data_5SYG
#
_model_server_result.job_id            M22bSVnKxHYauKuZo8904w 
_model_server_result.datetime_utc      '2025-07-02 23:40:51' 
_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          5syg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    5SYG 
#
_exptl.entry_id    5SYG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          3 
_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                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? 130-meric 130 'representative helical assembly' 1 
? pentameric 5 'helical asymmetric unit' 2 
? pentameric 5 'helical asymmetric unit, std helical frame' 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F 1 (1-26) 
A,B,C,D,E,F 2 14 
A,B,C,D,E,F 3 H 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 -56.4 
3 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 24.6 
4 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 -47 
5 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 34 
6 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 -37.6 
7 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 43.4 
8 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 -28.2 
9 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 52.8 
10 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 -18.8 
11 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 62.2 
12 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 -9.4 
13 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 71.6 
14 'helical symmetry operation' ? ? 1 0 0 0 1 0 0 0 1 0 0 81 
15 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 9.4 
16 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 90.4 
17 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 18.8 
18 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 99.8 
19 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 28.2 
20 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 109.2 
21 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 37.6 
22 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 118.6 
23 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 47 
24 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 128 
25 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 56.4 
26 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 137.4 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 OE1 GLU 71 A GLU 71 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc2 C O1B GTP . A GTP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
#
_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 174 n n 
PG O2G GTP sing 175 n n 
PG O3G GTP sing 176 n n 
PG O3B GTP sing 177 n n 
O2G HOG2 GTP sing 178 n n 
O3G HOG3 GTP sing 179 n n 
O3B PB GTP sing 180 n n 
PB O1B GTP doub 181 n n 
PB O2B GTP sing 182 n n 
PB O3A GTP sing 183 n n 
O2B HOB2 GTP sing 184 n n 
O3A PA GTP sing 185 n n 
PA O1A GTP doub 186 n n 
PA O2A GTP sing 187 n n 
PA O5' GTP sing 188 n n 
O2A HOA2 GTP sing 189 n n 
O5' C5' GTP sing 190 n n 
C5' C4' GTP sing 191 n n 
C5' H5' GTP sing 192 n n 
C5' "H5''" GTP sing 193 n n 
C4' O4' GTP sing 194 n n 
C4' C3' GTP sing 195 n n 
C4' H4' GTP sing 196 n n 
O4' C1' GTP sing 197 n n 
C3' O3' GTP sing 198 n n 
C3' C2' GTP sing 199 n n 
C3' H3' GTP sing 200 n n 
O3' HO3' GTP sing 201 n n 
C2' O2' GTP sing 202 n n 
C2' C1' GTP sing 203 n n 
C2' H2' GTP sing 204 n n 
O2' HO2' GTP sing 205 n n 
C1' N9 GTP sing 206 n n 
C1' H1' GTP sing 207 n n 
N9 C8 GTP sing 208 n y 
N9 C4 GTP sing 209 n y 
C8 N7 GTP doub 210 n y 
C8 H8 GTP sing 211 n n 
N7 C5 GTP sing 212 n y 
C5 C6 GTP sing 213 n n 
C5 C4 GTP doub 214 n y 
C6 O6 GTP doub 215 n n 
C6 N1 GTP sing 216 n n 
N1 C2 GTP sing 217 n n 
N1 HN1 GTP sing 218 n n 
C2 N2 GTP sing 219 n n 
C2 N3 GTP doub 220 n n 
N2 HN21 GTP sing 221 n n 
N2 HN22 GTP sing 222 n n 
N3 C4 GTP sing 223 n n 
#
_atom_sites.entry_id                     5SYG 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 3 GTP A 1 501 1 GTP GTP . 
D 4 MG A 1 502 2 MG MG . 
E 5 GDP B 1 501 1 GDP GDP . 
F 6 ZPN B 1 502 1 ZPN ZPN . 
