data_8U8A
#
_model_server_result.job_id            MbfCkIW4iWqhYVOmCu52HA 
_model_server_result.datetime_utc      '2024-12-01 06:23:51' 
_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          8u8a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2602}' 
#
_entry.id    8U8A 
#
_exptl.entry_id    8U8A 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            8U8A 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8U8A 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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    ? 
_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 
#
_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 153 n n 
PB O2B GDP sing 154 n n 
PB O3B GDP sing 155 n n 
PB O3A GDP sing 156 n n 
O2B HOB2 GDP sing 157 n n 
O3B HOB3 GDP sing 158 n n 
O3A PA GDP sing 159 n n 
PA O1A GDP doub 160 n n 
PA O2A GDP sing 161 n n 
PA O5' GDP sing 162 n n 
O2A HOA2 GDP sing 163 n n 
O5' C5' GDP sing 164 n n 
C5' C4' GDP sing 165 n n 
C5' H5' GDP sing 166 n n 
C5' "H5''" GDP sing 167 n n 
C4' O4' GDP sing 168 n n 
C4' C3' GDP sing 169 n n 
C4' H4' GDP sing 170 n n 
O4' C1' GDP sing 171 n n 
C3' O3' GDP sing 172 n n 
C3' C2' GDP sing 173 n n 
C3' H3' GDP sing 174 n n 
O3' HO3' GDP sing 175 n n 
C2' O2' GDP sing 176 n n 
C2' C1' GDP sing 177 n n 
C2' H2' GDP sing 178 n n 
O2' HO2' GDP sing 179 n n 
C1' N9 GDP sing 180 n n 
C1' H1' GDP sing 181 n n 
N9 C8 GDP sing 182 n y 
N9 C4 GDP sing 183 n y 
C8 N7 GDP doub 184 n y 
C8 H8 GDP sing 185 n n 
N7 C5 GDP sing 186 n y 
C5 C6 GDP sing 187 n n 
C5 C4 GDP doub 188 n y 
C6 O6 GDP doub 189 n n 
C6 N1 GDP sing 190 n n 
N1 C2 GDP sing 191 n n 
N1 HN1 GDP sing 192 n n 
C2 N2 GDP sing 193 n n 
C2 N3 GDP doub 194 n n 
N2 HN21 GDP sing 195 n n 
N2 HN22 GDP sing 196 n n 
N3 C4 GDP sing 197 n n 
#
_atom_sites.entry_id                     8U8A 
_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 2 0LI B 1 2601 2602 0LI 0LI . 
D 3 GDP B 1 2602 2601 GDP GDP . 
E 2 0LI C 1 2601 2603 0LI 0LI . 
F 3 GDP C 1 2602 2602 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 3 270.087 243.302 176.56 1 43.56 ? PB GDP 2602 B 1 
HETATM 2 O O1B GDP . . . D 3 271.023 244.449 176.715 1 36.44 ? O1B GDP 2602 B 1 
HETATM 3 O O2B GDP . . . D 3 269.013 243.404 177.609 1 35.57 ? O2B GDP 2602 B 1 
HETATM 4 O O3B GDP . . . D 3 270.872 242.036 176.721 1 35.79 ? O3B GDP 2602 B 1 
HETATM 5 O O3A GDP . . . D 3 269.497 243.375 175.079 1 39.38 ? O3A GDP 2602 B 1 
HETATM 6 P PA GDP . . . D 3 270.517 243.465 173.85 1 33.92 ? PA GDP 2602 B 1 
HETATM 7 O O1A GDP . . . D 3 271.338 242.215 173.767 1 38.57 ? O1A GDP 2602 B 1 
HETATM 8 O O2A GDP . . . D 3 271.388 244.668 173.988 1 30.33 ? O2A GDP 2602 B 1 
HETATM 9 O O5' GDP . . . D 3 269.607 243.609 172.54 1 36.28 ? O5' GDP 2602 B 1 
HETATM 10 C C5' GDP . . . D 3 270.218 244.084 171.348 1 34.35 ? C5' GDP 2602 B 1 
HETATM 11 C C4' GDP . . . D 3 269.186 244.339 170.257 1 37.54 ? C4' GDP 2602 B 1 
HETATM 12 O O4' GDP . . . D 3 269.345 245.669 169.767 1 40.47 ? O4' GDP 2602 B 1 
HETATM 13 C C3' GDP . . . D 3 269.424 243.424 169.078 1 40.77 ? C3' GDP 2602 B 1 
HETATM 14 O O3' GDP . . . D 3 268.171 242.92 168.617 1 38.64 ? O3' GDP 2602 B 1 
HETATM 15 C C2' GDP . . . D 3 270.054 244.276 168.001 1 36.4 ? C2' GDP 2602 B 1 
HETATM 16 O O2' GDP . . . D 3 269.499 243.978 166.723 1 41.05 ? O2' GDP 2602 B 1 
HETATM 17 C C1' GDP . . . D 3 269.735 245.699 168.395 1 36.18 ? C1' GDP 2602 B 1 
HETATM 18 N N9 GDP . . . D 3 270.939 246.541 168.266 1 31.34 ? N9 GDP 2602 B 1 
HETATM 19 C C8 GDP . . . D 3 271.833 246.738 169.239 1 37.78 ? C8 GDP 2602 B 1 
HETATM 20 N N7 GDP . . . D 3 272.818 247.569 168.834 1 42.45 ? N7 GDP 2602 B 1 
HETATM 21 C C5 GDP . . . D 3 272.554 247.916 167.573 1 33.99 ? C5 GDP 2602 B 1 
HETATM 22 C C6 GDP . . . D 3 273.206 248.774 166.571 1 36.37 ? C6 GDP 2602 B 1 
HETATM 23 O O6 GDP . . . D 3 274.264 249.363 166.843 1 43.32 ? O6 GDP 2602 B 1 
HETATM 24 N N1 GDP . . . D 3 272.637 248.894 165.377 1 36.71 ? N1 GDP 2602 B 1 
HETATM 25 C C2 GDP . . . D 3 271.497 248.256 165.078 1 42.6 ? C2 GDP 2602 B 1 
HETATM 26 N N2 GDP . . . D 3 270.977 248.427 163.841 1 44.62 ? N2 GDP 2602 B 1 
HETATM 27 N N3 GDP . . . D 3 270.845 247.452 165.956 1 42.46 ? N3 GDP 2602 B 1 
HETATM 28 C C4 GDP . . . D 3 271.316 247.245 167.202 1 31.98 ? C4 GDP 2602 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          23 
_model_server_stats.element_count           28 
#