data_5FBV
#
_model_server_result.job_id            tN5fsXuIJ9QoINoRaHsJxw 
_model_server_result.datetime_utc      '2025-08-03 07:19:09' 
_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          5fbv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    5FBV 
#
_exptl.entry_id    5FBV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_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         90 
_cell.entry_id            5FBV 
_cell.length_a            48.536 
_cell.length_b            102.782 
_cell.length_c            186.141 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5FBV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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 189 n n 
PG S1G GSP doub 190 n n 
PG O2G GSP sing 191 n n 
PG O3G GSP sing 192 n n 
O3B PB GSP sing 193 n n 
O2G HOG2 GSP sing 194 n n 
O3G HOG3 GSP sing 195 n n 
PB O1B GSP doub 196 n n 
PB O2B GSP sing 197 n n 
PB O3A GSP sing 198 n n 
O2B HOB2 GSP sing 199 n n 
PA O1A GSP doub 200 n n 
PA O2A GSP sing 201 n n 
PA O3A GSP sing 202 n n 
PA O5' GSP sing 203 n n 
O2A HOA2 GSP sing 204 n n 
O5' C5' GSP sing 205 n n 
C5' C4' GSP sing 206 n n 
C5' "H5'1" GSP sing 207 n n 
C5' "H5'2" GSP sing 208 n n 
C4' O4' GSP sing 209 n n 
C4' C3' GSP sing 210 n n 
C4' H4' GSP sing 211 n n 
O4' C1' GSP sing 212 n n 
C3' O3' GSP sing 213 n n 
C3' C2' GSP sing 214 n n 
C3' H3' GSP sing 215 n n 
O3' HO3' GSP sing 216 n n 
C2' O2' GSP sing 217 n n 
C2' C1' GSP sing 218 n n 
C2' H2' GSP sing 219 n n 
O2' HO2' GSP sing 220 n n 
C1' N9 GSP sing 221 n n 
C1' H1' GSP sing 222 n n 
N9 C8 GSP sing 223 n y 
N9 C4 GSP sing 224 n y 
C8 N7 GSP doub 225 n y 
C8 H8 GSP sing 226 n n 
N7 C5 GSP sing 227 n y 
C5 C6 GSP sing 228 n n 
C5 C4 GSP doub 229 n y 
C6 O6 GSP doub 230 n n 
C6 N1 GSP sing 231 n n 
N1 C2 GSP sing 232 n n 
N1 HN1 GSP sing 233 n n 
C2 N2 GSP sing 234 n n 
C2 N3 GSP doub 235 n n 
N2 HN21 GSP sing 236 n n 
N2 HN22 GSP sing 237 n n 
N3 C4 GSP sing 238 n n 
#
_atom_sites.entry_id                     5FBV 
_atom_sites.fract_transf_matrix[1][1]    0.020603 
_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]    0.009729 
_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]    0.005372 
_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 5W3 A 1 801 1 5W3 364 . 
D 4 GSP B 1 301 1 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 . . . D 4 31.213 57.332 77.725 1 109.55 ? PG GSP 301 B 1 
HETATM 2 O O3B GSP . . . D 4 32.508 56.438 77.765 1 96.78 ? O3B GSP 301 B 1 
HETATM 3 S S1G GSP . . . D 4 29.791 56.167 77.079 1 121.27 ? S1G GSP 301 B 1 
HETATM 4 O O2G GSP . . . D 4 31.435 58.558 76.761 1 102.45 ? O2G GSP 301 B 1 
HETATM 5 O O3G GSP . . . D 4 30.869 57.778 79.209 1 107.74 ? O3G GSP 301 B 1 
HETATM 6 P PB GSP . . . D 4 33.918 57.099 77.54 1 88.49 ? PB GSP 301 B 1 
HETATM 7 O O1B GSP . . . D 4 33.992 57.529 76.088 1 101.6 ? O1B GSP 301 B 1 
HETATM 8 O O2B GSP . . . D 4 35.062 56.216 77.938 1 85.36 -1 O2B GSP 301 B 1 