#
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 . . . C 3 315.808 449.186 346.833 1 148.21 ? PG GTP 501 A 1 
HETATM 2 O O1G GTP . . . C 3 316.246 447.969 346.055 1 148.21 ? O1G GTP 501 A 1 
HETATM 3 O O2G GTP . . . C 3 314.31 449.347 346.736 1 147.59 ? O2G GTP 501 A 1 
HETATM 4 O O3G GTP . . . C 3 316.457 450.423 346.254 1 147.2 ? O3G GTP 501 A 1 
HETATM 5 O O3B GTP . . . C 3 316.169 449.1 348.405 1 150.71 ? O3B GTP 501 A 1 
HETATM 6 P PB GTP . . . C 3 316.916 447.93 349.229 1 153.75 ? PB GTP 501 A 1 
HETATM 7 O O1B GTP . . . C 3 316.388 446.563 348.864 1 152.1 ? O1B GTP 501 A 1 
HETATM 8 O O2B GTP . . . C 3 316.702 448.215 350.698 1 152.74 ? O2B GTP 501 A 1 
HETATM 9 O O3A GTP . . . C 3 318.468 448.067 348.817 1 153.13 ? O3A GTP 501 A 1 
HETATM 10 P PA GTP . . . C 3 319.723 447.668 349.75 1 151.74 ? PA GTP 501 A 1 
HETATM 11 O O1A GTP . . . C 3 320.536 446.622 349.024 1 150.2 ? O1A GTP 501 A 1 
HETATM 12 O O2A GTP . . . C 3 319.305 447.182 351.12 1 150.19 ? O2A GTP 501 A 1 
HETATM 13 O O5' GTP . . . C 3 320.533 449.061 349.851 1 148 ? O5' GTP 501 A 1 
HETATM 14 C C5' GTP . . . C 3 321.883 449.23 349.469 1 144.92 ? C5' GTP 501 A 1 
HETATM 15 C C4' GTP . . . C 3 322.724 449.543 350.703 1 142.75 ? C4' GTP 501 A 1 
HETATM 16 O O4' GTP . . . C 3 322.677 448.418 351.555 1 140.64 ? O4' GTP 501 A 1 
HETATM 17 C C3' GTP . . . C 3 324.187 449.786 350.375 1 142.25 ? C3' GTP 501 A 1 
HETATM 18 O O3' GTP . . . C 3 324.697 450.74 351.28 1 141.91 ? O3' GTP 501 A 1 
HETATM 19 C C2' GTP . . . C 3 324.828 448.442 350.639 1 140.76 ? C2' GTP 501 A 1 
HETATM 20 O O2' GTP . . . C 3 326.175 448.562 351.033 1 140.37 ? O2' GTP 501 A 1 
HETATM 21 C C1' GTP . . . C 3 323.97 447.887 351.762 1 138.82 ? C1' GTP 501 A 1 
HETATM 22 N N9 GTP . . . C 3 323.863 446.421 351.718 1 135.93 ? N9 GTP 501 A 1 
HETATM 23 C C8 GTP . . . C 3 323.264 445.656 350.753 1 134.45 ? C8 GTP 501 A 1 
HETATM 24 N N7 GTP . . . C 3 323.367 444.354 351.108 1 134.26 ? N7 GTP 501 A 1 
HETATM 25 C C5 GTP . . . C 3 324.013 444.28 352.294 1 132.74 ? C5 GTP 501 A 1 
HETATM 26 C C6 GTP . . . C 3 324.38 443.215 353.11 1 130.67 ? C6 GTP 501 A 1 
HETATM 27 O O6 GTP . . . C 3 324.126 442.051 352.797 1 127.92 ? O6 GTP 501 A 1 
HETATM 28 N N1 GTP . . . C 3 325.048 443.482 354.287 1 130.92 ? N1 GTP 501 A 1 
HETATM 29 C C2 GTP . . . C 3 325.341 444.782 354.648 1 133.61 ? C2 GTP 501 A 1 
HETATM 30 N N2 GTP . . . C 3 325.979 445.031 355.782 1 132.93 ? N2 GTP 501 A 1 
HETATM 31 N N3 GTP . . . C 3 324.974 445.83 353.841 1 134.21 ? N3 GTP 501 A 1 
HETATM 32 C C4 GTP . . . C 3 324.322 445.577 352.687 1 133.62 ? C4 GTP 501 A 1 
#
_model_server_stats.io_time_ms              55 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          18 
_model_server_stats.element_count           32 
#