data_3JAK
#
_model_server_result.job_id            LhDZseG0Tox2Ty6_QkHhUw 
_model_server_result.datetime_utc      '2025-03-04 16:04:53' 
_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          3jak 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":501}' 
#
_entry.id    3JAK 
#
_exptl.entry_id    3JAK 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_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            3JAK 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3JAK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetradecameric 
_pdbx_struct_assembly.oligomeric_count      14 
_pdbx_struct_assembly.details               author_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,Y,Z,AA,BA,CA,DA,EA,FA 
_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
? 6 Q N N 
? 6 T N N 
? 6 W N N 
? 6 Z N N 
? 6 CA N N 
? 6 FA 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
metalc ? metalc1 A OE2 GLU 71 E GLU 71 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
metalc ? metalc2 O O1B GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc3 O O1G GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc4 D OE2 GLU 71 J GLU 71 1_555 S MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? 
metalc ? metalc5 R O1G GTP . J GTP 501 1_555 S MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc6 R O1B GTP . J GTP 501 1_555 S MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc7 F OE2 GLU 71 C GLU 71 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? 
metalc ? metalc8 U O1B GTP . C GTP 501 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc9 U O1G GTP . C GTP 501 1_555 V MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc10 H OE2 GLU 71 L GLU 71 1_555 Y MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? 
metalc ? metalc11 X O1B GTP . L GTP 501 1_555 Y MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc12 X O1G GTP . L GTP 501 1_555 Y MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc13 J OE2 GLU 71 A GLU 71 1_555 BA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? 
metalc ? metalc14 AA O1B GTP . A GTP 501 1_555 BA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc15 AA O1G GTP . A GTP 501 1_555 BA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc16 M OE2 GLU 71 K GLU 71 1_555 EA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc17 DA O1B GTP . K GTP 501 1_555 EA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc18 DA O1G GTP . K GTP 501 1_555 EA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3 S' 
_chem_comp.formula_weight    539.246 
_chem_comp.id                GSP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_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 O3B GSP sing 129 n n 
PG S1G GSP doub 130 n n 
PG O2G GSP sing 131 n n 
PG O3G GSP sing 132 n n 
O3B PB GSP sing 133 n n 
O2G HOG2 GSP sing 134 n n 
O3G HOG3 GSP sing 135 n n 
PB O1B GSP doub 136 n n 
PB O2B GSP sing 137 n n 
PB O3A GSP sing 138 n n 
O2B HOB2 GSP sing 139 n n 
PA O1A GSP doub 140 n n 
PA O2A GSP sing 141 n n 
PA O3A GSP sing 142 n n 
PA O5' GSP sing 143 n n 
O2A HOA2 GSP sing 144 n n 
O5' C5' GSP sing 145 n n 
C5' C4' GSP sing 146 n n 
C5' "H5'1" GSP sing 147 n n 
C5' "H5'2" GSP sing 148 n n 
C4' O4' GSP sing 149 n n 
C4' C3' GSP sing 150 n n 
C4' H4' GSP sing 151 n n 
O4' C1' GSP sing 152 n n 
C3' O3' GSP sing 153 n n 
C3' C2' GSP sing 154 n n 
C3' H3' GSP sing 155 n n 
O3' HO3' GSP sing 156 n n 
C2' O2' GSP sing 157 n n 
C2' C1' GSP sing 158 n n 
C2' H2' GSP sing 159 n n 
O2' HO2' GSP sing 160 n n 
C1' N9 GSP sing 161 n n 
C1' H1' GSP sing 162 n n 
N9 C8 GSP sing 163 n y 
N9 C4 GSP sing 164 n y 
C8 N7 GSP doub 165 n y 
C8 H8 GSP sing 166 n n 
N7 C5 GSP sing 167 n y 
C5 C6 GSP sing 168 n n 
C5 C4 GSP doub 169 n y 
C6 O6 GSP doub 170 n n 
C6 N1 GSP sing 171 n n 
N1 C2 GSP sing 172 n n 
N1 HN1 GSP sing 173 n n 
C2 N2 GSP sing 174 n n 
C2 N3 GSP doub 175 n n 
N2 HN21 GSP sing 176 n n 
N2 HN22 GSP sing 177 n n 
N3 C4 GSP sing 178 n n 
#
_atom_sites.entry_id                     3JAK 
_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
O 4 GTP E 1 501 501 GTP GTP . 
P 5 MG E 1 502 502 MG MG . 
Q 6 GSP F 1 501 501 GSP GSP . 
R 4 GTP J 1 501 501 GTP GTP . 
S 5 MG J 1 502 502 MG MG . 
T 6 GSP G 1 501 501 GSP GSP . 
U 4 GTP C 1 501 501 GTP GTP . 
V 5 MG C 1 502 502 MG MG . 
W 6 GSP D 1 501 501 GSP GSP . 
X 4 GTP L 1 501 501 GTP GTP . 
Y 5 MG L 1 502 502 MG MG . 
