data_5FBQ
#
_model_server_result.job_id            inO6lHHyo5KSqqZgm_YkPw 
_model_server_result.datetime_utc      '2024-11-04 22:56:28' 
_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          5fbq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    5FBQ 
#
_exptl.entry_id    5FBQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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            5FBQ 
_cell.length_a            48.759 
_cell.length_b            101.155 
_cell.length_c            188.486 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5FBQ 
_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 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
PB O1B GDP doub 154 n n 
PB O2B GDP sing 155 n n 
PB O3B GDP sing 156 n n 
PB O3A GDP sing 157 n n 
O2B HOB2 GDP sing 158 n n 
O3B HOB3 GDP sing 159 n n 
O3A PA GDP sing 160 n n 
PA O1A GDP doub 161 n n 
PA O2A GDP sing 162 n n 
PA O5' GDP sing 163 n n 
O2A HOA2 GDP sing 164 n n 
O5' C5' GDP sing 165 n n 
C5' C4' GDP sing 166 n n 
C5' H5' GDP sing 167 n n 
C5' "H5''" GDP sing 168 n n 
C4' O4' GDP sing 169 n n 
C4' C3' GDP sing 170 n n 
C4' H4' GDP sing 171 n n 
O4' C1' GDP sing 172 n n 
C3' O3' GDP sing 173 n n 
C3' C2' GDP sing 174 n n 
C3' H3' GDP sing 175 n n 
O3' HO3' GDP sing 176 n n 
C2' O2' GDP sing 177 n n 
C2' C1' GDP sing 178 n n 
C2' H2' GDP sing 179 n n 
O2' HO2' GDP sing 180 n n 
C1' N9 GDP sing 181 n n 
C1' H1' GDP sing 182 n n 
N9 C8 GDP sing 183 n y 
N9 C4 GDP sing 184 n y 
C8 N7 GDP doub 185 n y 
C8 H8 GDP sing 186 n n 
N7 C5 GDP sing 187 n y 
C5 C6 GDP sing 188 n n 
C5 C4 GDP doub 189 n y 
C6 O6 GDP doub 190 n n 
C6 N1 GDP sing 191 n n 
N1 C2 GDP sing 192 n n 
N1 HN1 GDP sing 193 n n 
C2 N2 GDP sing 194 n n 
C2 N3 GDP doub 195 n n 
N2 HN21 GDP sing 196 n n 
N2 HN22 GDP sing 197 n n 
N3 C4 GDP sing 198 n n 
#
_atom_sites.entry_id                     5FBQ 
_atom_sites.fract_transf_matrix[1][1]    0.020509 
_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]    0.009886 
_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]    0.005305 
_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 5W6 A 1 801 1 5W6 358 . 
D 4 GDP B 1 301 1 GDP GDP . 
#
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 PB GDP . . . D 4 -9.713 -45.131 16.874 1 123.13 ? PB GDP 301 B 1 
HETATM 2 O O1B GDP . . . D 4 -10.484 -45.927 15.848 1 118.7 ? O1B GDP 301 B 1 
HETATM 3 O O2B GDP . . . D 4 -9.869 -45.637 18.287 1 114.59 ? O2B GDP 301 B 1 
HETATM 4 O O3B GDP . . . D 4 -8.289 -44.817 16.485 1 129.9 ? O3B GDP 301 B 1 
HETATM 5 O O3A GDP . . . D 4 -10.439 -43.692 16.894 1 114.97 ? O3A GDP 301 B 1 
HETATM 6 P PA GDP . . . D 4 -10.77 -42.904 15.528 1 104.39 ? PA GDP 301 B 1 
HETATM 7 O O1A GDP . . . D 4 -9.686 -43.221 14.527 1 105.96 ? O1A GDP 301 B 1 
