data_8DHB
#
_model_server_result.job_id            KgamjxVXPudKCh9FjwqhSg 
_model_server_result.datetime_utc      '2024-12-23 04:12:38' 
_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          8dhb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":500}' 
#
_entry.id    8DHB 
#
_exptl.entry_id    8DHB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          13 
_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            8DHB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DHB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M 
_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                      13 
_struct_asym.id                             M 
_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
disulf ? disulf1 J SG CYS 51 J CYS 8 1_555 J SG CYS 168 J CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc1 K O12 CZC . A CZC 501 1_555 L BE BEF . A BEF 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.779 ? 
#
_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 130 n n 
PB O2B GDP sing 131 n n 
PB O3B GDP sing 132 n n 
PB O3A GDP sing 133 n n 
O2B HOB2 GDP sing 134 n n 
O3B HOB3 GDP sing 135 n n 
O3A PA GDP sing 136 n n 
PA O1A GDP doub 137 n n 
PA O2A GDP sing 138 n n 
PA O5' GDP sing 139 n n 
O2A HOA2 GDP sing 140 n n 
O5' C5' GDP sing 141 n n 
C5' C4' GDP sing 142 n n 
C5' H5' GDP sing 143 n n 
C5' "H5''" GDP sing 144 n n 
C4' O4' GDP sing 145 n n 
C4' C3' GDP sing 146 n n 
C4' H4' GDP sing 147 n n 
O4' C1' GDP sing 148 n n 
C3' O3' GDP sing 149 n n 
C3' C2' GDP sing 150 n n 
C3' H3' GDP sing 151 n n 
O3' HO3' GDP sing 152 n n 
C2' O2' GDP sing 153 n n 
C2' C1' GDP sing 154 n n 
C2' H2' GDP sing 155 n n 
O2' HO2' GDP sing 156 n n 
C1' N9 GDP sing 157 n n 
C1' H1' GDP sing 158 n n 
N9 C8 GDP sing 159 n y 
N9 C4 GDP sing 160 n y 
C8 N7 GDP doub 161 n y 
C8 H8 GDP sing 162 n n 
N7 C5 GDP sing 163 n y 
C5 C6 GDP sing 164 n n 
C5 C4 GDP doub 165 n y 
C6 O6 GDP doub 166 n n 
C6 N1 GDP sing 167 n n 
N1 C2 GDP sing 168 n n 
N1 HN1 GDP sing 169 n n 
C2 N2 GDP sing 170 n n 
C2 N3 GDP doub 171 n n 
N2 HN21 GDP sing 172 n n 
N2 HN22 GDP sing 173 n n 
N3 C4 GDP sing 174 n n 
#
_atom_sites.entry_id                     8DHB 
_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
K 11 CZC A 1 501 502 CZC XDP . 
L 12 BEF A 1 502 503 BEF BEF . 
M 13 GDP B 1 500 500 GDP GDP . 
#
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 . . . M 13 235.563 271.549 236.533 1 32.75 ? PB GDP 500 B 1 
HETATM 2 O O1B GDP . . . M 13 234.318 272.4 236.475 1 32.75 ? O1B GDP 500 B 1 
HETATM 3 O O2B GDP . . . M 13 236.783 272.438 236.498 1 32.75 -1 O2B GDP 500 B 1 
HETATM 4 O O3B GDP . . . M 13 235.565 270.742 237.808 1 32.75 ? O3B GDP 500 B 1 
HETATM 5 O O3A GDP . . . M 13 235.58 270.545 235.276 1 32.75 ? O3A GDP 500 B 1 
HETATM 6 P PA GDP . . . M 13 234.441 269.417 235.124 1 32.75 ? PA GDP 500 B 1 
HETATM 7 O O1A GDP . . . M 13 233.09 270.057 234.913 1 32.75 ? O1A GDP 500 B 1 
HETATM 8 O O2A GDP . . . M 13 234.419 268.509 236.33 1 32.75 -1 O2A GDP 500 B 1 
HETATM 9 O O5' GDP . . . M 13 234.891 268.599 233.813 1 32.75 ? O5' GDP 500 B 1 
HETATM 10 C C5' GDP . . . M 13 234.604 267.207 233.723 1 32.75 ? C5' GDP 500 B 1 
HETATM 11 C C4' GDP . . . M 13 234.823 266.692 232.31 1 32.75 ? C4' GDP 500 B 1 
HETATM 12 O O4' GDP . . . M 13 236.169 266.92 231.897 1 32.75 ? O4' GDP 500 B 1 
HETATM 13 C C3' GDP . . . M 13 234.603 265.192 232.289 1 32.75 ? C3' GDP 500 B 1 
HETATM 14 O O3' GDP . . . M 13 233.428 264.886 231.536 1 32.75 ? O3' GDP 500 B 1 
HETATM 15 C C2' GDP . . . M 13 235.823 264.589 231.628 1 32.75 ? C2' GDP 500 B 1 
HETATM 16 O O2' GDP . . . M 13 235.438 263.801 230.5 1 32.75 ? O2' GDP 500 B 1 
HETATM 17 C C1' GDP . . . M 13 236.662 265.777 231.193 1 32.75 ? C1' GDP 500 B 1 
HETATM 18 N N9 GDP . . . M 13 238.081 265.52 231.536 1 32.75 ? N9 GDP 500 B 1 
HETATM 19 C C8 GDP . . . M 13 238.736 266.036 232.59 1 32.75 ? C8 GDP 500 B 1 
HETATM 20 N N7 GDP . . . M 13 240.022 265.602 232.625 1 32.75 ? N7 GDP 500 B 1 
HETATM 21 C C5 GDP . . . M 13 240.207 264.78 231.573 1 32.75 ? C5 GDP 500 B 1 
HETATM 22 C C6 GDP . . . M 13 241.323 263.977 231.009 1 32.75 ? C6 GDP 500 B 1 
HETATM 23 O O6 GDP . . . M 13 242.452 263.95 231.536 1 32.75 ? O6 GDP 500 B 1 
HETATM 24 N N1 GDP . . . M 13 241.096 263.266 229.905 1 32.75 ? N1 GDP 500 B 1 
HETATM 25 C C2 GDP . . . M 13 239.902 263.257 229.295 1 32.75 ? C2 GDP 500 B 1 
HETATM 26 N N2 GDP . . . M 13 239.769 262.505 228.177 1 32.75 ? N2 GDP 500 B 1 
HETATM 27 N N3 GDP . . . M 13 238.835 263.964 229.749 1 32.75 ? N3 GDP 500 B 1 
HETATM 28 C C4 GDP . . . M 13 238.922 264.73 230.862 1 32.75 ? C4 GDP 500 B 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#