HETATM 9 P PA GSP . . . D 4 35.21 59.33 78.564 1 93.57 ? PA GSP 301 B 1 
HETATM 10 O O1A GSP . . . D 4 36.281 58.87 77.639 1 90.46 -1 O1A GSP 301 B 1 
HETATM 11 O O2A GSP . . . D 4 34.727 60.744 78.33 1 91.08 ? O2A GSP 301 B 1 
HETATM 12 O O3A GSP . . . D 4 33.96 58.396 78.457 1 96.95 ? O3A GSP 301 B 1 
HETATM 13 O O5' GSP . . . D 4 35.94 59.102 79.971 1 102.62 ? O5' GSP 301 B 1 
HETATM 14 C C5' GSP . . . D 4 35.481 59.839 81.131 1 100.65 ? C5' GSP 301 B 1 
HETATM 15 C C4' GSP . . . D 4 36.544 59.76 82.201 1 93.25 ? C4' GSP 301 B 1 
HETATM 16 O O4' GSP . . . D 4 37.484 58.915 81.92 1 84.62 ? O4' GSP 301 B 1 
HETATM 17 C C3' GSP . . . D 4 37.225 61.276 82.304 1 98.73 ? C3' GSP 301 B 1 
HETATM 18 O O3' GSP . . . D 4 37.068 61.753 83.678 1 101.31 ? O3' GSP 301 B 1 
HETATM 19 C C2' GSP . . . D 4 38.409 61.138 81.924 1 97.45 ? C2' GSP 301 B 1 
HETATM 20 O O2' GSP . . . D 4 39.362 62.097 82.596 1 105.95 ? O2' GSP 301 B 1 
HETATM 21 C C1' GSP . . . D 4 38.743 59.657 82.352 1 93.56 ? C1' GSP 301 B 1 
HETATM 22 N N9 GSP . . . D 4 39.878 59.253 81.848 1 92.84 ? N9 GSP 301 B 1 
HETATM 23 C C8 GSP . . . D 4 39.678 59.047 80.529 1 96.42 ? C8 GSP 301 B 1 
HETATM 24 N N7 GSP . . . D 4 40.865 58.635 80.008 1 95.99 ? N7 GSP 301 B 1 
HETATM 25 C C5 GSP . . . D 4 41.795 58.588 80.978 1 90.87 ? C5 GSP 301 B 1 
HETATM 26 C C6 GSP . . . D 4 43.268 58.201 80.974 1 92.23 ? C6 GSP 301 B 1 
HETATM 27 O O6 GSP . . . D 4 43.804 57.86 79.954 1 94.21 ? O6 GSP 301 B 1 
HETATM 28 N N1 GSP . . . D 4 44.012 58.241 82.163 1 97.81 ? N1 GSP 301 B 1 
HETATM 29 C C2 GSP . . . D 4 43.377 58.651 83.372 1 99.65 ? C2 GSP 301 B 1 
HETATM 30 N N2 GSP . . . D 4 44.115 58.703 84.598 1 96.35 ? N2 GSP 301 B 1 
HETATM 31 N N3 GSP . . . D 4 41.943 59.022 83.368 1 101.4 ? N3 GSP 301 B 1 
HETATM 32 C C4 GSP . . . D 4 41.18 58.977 82.123 1 96.55 ? C4 GSP 301 B 1 
HETATM 33 H HOG2 GSP . . . D 4 31.041 59.297 77.115 1 122.94 ? HOG2 GSP 301 B 1 
HETATM 34 H HOG3 GSP . . . D 4 30.127 57.394 79.465 1 129.29 ? HOG3 GSP 301 B 1 
HETATM 35 H "H5'1" GSP . . . D 4 34.641 59.443 81.467 1 120.78 ? "H5'1" GSP 301 B 1 
HETATM 36 H "H5'2" GSP . . . D 4 35.327 60.778 80.886 1 120.78 ? "H5'2" GSP 301 B 1 
HETATM 37 H H4' GSP . . . D 4 36.133 59.523 83.061 1 111.9 ? H4' GSP 301 B 1 
HETATM 38 H H3' GSP . . . D 4 36.756 61.888 81.689 1 118.47 ? H3' GSP 301 B 1 
HETATM 39 H HO3' GSP . . . D 4 36.223 61.96 83.822 1 121.57 ? HO3' GSP 301 B 1 
HETATM 40 H H2' GSP . . . D 4 38.466 61.229 80.95 1 116.94 ? H2' GSP 301 B 1 
HETATM 41 H HO2' GSP . . . D 4 39.54 61.809 83.424 1 127.14 ? HO2' GSP 301 B 1 
HETATM 42 H H1' GSP . . . D 4 38.807 59.62 83.336 1 112.28 ? H1' GSP 301 B 1 
HETATM 43 H H8 GSP . . . D 4 38.827 59.171 80.034 1 115.71 ? H8 GSP 301 B 1 
HETATM 44 H HN1 GSP . . . D 4 44.91 58.01 82.161 1 117.37 ? HN1 GSP 301 B 1 
HETATM 45 H HN21 GSP . . . D 4 44.996 58.475 84.61 1 115.62 ? HN21 GSP 301 B 1 
HETATM 46 H HN22 GSP . . . D 4 43.699 58.965 85.375 1 115.62 ? HN22 GSP 301 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           46 
#