data_5ND4
#
_model_server_result.job_id            z4CXHTdPPyoDts5I3BeYJQ 
_model_server_result.datetime_utc      '2024-11-04 23:23:14' 
_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          5nd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":600}' 
#
_entry.id    5ND4 
#
_exptl.entry_id    5ND4 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          8 
_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,H,I,J 
_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                      8 
_struct_asym.id                             I 
_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
metalc ? metalc1 A OG SER 357 C SER 377 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc2 D O2B ADP . C ADP 601 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc3 G O2G GTP . A GTP 500 1_555 H MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? 
#
_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 131 n n 
PB O2B GDP sing 132 n n 
PB O3B GDP sing 133 n n 
PB O3A GDP sing 134 n n 
O2B HOB2 GDP sing 135 n n 
O3B HOB3 GDP sing 136 n n 
O3A PA GDP sing 137 n n 
PA O1A GDP doub 138 n n 
PA O2A GDP sing 139 n n 
PA O5' GDP sing 140 n n 
O2A HOA2 GDP sing 141 n n 
O5' C5' GDP sing 142 n n 
C5' C4' GDP sing 143 n n 
C5' H5' GDP sing 144 n n 
C5' "H5''" GDP sing 145 n n 
C4' O4' GDP sing 146 n n 
C4' C3' GDP sing 147 n n 
C4' H4' GDP sing 148 n n 
O4' C1' GDP sing 149 n n 
C3' O3' GDP sing 150 n n 
C3' C2' GDP sing 151 n n 
C3' H3' GDP sing 152 n n 
O3' HO3' GDP sing 153 n n 
C2' O2' GDP sing 154 n n 
C2' C1' GDP sing 155 n n 
C2' H2' GDP sing 156 n n 
O2' HO2' GDP sing 157 n n 
C1' N9 GDP sing 158 n n 
C1' H1' GDP sing 159 n n 
N9 C8 GDP sing 160 n y 
N9 C4 GDP sing 161 n y 
C8 N7 GDP doub 162 n y 
C8 H8 GDP sing 163 n n 
N7 C5 GDP sing 164 n y 
C5 C6 GDP sing 165 n n 
C5 C4 GDP doub 166 n y 
C6 O6 GDP doub 167 n n 
C6 N1 GDP sing 168 n n 
N1 C2 GDP sing 169 n n 
N1 HN1 GDP sing 170 n n 
C2 N2 GDP sing 171 n n 
C2 N3 GDP doub 172 n n 
N2 HN21 GDP sing 173 n n 
N2 HN22 GDP sing 174 n n 
N3 C4 GDP sing 175 n n 
#
_atom_sites.entry_id                     5ND4 
_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 ADP C 1 601 511 ADP ADP . 
E 5 MG C 1 602 512 MG MG . 
F 6 ALF C 1 603 513 ALF ALF . 
G 7 GTP A 1 500 500 GTP GTP . 
H 5 MG A 1 501 501 MG MG . 
I 8 GDP B 1 600 600 GDP GDP . 
J 9 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 . . . I 8 223.119 218.673 346.611 1 0 ? PB GDP 600 B 1 
HETATM 2 O O1B GDP . . . I 8 222.248 218.802 345.428 1 0 ? O1B GDP 600 B 1 
HETATM 3 O O2B GDP . . . I 8 224.052 219.696 346.803 1 0 ? O2B GDP 600 B 1 
HETATM 4 O O3B GDP . . . I 8 222.177 218.38 347.914 1 0 ? O3B GDP 600 B 1 
HETATM 5 O O3A GDP . . . I 8 223.992 217.384 346.368 1 0 ? O3A GDP 600 B 1 
HETATM 6 P PA GDP . . . I 8 225.654 217.205 346.318 1 0 ? PA GDP 600 B 1 
HETATM 7 O O1A GDP . . . I 8 226.187 217.941 345.137 1 0 ? O1A GDP 600 B 1 
HETATM 8 O O2A GDP . . . I 8 226.172 217.672 347.668 1 0 ? O2A GDP 600 B 1 
HETATM 9 O O5' GDP . . . I 8 225.779 215.679 346.048 1 0 ? O5' GDP 600 B 1 
HETATM 10 C C5' GDP . . . I 8 226.982 214.939 346.422 1 0 ? C5' GDP 600 B 1 
HETATM 11 C C4' GDP . . . I 8 227.645 214.255 345.325 1 0 ? C4' GDP 600 B 1 
HETATM 12 O O4' GDP . . . I 8 228.133 215.271 344.362 1 0 ? O4' GDP 600 B 1 
HETATM 13 C C3' GDP . . . I 8 228.982 213.521 345.701 1 0 ? C3' GDP 600 B 1 
HETATM 14 O O3' GDP . . . I 8 229.001 212.283 344.902 1 0 ? O3' GDP 600 B 1 
HETATM 15 C C2' GDP . . . I 8 230.182 214.395 345.268 1 0 ? C2' GDP 600 B 1 
HETATM 16 O O2' GDP . . . I 8 231.397 213.756 344.84 1 0 ? O2' GDP 600 B 1 
HETATM 17 C C1' GDP . . . I 8 229.606 215.221 344.12 1 0 ? C1' GDP 600 B 1 
HETATM 18 N N9 GDP . . . I 8 230.094 216.599 344.056 1 0 ? N9 GDP 600 B 1 
HETATM 19 C C8 GDP . . . I 8 229.656 217.58 345.107 1 0 ? C8 GDP 600 B 1 
HETATM 20 N N7 GDP . . . I 8 230.382 218.641 344.539 1 0 ? N7 GDP 600 B 1 
HETATM 21 C C5 GDP . . . I 8 231.108 218.456 343.441 1 0 ? C5 GDP 600 B 1 
HETATM 22 C C6 GDP . . . I 8 231.973 219.05 342.498 1 0 ? C6 GDP 600 B 1 
HETATM 23 O O6 GDP . . . I 8 232.233 220.357 342.675 1 0 ? O6 GDP 600 B 1 
HETATM 24 N N1 GDP . . . I 8 232.515 218.408 341.439 1 0 ? N1 GDP 600 B 1 
HETATM 25 C C2 GDP . . . I 8 232.201 216.966 341.255 1 0 ? C2 GDP 600 B 1 
HETATM 26 N N2 GDP . . . I 8 232.844 216.547 340.187 1 0 ? N2 GDP 600 B 1 
HETATM 27 N N3 GDP . . . I 8 231.445 216.367 342.078 1 0 ? N3 GDP 600 B 1 
HETATM 28 C C4 GDP . . . I 8 230.901 217.057 343.097 1 0 ? C4 GDP 600 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#