data_5ND3
#
_model_server_result.job_id            rWFQsSJDRWgT-NjO4FkYoA 
_model_server_result.datetime_utc      '2024-11-22 07:01:02' 
_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":"D","auth_seq_id":500}' 
#
_entry.id    5ND3 
#
_exptl.entry_id    5ND3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-TRIPHOSPHATE" 
_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                      4 
_struct_asym.id                             D 
_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 H16 N5 O14 P3' 
_chem_comp.formula_weight    523.18 
_chem_comp.id                GTP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-TRIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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 PG GTP . . . D 4 222.837 217.878 307.212 1 29.97 ? PG GTP 500 A 1 
HETATM 2 O O1G GTP . . . D 4 221.394 218.328 307.475 1 34.97 ? O1G GTP 500 A 1 
HETATM 3 O O2G GTP . . . D 4 223.854 218.739 307.933 1 28.7 ? O2G GTP 500 A 1 
HETATM 4 O O3G GTP . . . D 4 222.861 216.429 307.688 1 32.1 ? O3G GTP 500 A 1 
HETATM 5 O O3B GTP . . . D 4 223.29 218 305.621 1 35.17 ? O3B GTP 500 A 1 
HETATM 6 P PB GTP . . . D 4 224.767 217.619 304.997 1 41.4 ? PB GTP 500 A 1 
HETATM 7 O O1B GTP . . . D 4 224.485 216.649 303.862 1 42.02 ? O1B GTP 500 A 1 
HETATM 8 O O2B GTP . . . D 4 225.53 218.826 304.706 1 41.17 ? O2B GTP 500 A 1 
HETATM 9 O O3A GTP . . . D 4 225.421 216.737 306.062 1 39.24 ? O3A GTP 500 A 1 
HETATM 10 P PA GTP . . . D 4 226.829 216.22 306.338 1 41.34 ? PA GTP 500 A 1 
HETATM 11 O O1A GTP . . . D 4 227.83 217.304 306.301 1 44.48 ? O1A GTP 500 A 1 
HETATM 12 O O2A GTP . . . D 4 226.774 215.427 307.6 1 43.37 ? O2A GTP 500 A 1 
HETATM 13 O O5' GTP . . . D 4 227.081 215.142 305.12 1 34.27 ? O5' GTP 500 A 1 
HETATM 14 C C5' GTP . . . D 4 228.356 214.531 305.182 1 25.47 ? C5' GTP 500 A 1 
HETATM 15 C C4' GTP . . . D 4 228.66 213.531 304.112 1 17.26 ? C4' GTP 500 A 1 
HETATM 16 O O4' GTP . . . D 4 229.232 214.187 302.95 1 18.2 ? O4' GTP 500 A 1 
HETATM 17 C C3' GTP . . . D 4 229.729 212.593 304.625 1 18.14 ? C3' GTP 500 A 1 
HETATM 18 O O3' GTP . . . D 4 229.64 211.355 303.956 1 19.98 ? O3' GTP 500 A 1 
HETATM 19 C C2' GTP . . . D 4 231.002 213.362 304.307 1 17.5 ? C2' GTP 500 A 1 
HETATM 20 O O2' GTP . . . D 4 232.087 212.444 304.151 1 19.33 ? O2' GTP 500 A 1 
HETATM 21 C C1' GTP . . . D 4 230.665 214.093 302.998 1 18.43 ? C1' GTP 500 A 1 
HETATM 22 N N9 GTP . . . D 4 231.214 215.455 302.87 1 9.96 ? N9 GTP 500 A 1 
HETATM 23 C C8 GTP . . . D 4 231.004 216.515 303.717 1 11.6 ? C8 GTP 500 A 1 
HETATM 24 N N7 GTP . . . D 4 231.621 217.605 303.351 1 7.31 ? N7 GTP 500 A 1 
HETATM 25 C C5 GTP . . . D 4 232.291 217.25 302.205 1 2 ? C5 GTP 500 A 1 
HETATM 26 C C6 GTP . . . D 4 233.125 217.998 301.376 1 3.48 ? C6 GTP 500 A 1 
HETATM 27 O O6 GTP . . . D 4 233.424 219.181 301.516 1 2.56 ? O6 GTP 500 A 1 
HETATM 28 N N1 GTP . . . D 4 233.624 217.265 300.277 1 2 ? N1 GTP 500 A 1 
HETATM 29 C C2 GTP . . . D 4 233.344 215.94 300.025 1 2 ? C2 GTP 500 A 1 
HETATM 30 N N2 GTP . . . D 4 233.899 215.416 298.97 1 2 ? N2 GTP 500 A 1 
HETATM 31 N N3 GTP . . . D 4 232.556 215.208 300.811 1 2 ? N3 GTP 500 A 1 
HETATM 32 C C4 GTP . . . D 4 232.053 215.91 301.877 1 3.56 ? C4 GTP 500 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    79 
_model_server_stats.query_time_ms           1531 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           32 
#