 HOH HOH . D 4 HOH A 11 611 5 HOH HOH . D 4 HOH A 12 612 3 HOH HOH . D 4 HOH A 13 613 70 HOH HOH . D 4 HOH A 14 614 45 HOH HOH . D 4 HOH A 15 615 55 HOH HOH . D 4 HOH A 16 616 28 HOH HOH . D 4 HOH A 17 617 27 HOH HOH . D 4 HOH A 18 618 69 HOH HOH . D 4 HOH A 19 619 17 HOH HOH . D 4 HOH A 20 620 23 HOH HOH . D 4 HOH A 21 621 4 HOH HOH . D 4 HOH A 22 622 21 HOH HOH . D 4 HOH A 23 623 11 HOH HOH . D 4 HOH A 24 624 68 HOH HOH . D 4 HOH A 25 625 2 HOH HOH . D 4 HOH A 26 626 20 HOH HOH . D 4 HOH A 27 627 1 HOH HOH . D 4 HOH A 28 628 40 HOH HOH . D 4 HOH A 29 629 6 HOH HOH . D 4 HOH A 30 630 61 HOH HOH . D 4 HOH A 31 631 47 HOH HOH . D 4 HOH A 32 632 22 HOH HOH . D 4 HOH A 33 633 48 HOH HOH . D 4 HOH A 34 634 18 HOH HOH . D 4 HOH A 35 635 50 HOH HOH . D 4 HOH A 36 636 49 HOH HOH . D 4 HOH A 37 637 9 HOH HOH . D 4 HOH A 38 638 7 HOH HOH . D 4 HOH A 39 639 8 HOH HOH . D 4 HOH A 40 640 30 HOH HOH . D 4 HOH A 41 641 14 HOH HOH . D 4 HOH A 42 642 34 HOH HOH . D 4 HOH A 43 643 10 HOH HOH . D 4 HOH A 44 644 58 HOH HOH . D 4 HOH A 45 645 67 HOH HOH . D 4 HOH A 46 646 15 HOH HOH . D 4 HOH A 47 647 52 HOH HOH . D 4 HOH A 48 648 53 HOH HOH . D 4 HOH A 49 649 57 HOH HOH . D 4 HOH A 50 650 26 HOH HOH . D 4 HOH A 51 651 65 HOH HOH . D 4 HOH A 52 652 36 HOH HOH . D 4 HOH A 53 653 35 HOH HOH . D 4 HOH A 54 654 31 HOH HOH . D 4 HOH A 55 655 46 HOH HOH . D 4 HOH A 56 656 63 HOH HOH . D 4 HOH A 57 657 62 HOH HOH . D 4 HOH A 58 658 54 HOH HOH . D 4 HOH A 59 659 33 HOH HOH . D 4 HOH A 60 660 24 HOH HOH . D 4 HOH A 61 661 42 HOH HOH . D 4 HOH A 62 662 44 HOH HOH . D 4 HOH A 63 663 19 HOH HOH . D 4 HOH A 64 664 39 HOH HOH . D 4 HOH A 65 665 12 HOH HOH . D 4 HOH A 66 666 66 HOH HOH . D 4 HOH A 67 667 38 HOH HOH . D 4 HOH A 68 668 41 HOH HOH . D 4 HOH A 69 669 64 HOH HOH . D 4 HOH A 70 670 13 HOH HOH . D 4 HOH A 71 671 56 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 . . . B 2 25.527 -15.996 -4.915 1 80.68 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . B 2 26.282 -14.828 -5.418 1 66.71 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . B 2 24.607 -16.556 -5.942 1 67.47 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . B 2 24.817 -15.694 -3.631 1 64.9 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . B 2 26.563 -17.179 -4.539 1 56.21 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . B 2 27.998 -17.123 -3.847 1 40.66 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . B 2 27.991 -15.984 -2.895 1 46.92 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . B 2 28.939 -17.135 -4.99 1 38.87 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . B 2 28.165 -18.472 -2.997 1 58.12 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . B 2 28.475 -18.872 -1.461 1 71.74 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . B 2 27.601 -18.11 -0.531 1 64.56 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . B 2 29.913 -18.809 -1.092 1 44.21 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . B 2 28.008 -20.402 -1.478 1 73.04 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . B 2 28.833 -21.393 -2.139 1 64.34 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . B 2 28.916 -22.615 -1.26 1 62.21 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . B 2 30.07 -23.401 -1.646 1 69.93 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . B 2 29.136 -22.34 0.229 1 68.17 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . B 2 28.674 -23.434 1.008 1 66.48 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . B 2 30.658 -22.182 0.278 1 72.08 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . B 2 31.204 -22.34 1.569 1 77.03 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . B 2 31.082 -23.296 -0.67 1 68.86 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . B 2 32.345 -23.054 -1.353 1 63.99 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . B 2 32.566 -22.19 -2.394 1 57.5 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . B 2 33.802 -22.203 -2.826 1 61.36 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . B 2 34.436 -23.134 -2.014 1 63.94 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . B 2 35.784 -23.565 -2.004 1 56.12 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . B 2 36.709 -23.205 -2.743 1 54.27 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . B 2 36.007 -24.516 -1.01 1 63.38 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . B 2 35.056 -24.995 -0.144 1 65.07 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . B 2 35.46 -25.914 0.742 1 55.46 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . B 2 33.786 -24.593 -0.148 1 59.04 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . B 2 33.55 -23.665 -1.103 1 64.2 ? C4 GTP 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #