data_5KDL
#
_model_server_result.job_id            let6IVbFxe_9QAk7pBg0Sg 
_model_server_result.datetime_utc      '2024-10-18 18:19:35' 
_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          5kdl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":402}' 
#
_entry.id    5KDL 
#
_exptl.entry_id    5KDL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_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          99.86 
_cell.angle_gamma         90 
_cell.entry_id            5KDL 
_cell.length_a            61.742 
_cell.length_b            77.351 
_cell.length_c            73.095 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KDL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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
? 3 D N N 
? 3 F 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 OG SER 47 A SER 47 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
metalc ? metalc2 A OG1 THR 181 A THR 181 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc3 C MG MG . A MG 401 1_555 D O2G GSP . A GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc4 C MG MG . A MG 401 1_555 D O1B GSP . A GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc5 C MG MG . A MG 401 1_555 G O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? 
metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? 
metalc ? metalc7 B OG SER 47 B SER 47 1_555 E MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
metalc ? metalc8 B OG1 THR 181 B THR 181 1_555 E MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc9 E MG MG . B MG 401 1_555 F O2B GSP . B GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc10 E MG MG . B MG 401 1_555 F O2G GSP . B GSP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc11 E MG MG . B MG 401 1_555 H O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? 
metalc ? metalc12 E MG MG . B MG 401 1_555 H O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
#
_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                     5KDL 
_atom_sites.fract_transf_matrix[1][1]    0.016196 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002814 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012928 
_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]    0.013886 
_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 2 MG A 1 401 356 MG MG . 
D 3 GSP A 1 402 355 GSP GSP . 
E 2 MG B 1 401 356 MG MG . 
F 3 GSP B 1 402 355 GSP GSP . 
G 4 HOH A 1 501 2 HOH HOH . 
G 4 HOH A 2 502 1 HOH HOH . 
H 4 HOH B 1 501 4 HOH HOH . 
H 4 HOH B 2 502 3 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 GSP . . . F 3 11.269 7.915 30.403 1 52.46 ? PG GSP 402 B 1 
HETATM 2 O O3B GSP . . . F 3 11.53 7.258 28.959 1 55.64 ? O3B GSP 402 B 1 
HETATM 3 S S1G GSP . . . F 3 9.7 8.58 30.371 1 53.34 ? S1G GSP 402 B 1 
HETATM 4 O O2G GSP . . . F 3 11.405 6.832 31.494 1 46.78 ? O2G GSP 402 B 1 
HETATM 5 O O3G GSP . . . F 3 12.275 9.023 30.729 1 48.97 ? O3G GSP 402 B 1 
HETATM 6 P PB GSP . . . F 3 12.721 6.201 28.738 1 48.63 ? PB GSP 402 B 1 
HETATM 7 O O1B GSP . . . F 3 13.98 6.919 28.445 1 47.57 ? O1B GSP 402 B 1 
HETATM 8 O O2B GSP . . . F 3 12.855 5.311 29.911 1 42.27 ? O2B GSP 402 B 1 
HETATM 9 P PA GSP . . . F 3 11.861 3.819 27.524 1 41.81 ? PA GSP 402 B 1 
HETATM 10 O O1A GSP . . . F 3 13.104 3.047 27.729 1 53.56 ? O1A GSP 402 B 1 
HETATM 11 O O2A GSP . . . F 3 10.876 3.541 28.596 1 43.11 ? O2A GSP 402 B 1 
HETATM 12 O O3A GSP . . . F 3 12.25 5.378 27.439 1 46.45 ? O3A GSP 402 B 1 
HETATM 13 O O5' GSP . . . F 3 11.256 3.515 26.061 1 54.93 ? O5' GSP 402 B 1 
HETATM 14 C C5' GSP . . . F 3 9.956 3.949 25.727 1 47 ? C5' GSP 402 B 1 
HETATM 15 C C4' GSP . . . F 3 9.217 2.856 24.974 1 41.69 ? C4' GSP 402 B 1 
HETATM 16 O O4' GSP . . . F 3 9.666 2.822 23.634 1 42.85 ? O4' GSP 402 B 1 
HETATM 17 C C3' GSP . . . F 3 9.437 1.482 25.575 1 49.72 ? C3' GSP 402 B 1 
HETATM 18 O O3' GSP . . . F 3 8.189 0.912 25.882 1 47.24 ? O3' GSP 402 B 1 
HETATM 19 C C2' GSP . . . F 3 10.151 0.67 24.519 1 48.5 ? C2' GSP 402 B 1 
HETATM 20 O O2' GSP . . . F 3 9.491 -0.555 24.333 1 67.16 ? O2' GSP 402 B 1 
HETATM 21 C C1' GSP . . . F 3 10.118 1.535 23.267 1 47.05 ? C1' GSP 402 B 1 
HETATM 22 N N9 GSP . . . F 3 11.462 1.658 22.69 1 51.2 ? N9 GSP 402 B 1 
HETATM 23 C C8 GSP . . . F 3 12.559 2.185 23.321 1 52.99 ? C8 GSP 402 B 1 
HETATM 24 N N7 GSP . . . F 3 13.605 2.129 22.474 1 53.67 ? N7 GSP 402 B 1 
HETATM 25 C C5 GSP . . . F 3 13.188 1.581 21.315 1 52.04 ? C5 GSP 402 B 1 
HETATM 26 C C6 GSP . . . F 3 13.864 1.307 20.14 1 47.85 ? C6 GSP 402 B 1 
HETATM 27 O O6 GSP . . . F 3 15.057 1.584 20.058 1 57.17 ? O6 GSP 402 B 1 
HETATM 28 N N1 GSP . . . F 3 13.193 0.733 19.083 1 51.17 ? N1 GSP 402 B 1 
HETATM 29 C C2 GSP . . . F 3 11.85 0.437 19.213 1 48.95 ? C2 GSP 402 B 1 
HETATM 30 N N2 GSP . . . F 3 11.192 -0.124 18.205 1 58.93 ? N2 GSP 402 B 1 
HETATM 31 N N3 GSP . . . F 3 11.184 0.715 20.391 1 40.59 ? N3 GSP 402 B 1 
HETATM 32 C C4 GSP . . . F 3 11.842 1.278 21.43 1 44.75 ? C4 GSP 402 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           32 
#