data_1TVK
#
_model_server_result.job_id            aZ0Tusl8IuYD4P09B7ug1g 
_model_server_result.datetime_utc      '2024-12-15 17:03:21' 
_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          1tvk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1500}' 
#
_entry.id    1TVK 
#
_exptl.entry_id    1TVK 
_exptl.method      'ELECTRON CRYSTALLOGRAPHY' 
#
_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            1TVK 
_cell.length_a            81.2 
_cell.length_b            93.5 
_cell.length_c            90 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1TVK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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,E 
_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 158 n n 
PB O2B GDP sing 159 n n 
PB O3B GDP sing 160 n n 
PB O3A GDP sing 161 n n 
O2B HOB2 GDP sing 162 n n 
O3B HOB3 GDP sing 163 n n 
O3A PA GDP sing 164 n n 
PA O1A GDP doub 165 n n 
PA O2A GDP sing 166 n n 
PA O5' GDP sing 167 n n 
O2A HOA2 GDP sing 168 n n 
O5' C5' GDP sing 169 n n 
C5' C4' GDP sing 170 n n 
C5' H5' GDP sing 171 n n 
C5' "H5''" GDP sing 172 n n 
C4' O4' GDP sing 173 n n 
C4' C3' GDP sing 174 n n 
C4' H4' GDP sing 175 n n 
O4' C1' GDP sing 176 n n 
C3' O3' GDP sing 177 n n 
C3' C2' GDP sing 178 n n 
C3' H3' GDP sing 179 n n 
O3' HO3' GDP sing 180 n n 
C2' O2' GDP sing 181 n n 
C2' C1' GDP sing 182 n n 
C2' H2' GDP sing 183 n n 
O2' HO2' GDP sing 184 n n 
C1' N9 GDP sing 185 n n 
C1' H1' GDP sing 186 n n 
N9 C8 GDP sing 187 n y 
N9 C4 GDP sing 188 n y 
C8 N7 GDP doub 189 n y 
C8 H8 GDP sing 190 n n 
N7 C5 GDP sing 191 n y 
C5 C6 GDP sing 192 n n 
C5 C4 GDP doub 193 n y 
C6 O6 GDP doub 194 n n 
C6 N1 GDP sing 195 n n 
N1 C2 GDP sing 196 n n 
N1 HN1 GDP sing 197 n n 
C2 N2 GDP sing 198 n n 
C2 N3 GDP doub 199 n n 
N2 HN21 GDP sing 200 n n 
N2 HN22 GDP sing 201 n n 
N3 C4 GDP sing 202 n n 
#
_atom_sites.entry_id                     1TVK 
_atom_sites.fract_transf_matrix[1][1]    0.012315 
_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]    0.010695 
_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]    0.011111 
_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 GTP A 1 9500 9500 GTP GTP . 
D 4 GDP B 1 1500 1500 GDP GDP . 
E 5 EP B 1 1001 1001 EP EP . 
#
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 -17.074 2.843 5.349 1 107.99 ? PB GDP 1500 B 1 
HETATM 2 O O1B GDP . . . D 4 -15.812 3.553 5.013 1 107.99 ? O1B GDP 1500 B 1 
HETATM 3 O O2B GDP . . . D 4 -17.397 2.544 6.77 1 107.99 ? O2B GDP 1500 B 1 
HETATM 4 O O3B GDP . . . D 4 -18.209 3.636 4.806 1 107.99 ? O3B GDP 1500 B 1 
HETATM 5 O O3A GDP . . . D 4 -16.973 1.564 4.612 1 107.99 ? O3A GDP 1500 B 1 
HETATM 6 P PA GDP . . . D 4 -16.089 0.43 4.971 1 107.99 ? PA GDP 1500 B 1 
HETATM 7 O O1A GDP . . . D 4 -14.888 1.021 5.596 1 107.99 ? O1A GDP 1500 B 1 
HETATM 8 O O2A GDP . . . D 4 -16.907 -0.535 5.749 1 107.99 ? O2A GDP 1500 B 1 
HETATM 9 O O5' GDP . . . D 4 -15.615 -0.275 3.617 1 107.99 ? O5' GDP 1500 B 1 
HETATM 10 C C5' GDP . . . D 4 -16.384 -1.322 3.02 1 107.99 ? C5' GDP 1500 B 1 
HETATM 11 C C4' GDP . . . D 4 -15.477 -2.377 2.429 1 107.99 ? C4' GDP 1500 B 1 
HETATM 12 O O4' GDP . . . D 4 -14.379 -2.652 3.329 1 107.99 ? O4' GDP 1500 B 1 
HETATM 13 C C3' GDP . . . D 4 -16.181 -3.699 2.214 1 107.99 ? C3' GDP 1500 B 1 
HETATM 14 O O3' GDP . . . D 4 -16.734 -3.729 0.904 1 107.99 ? O3' GDP 1500 B 1 
HETATM 15 C C2' GDP . . . D 4 -15.087 -4.743 2.41 1 107.99 ? C2' GDP 1500 B 1 
HETATM 16 O O2' GDP . . . D 4 -14.392 -5.073 1.229 1 107.99 ? O2' GDP 1500 B 1 
HETATM 17 C C1' GDP . . . D 4 -14.149 -4.046 3.394 1 107.99 ? C1' GDP 1500 B 1 
HETATM 18 N N9 GDP . . . D 4 -14.238 -4.444 4.793 1 107.99 ? N9 GDP 1500 B 1 
HETATM 19 C C8 GDP . . . D 4 -15.212 -4.095 5.696 1 107.99 ? C8 GDP 1500 B 1 
HETATM 20 N N7 GDP . . . D 4 -14.943 -4.483 6.913 1 107.99 ? N7 GDP 1500 B 1 
HETATM 21 C C5 GDP . . . D 4 -13.732 -5.15 6.799 1 107.99 ? C5 GDP 1500 B 1 
HETATM 22 C C6 GDP . . . D 4 -12.916 -5.758 7.791 1 107.99 ? C6 GDP 1500 B 1 
HETATM 23 O O6 GDP . . . D 4 -13.092 -5.804 9.014 1 107.99 ? O6 GDP 1500 B 1 
HETATM 24 N N1 GDP . . . D 4 -11.786 -6.342 7.232 1 107.99 ? N1 GDP 1500 B 1 
HETATM 25 C C2 GDP . . . D 4 -11.476 -6.339 5.9 1 107.99 ? C2 GDP 1500 B 1 
HETATM 26 N N2 GDP . . . D 4 -10.362 -6.975 5.563 1 107.99 ? N2 GDP 1500 B 1 
HETATM 27 N N3 GDP . . . D 4 -12.207 -5.756 4.969 1 107.99 ? N3 GDP 1500 B 1 
HETATM 28 C C4 GDP . . . D 4 -13.311 -5.179 5.487 1 107.99 ? C4 GDP 1500 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           362 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#