HETATM 8 O O2A GDP . . . D 4 -11.071 -41.467 15.878 1 112.79 ? O2A GDP 301 B 1 
HETATM 9 O O5' GDP . . . D 4 -12.145 -43.591 15.049 1 111.76 ? O5' GDP 301 B 1 
HETATM 10 C C5' GDP . . . D 4 -12.23 -44.356 13.847 1 117.03 ? C5' GDP 301 B 1 
HETATM 11 C C4' GDP . . . D 4 -12.481 -43.512 12.605 1 109.09 ? C4' GDP 301 B 1 
HETATM 12 O O4' GDP . . . D 4 -13.65 -44.01 11.941 1 102.54 ? O4' GDP 301 B 1 
HETATM 13 C C3' GDP . . . D 4 -12.703 -42.016 12.833 1 112.19 ? C3' GDP 301 B 1 
HETATM 14 O O3' GDP . . . D 4 -11.51 -41.265 12.576 1 130.54 ? O3' GDP 301 B 1 
HETATM 15 C C2' GDP . . . D 4 -13.835 -41.657 11.894 1 100.53 ? C2' GDP 301 B 1 
HETATM 16 O O2' GDP . . . D 4 -13.364 -41.132 10.651 1 111.5 ? O2' GDP 301 B 1 
HETATM 17 C C1' GDP . . . D 4 -14.577 -42.961 11.661 1 97.61 ? C1' GDP 301 B 1 
HETATM 18 N N9 GDP . . . D 4 -15.749 -43.063 12.567 1 98.34 ? N9 GDP 301 B 1 
HETATM 19 C C8 GDP . . . D 4 -15.737 -42.953 13.906 1 112.89 ? C8 GDP 301 B 1 
HETATM 20 N N7 GDP . . . D 4 -16.997 -43.102 14.372 1 114.74 ? N7 GDP 301 B 1 
HETATM 21 C C5 GDP . . . D 4 -17.797 -43.309 13.312 1 109.39 ? C5 GDP 301 B 1 
HETATM 22 C C6 GDP . . . D 4 -19.251 -43.539 13.146 1 112.98 ? C6 GDP 301 B 1 
HETATM 23 O O6 GDP . . . D 4 -20.011 -43.571 14.137 1 113.18 ? O6 GDP 301 B 1 
HETATM 24 N N1 GDP . . . D 4 -19.73 -43.713 11.911 1 111.06 ? N1 GDP 301 B 1 
HETATM 25 C C2 GDP . . . D 4 -18.916 -43.68 10.842 1 106.12 ? C2 GDP 301 B 1 
HETATM 26 N N2 GDP . . . D 4 -19.44 -43.861 9.606 1 101.53 ? N2 GDP 301 B 1 
HETATM 27 N N3 GDP . . . D 4 -17.583 -43.471 10.966 1 106.12 ? N3 GDP 301 B 1 
HETATM 28 C C4 GDP . . . D 4 -17.008 -43.285 12.18 1 101.09 ? C4 GDP 301 B 1 
HETATM 29 H H5' GDP . . . D 4 -11.299 -44.912 13.716 1 140.43 ? H5' GDP 301 B 1 
HETATM 30 H "H5''" GDP . . . D 4 -13.035 -45.086 13.948 1 140.43 ? "H5''" GDP 301 B 1 
HETATM 31 H H4' GDP . . . D 4 -11.614 -43.627 11.939 1 130.9 ? H4' GDP 301 B 1 
HETATM 32 H H3' GDP . . . D 4 -13.034 -41.858 13.869 1 134.63 ? H3' GDP 301 B 1 
HETATM 33 H HO3' GDP . . . D 4 -11.21 -41.435 11.672 1 156.64 ? HO3' GDP 301 B 1 
HETATM 34 H H2' GDP . . . D 4 -14.505 -40.94 12.388 1 120.64 ? H2' GDP 301 B 1 
HETATM 35 H HO2' GDP . . . D 4 -12.894 -40.302 10.81 1 133.8 ? HO2' GDP 301 B 1 
HETATM 36 H H1' GDP . . . D 4 -14.9 -43.009 10.611 1 117.13 ? H1' GDP 301 B 1 
HETATM 37 H H8 GDP . . . D 4 -14.859 -42.77 14.513 1 135.47 ? H8 GDP 301 B 1 
HETATM 38 H HN1 GDP . . . D 4 -20.748 -43.877 11.775 1 133.27 ? HN1 GDP 301 B 1 
HETATM 39 H HN21 GDP . . . D 4 -18.839 -43.838 8.795 1 121.84 ? HN21 GDP 301 B 1 
HETATM 40 H HN22 GDP . . . D 4 -20.431 -44.018 9.496 1 121.84 ? HN22 GDP 301 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           40 
#