data_5ND3
#
_model_server_result.job_id            HC0KJu9JDI1qh87kpJJNgg 
_model_server_result.datetime_utc      '2024-10-28 02:42:52' 
_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          5nd3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":600}' 
#
_entry.id    5ND3 
#
_exptl.entry_id    5ND3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          6 
_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                     ? 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,F,G 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
covale ? covale1 B ND2 ASN 101 A ASN 101 1_555 D O3G GTP . A GTP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.219 ? 
metalc ? metalc1 D O2G GTP . A GTP 500 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
#
_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     ? 
#
_atom_sites.entry_id                     5ND3 
_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
D 4 GTP A 1 500 500 GTP GTP . 
E 5 MG A 1 501 501 MG MG . 
F 6 GDP B 1 600 600 GDP GDP . 
G 7 TA1 B 1 601 601 TA1 TA1 . 
#
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 . . . F 6 222.782 219.016 346.766 1 22.28 ? PB GDP 600 B 1 
HETATM 2 O O1B GDP . . . F 6 221.923 219.124 345.571 1 23.59 ? O1B GDP 600 B 1 
HETATM 3 O O2B GDP . . . F 6 223.712 220.042 346.95 1 23.44 ? O2B GDP 600 B 1 
HETATM 4 O O3B GDP . . . F 6 221.825 218.746 348.064 1 25.3 ? O3B GDP 600 B 1 
HETATM 5 O O3A GDP . . . F 6 223.657 217.723 346.556 1 19.52 ? O3A GDP 600 B 1 
HETATM 6 P PA GDP . . . F 6 225.32 217.542 346.526 1 20.51 ? PA GDP 600 B 1 
HETATM 7 O O1A GDP . . . F 6 225.864 218.256 345.338 1 23.36 ? O1A GDP 600 B 1 
HETATM 8 O O2A GDP . . . F 6 225.823 218.033 347.873 1 18 ? O2A GDP 600 B 1 
HETATM 9 O O5' GDP . . . F 6 225.447 216.012 346.284 1 16.66 ? O5' GDP 600 B 1 
HETATM 10 C C5' GDP . . . F 6 226.645 215.278 346.683 1 7.65 ? C5' GDP 600 B 1 
HETATM 11 C C4' GDP . . . F 6 227.319 214.575 345.606 1 2.51 ? C4' GDP 600 B 1 
HETATM 12 O O4' GDP . . . F 6 227.817 215.574 344.631 1 2 ? O4' GDP 600 B 1 
HETATM 13 C C3' GDP . . . F 6 228.652 213.847 346.01 1 3.46 ? C3' GDP 600 B 1 
HETATM 14 O O3' GDP . . . F 6 228.679 212.596 345.233 1 2.32 ? O3' GDP 600 B 1 
HETATM 15 C C2' GDP . . . F 6 229.858 214.714 345.575 1 2.23 ? C2' GDP 600 B 1 
HETATM 16 O O2' GDP . . . F 6 231.076 214.066 345.17 1 2 ? O2' GDP 600 B 1 
HETATM 17 C C1' GDP . . . F 6 229.294 215.52 344.406 1 2 ? C1' GDP 600 B 1 
HETATM 18 N N9 GDP . . . F 6 229.782 216.897 344.323 1 5.88 ? N9 GDP 600 B 1 
HETATM 19 C C8 GDP . . . F 6 229.334 217.896 345.35 1 9.42 ? C8 GDP 600 B 1 
HETATM 20 N N7 GDP . . . F 6 230.067 218.946 344.773 1 10.36 ? N7 GDP 600 B 1 
HETATM 21 C C5 GDP . . . F 6 230.804 218.742 343.685 1 10.45 ? C5 GDP 600 B 1 
HETATM 22 C C6 GDP . . . F 6 231.679 219.32 342.741 1 13.51 ? C6 GDP 600 B 1 
HETATM 23 O O6 GDP . . . F 6 231.937 220.629 342.898 1 11.34 ? O6 GDP 600 B 1 
HETATM 24 N N1 GDP . . . F 6 232.232 218.659 341.7 1 10.31 ? N1 GDP 600 B 1 
HETATM 25 C C2 GDP . . . F 6 231.919 217.213 341.538 1 5.81 ? C2 GDP 600 B 1 
HETATM 26 N N2 GDP . . . F 6 232.575 216.776 340.484 1 6.23 ? N2 GDP 600 B 1 
HETATM 27 N N3 GDP . . . F 6 231.155 216.629 342.363 1 4.23 ? N3 GDP 600 B 1 
HETATM 28 C C4 GDP . . . F 6 230.6 217.337 343.365 1 7.64 ? C4 GDP 600 B 1 
#
_model_server_stats.io_time_ms              75 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    105 
_model_server_stats.query_time_ms           1152 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#