data_5ND2
#
_model_server_result.job_id            uMszDlM8q1vZ01jOhZH2sA 
_model_server_result.datetime_utc      '2024-11-04 23:19:24' 
_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          5nd2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":600}' 
#
_entry.id    5ND2 
#
_exptl.entry_id    5ND2 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          7 
_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 
_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                      7 
_struct_asym.id                             H 
_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 OG1 THR 146 C THR 166 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.704 ? 
metalc ? metalc2 D O3B ADP . C ADP 601 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc3 B OE1 GLN 11 A GLN 11 1_555 G MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.985 ? 
metalc ? metalc4 F O2G GTP . A GTP 500 1_555 G MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? 
#
_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 127 n n 
PB O2B GDP sing 128 n n 
PB O3B GDP sing 129 n n 
PB O3A GDP sing 130 n n 
O2B HOB2 GDP sing 131 n n 
O3B HOB3 GDP sing 132 n n 
O3A PA GDP sing 133 n n 
PA O1A GDP doub 134 n n 
PA O2A GDP sing 135 n n 
PA O5' GDP sing 136 n n 
O2A HOA2 GDP sing 137 n n 
O5' C5' GDP sing 138 n n 
C5' C4' GDP sing 139 n n 
C5' H5' GDP sing 140 n n 
C5' "H5''" GDP sing 141 n n 
C4' O4' GDP sing 142 n n 
C4' C3' GDP sing 143 n n 
C4' H4' GDP sing 144 n n 
O4' C1' GDP sing 145 n n 
C3' O3' GDP sing 146 n n 
C3' C2' GDP sing 147 n n 
C3' H3' GDP sing 148 n n 
O3' HO3' GDP sing 149 n n 
C2' O2' GDP sing 150 n n 
C2' C1' GDP sing 151 n n 
C2' H2' GDP sing 152 n n 
O2' HO2' GDP sing 153 n n 
C1' N9 GDP sing 154 n n 
C1' H1' GDP sing 155 n n 
N9 C8 GDP sing 156 n y 
N9 C4 GDP sing 157 n y 
C8 N7 GDP doub 158 n y 
C8 H8 GDP sing 159 n n 
N7 C5 GDP sing 160 n y 
C5 C6 GDP sing 161 n n 
C5 C4 GDP doub 162 n y 
C6 O6 GDP doub 163 n n 
C6 N1 GDP sing 164 n n 
N1 C2 GDP sing 165 n n 
N1 HN1 GDP sing 166 n n 
C2 N2 GDP sing 167 n n 
C2 N3 GDP doub 168 n n 
N2 HN21 GDP sing 169 n n 
N2 HN22 GDP sing 170 n n 
N3 C4 GDP sing 171 n n 
#
_atom_sites.entry_id                     5ND2 
_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 1 601 504 ADP ADP . 
E 5 MG C 1 602 505 MG MG . 
F 6 GTP A 1 500 500 GTP GTP . 
G 5 MG A 1 501 501 MG MG . 
H 7 GDP B 1 600 600 GDP GDP . 
I 8 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 . . . H 7 223.495 219.005 346.766 1 0.13 ? PB GDP 600 B 1 
HETATM 2 O O1B GDP . . . H 7 222.606 219.139 345.597 1 0.13 ? O1B GDP 600 B 1 
HETATM 3 O O2B GDP . . . H 7 224.437 220.023 346.943 1 0.13 ? O2B GDP 600 B 1 
HETATM 4 O O3B GDP . . . H 7 222.57 218.72 348.084 1 0.13 ? O3B GDP 600 B 1 
HETATM 5 O O3A GDP . . . H 7 224.355 217.709 346.512 1 0.13 ? O3A GDP 600 B 1 
HETATM 6 P PA GDP . . . H 7 226.015 217.518 346.436 1 0.13 ? PA GDP 600 B 1 
HETATM 7 O O1A GDP . . . H 7 226.534 218.249 345.247 1 0.13 ? O1A GDP 600 B 1 
HETATM 8 O O2A GDP . . . H 7 226.556 217.984 347.778 1 0.13 ? O2A GDP 600 B 1 
HETATM 9 O O5' GDP . . . H 7 226.125 215.991 346.166 1 0.13 ? O5' GDP 600 B 1 
HETATM 10 C C5' GDP . . . H 7 227.328 215.244 346.522 1 0.13 ? C5' GDP 600 B 1 
HETATM 11 C C4' GDP . . . H 7 227.969 214.555 345.417 1 0.13 ? C4' GDP 600 B 1 
HETATM 12 O O4' GDP . . . H 7 228.45 215.566 344.445 1 0.13 ? O4' GDP 600 B 1 
HETATM 13 C C3' GDP . . . H 7 229.307 213.811 345.774 1 0.13 ? C3' GDP 600 B 1 
HETATM 14 O O3' GDP . . . H 7 229.305 212.572 344.975 1 0.13 ? O3' GDP 600 B 1 
HETATM 15 C C2' GDP . . . H 7 230.508 214.677 345.322 1 0.13 ? C2' GDP 600 B 1 
HETATM 16 O O2' GDP . . . H 7 231.71 214.028 344.876 1 0.13 ? O2' GDP 600 B 1 
HETATM 17 C C1' GDP . . . H 7 229.918 215.506 344.181 1 0.13 ? C1' GDP 600 B 1 
HETATM 18 N N9 GDP . . . H 7 230.415 216.88 344.109 1 0.13 ? N9 GDP 600 B 1 
HETATM 19 C C8 GDP . . . H 7 230 217.865 345.164 1 0.13 ? C8 GDP 600 B 1 
HETATM 20 N N7 GDP . . . H 7 230.725 218.921 344.584 1 0.13 ? N7 GDP 600 B 1 
HETATM 21 C C5 GDP . . . H 7 231.432 218.729 343.476 1 0.13 ? C5 GDP 600 B 1 
HETATM 22 C C6 GDP . . . H 7 232.287 219.316 342.518 1 0.13 ? C6 GDP 600 B 1 
HETATM 23 O O6 GDP . . . H 7 232.559 220.622 342.691 1 0.13 ? O6 GDP 600 B 1 
HETATM 24 N N1 GDP . . . H 7 232.809 218.67 341.453 1 0.13 ? N1 GDP 600 B 1 
HETATM 25 C C2 GDP . . . H 7 232.482 217.23 341.275 1 0.13 ? C2 GDP 600 B 1 
HETATM 26 N N2 GDP . . . H 7 233.106 216.805 340.198 1 0.13 ? N2 GDP 600 B 1 
HETATM 27 N N3 GDP . . . H 7 231.735 216.637 342.11 1 0.13 ? N3 GDP 600 B 1 
HETATM 28 C C4 GDP . . . H 7 231.211 217.331 343.137 1 0.13 ? C4 GDP 600 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    58 
_model_server_stats.query_time_ms           1353 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#