Z 6 GSP I 1 501 501 GSP GSP . 
AA 4 GTP A 1 501 501 GTP GTP . 
BA 5 MG A 1 502 502 MG MG . 
CA 6 GSP B 1 501 501 GSP GSP . 
DA 4 GTP K 1 501 501 GTP GTP . 
EA 5 MG K 1 502 502 MG MG . 
FA 6 GSP H 1 501 501 GSP GSP . 
#
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 GSP . . . Q 6 263.917 422.032 332.861 1 17.27 ? PG GSP 501 F 1 
HETATM 2 O O3B GSP . . . Q 6 265.07 422.532 333.849 1 16.91 ? O3B GSP 501 F 1 
HETATM 3 S S1G GSP . . . Q 6 264.709 422.156 331.093 1 18 ? S1G GSP 501 F 1 
HETATM 4 O O2G GSP . . . Q 6 263.465 420.519 333.165 1 17.39 ? O2G GSP 501 F 1 
HETATM 5 O O3G GSP . . . Q 6 262.71 423.095 332.822 1 17.12 ? O3G GSP 501 F 1 
HETATM 6 P PB GSP . . . Q 6 264.886 422.405 335.429 1 16.47 ? PB GSP 501 F 1 
HETATM 7 O O1B GSP . . . Q 6 263.541 422.977 335.808 1 16.52 ? O1B GSP 501 F 1 
HETATM 8 O O2B GSP . . . Q 6 265.157 420.979 335.834 1 16.49 ? O2B GSP 501 F 1 
HETATM 9 P PA GSP . . . Q 6 267.555 423.07 335.663 1 15.97 ? PA GSP 501 F 1 
HETATM 10 O O1A GSP . . . Q 6 267.753 423.156 334.169 1 16.03 ? O1A GSP 501 F 1 
HETATM 11 O O2A GSP . . . Q 6 267.959 421.851 336.448 1 16.02 ? O2A GSP 501 F 1 
HETATM 12 O O3A GSP . . . Q 6 266.023 423.353 336.041 1 16.24 ? O3A GSP 501 F 1 
HETATM 13 O O5' GSP . . . Q 6 268.284 424.311 336.362 1 15.87 ? O5' GSP 501 F 1 
HETATM 14 C C5' GSP . . . Q 6 268.628 425.485 335.638 1 15.75 ? C5' GSP 501 F 1 
HETATM 15 C C4' GSP . . . Q 6 269.47 426.377 336.543 1 15.62 ? C4' GSP 501 F 1 
HETATM 16 O O4' GSP . . . Q 6 270.009 425.61 337.624 1 15.39 ? O4' GSP 501 F 1 
HETATM 17 C C3' GSP . . . Q 6 270.659 427.005 335.847 1 15.49 ? C3' GSP 501 F 1 
HETATM 18 O O3' GSP . . . Q 6 270.829 428.318 336.393 1 15.6 ? O3' GSP 501 F 1 
HETATM 19 C C2' GSP . . . Q 6 271.836 426.138 336.23 1 15.32 ? C2' GSP 501 F 1 
HETATM 20 O O2' GSP . . . Q 6 273.015 426.946 336.304 1 15.34 ? O2' GSP 501 F 1 
HETATM 21 C C1' GSP . . . Q 6 271.436 425.554 337.583 1 15.26 ? C1' GSP 501 F 1 
HETATM 22 N N9 GSP . . . Q 6 271.849 424.14 337.658 1 15.05 ? N9 GSP 501 F 1 
HETATM 23 C C8 GSP . . . Q 6 271.509 423.149 336.818 1 15.05 ? C8 GSP 501 F 1 
HETATM 24 N N7 GSP . . . Q 6 272.079 421.98 337.208 1 15.06 ? N7 GSP 501 F 1 
HETATM 25 C C5 GSP . . . Q 6 272.787 422.216 338.324 1 15 ? C5 GSP 501 F 1 
HETATM 26 C C6 GSP . . . Q 6 273.628 421.423 339.257 1 14.96 ? C6 GSP 501 F 1 
HETATM 27 O O6 GSP . . . Q 6 273.813 420.204 339.077 1 14.89 ? O6 GSP 501 F 1 
HETATM 28 N N1 GSP . . . Q 6 274.187 422.054 340.3 1 14.99 ? N1 GSP 501 F 1 
HETATM 29 C C2 GSP . . . Q 6 274.004 423.376 340.523 1 15.02 ? C2 GSP 501 F 1 
HETATM 30 N N2 GSP . . . Q 6 274.601 423.948 341.598 1 15.02 ? N2 GSP 501 F 1 
HETATM 31 N N3 GSP . . . Q 6 273.249 424.163 339.706 1 14.95 ? N3 GSP 501 F 1 
HETATM 32 C C4 GSP . . . Q 6 272.629 423.647 338.616 1 14.98 ? C4 GSP 501 F 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    46 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           32 
#