data_8DNK
#
_model_server_result.job_id            vrJREJztDad0FhfSKeP74Q 
_model_server_result.datetime_utc      '2025-08-31 06:26:40' 
_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          8dnk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    8DNK 
#
_exptl.entry_id    8DNK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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            8DNK 
_cell.length_a            91.181 
_cell.length_b            91.181 
_cell.length_c            91.181 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DNK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        195 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 3' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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    x,y,z 
_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                      3 
_struct_asym.id                             C 
_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 A SG CYS 27 A CYS 12 1_555 D C23 U50 . A U50 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.807 ? 
metalc ? metalc1 A OG SER 32 A SER 17 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc2 B MG MG . A MG 301 1_555 C O2B GDP . A GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc3 B MG MG . A MG 301 1_555 F O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc4 B MG MG . A MG 301 1_555 F O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc5 B MG MG . A MG 301 1_555 F O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc6 B MG MG . A MG 301 1_555 F O HOH . A HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
#
_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 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     8DNK 
_atom_sites.fract_transf_matrix[1][1]    0.010967 
_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]    0.010967 
_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]    0.010967 
_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
B 2 MG A 1 301 301 MG MG . 
C 3 GDP A 1 302 501 GDP GDP . 
D 4 U50 A 1 303 701 U50 UNL . 
E 5 SO4 A 1 304 1 SO4 SO4 . 
F 6 HOH A 1 401 403 HOH HOH . 
F 6 HOH A 2 402 3 HOH HOH . 
F 6 HOH A 3 403 37 HOH HOH . 
F 6 HOH A 4 404 11 HOH HOH . 
F 6 HOH A 5 405 401 HOH HOH . 
F 6 HOH A 6 406 404 HOH HOH . 
F 6 HOH A 7 407 402 HOH HOH . 
F 6 HOH A 8 408 15 HOH HOH . 
F 6 HOH A 9 409 20 HOH HOH . 
F 6 HOH A 10 410 6 HOH HOH . 
F 6 HOH A 11 411 12 HOH HOH . 
F 6 HOH A 12 412 25 HOH HOH . 
F 6 HOH A 13 413 13 HOH HOH . 
F 6 HOH A 14 414 22 HOH HOH . 
F 6 HOH A 15 415 16 HOH HOH . 
F 6 HOH A 16 416 10 HOH HOH . 
F 6 HOH A 17 417 8 HOH HOH . 
F 6 HOH A 18 418 19 HOH HOH . 
F 6 HOH A 19 419 17 HOH HOH . 
F 6 HOH A 20 420 18 HOH HOH . 
F 6 HOH A 21 421 27 HOH HOH . 
F 6 HOH A 22 422 7 HOH HOH . 
F 6 HOH A 23 423 9 HOH HOH . 
F 6 HOH A 24 424 21 HOH HOH . 
F 6 HOH A 25 425 1 HOH HOH . 
F 6 HOH A 26 426 32 HOH HOH . 
F 6 HOH A 27 427 28 HOH HOH . 
F 6 HOH A 28 428 5 HOH HOH . 
F 6 HOH A 29 429 36 HOH HOH . 
F 6 HOH A 30 430 14 HOH HOH . 
F 6 HOH A 31 431 30 HOH HOH . 
F 6 HOH A 32 432 33 HOH HOH . 
F 6 HOH A 33 433 4 HOH HOH . 
F 6 HOH A 34 434 38 HOH HOH . 
F 6 HOH A 35 435 2 HOH HOH . 
F 6 HOH A 36 436 23 HOH HOH . 
F 6 HOH A 37 437 35 HOH HOH . 
F 6 HOH A 38 438 26 HOH HOH . 
F 6 HOH A 39 439 31 HOH HOH . 
F 6 HOH A 40 440 29 HOH HOH . 
F 6 HOH A 41 441 34 HOH HOH . 
F 6 HOH A 42 442 24 HOH HOH . 
#
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 . . . C 3 20.36 42.139 -35.742 1 27.45 ? PB GDP 302 A 1 
HETATM 2 O O1B GDP . . . C 3 21.745 41.981 -36.263 1 32.02 ? O1B GDP 302 A 1 
HETATM 3 O O2B GDP . . . C 3 19.716 43.375 -36.213 1 27.95 ? O2B GDP 302 A 1 
HETATM 4 O O3B GDP . . . C 3 20.247 41.773 -34.301 1 24.06 ? O3B GDP 302 A 1 
HETATM 5 O O3A GDP . . . C 3 19.499 40.939 -36.508 1 28.41 ? O3A GDP 302 A 1 
HETATM 6 P PA GDP . . . C 3 18.413 41.122 -37.709 1 31.66 ? PA GDP 302 A 1 
HETATM 7 O O1A GDP . . . C 3 19.097 41.688 -38.861 1 28.12 ? O1A GDP 302 A 1 
HETATM 8 O O2A GDP . . . C 3 17.116 41.752 -37.322 1 30.89 ? O2A GDP 302 A 1 
HETATM 9 O O5' GDP . . . C 3 18.017 39.628 -38.063 1 28.16 ? O5' GDP 302 A 1 
HETATM 10 C C5' GDP . . . C 3 19.065 38.673 -38.315 1 29.87 ? C5' GDP 302 A 1 
HETATM 11 C C4' GDP . . . C 3 18.576 37.436 -39.08 1 26.65 ? C4' GDP 302 A 1 
HETATM 12 O O4' GDP . . . C 3 17.661 36.658 -38.308 1 26.23 ? O4' GDP 302 A 1 
HETATM 13 C C3' GDP . . . C 3 17.762 37.893 -40.282 1 27.55 ? C3' GDP 302 A 1 
HETATM 14 O O3' GDP . . . C 3 17.87 36.899 -41.279 1 28.18 ? O3' GDP 302 A 1 
HETATM 15 C C2' GDP . . . C 3 16.338 37.843 -39.85 1 27.08 ? C2' GDP 302 A 1 
HETATM 16 O O2' GDP . . . C 3 15.474 37.627 -40.949 1 31.11 ? O2' GDP 302 A 1 
HETATM 17 C C1' GDP . . . C 3 16.34 36.642 -38.929 1 26.82 ? C1' GDP 302 A 1 
HETATM 18 N N9 GDP . . . C 3 15.308 36.708 -37.893 1 24.6 ? N9 GDP 302 A 1 
HETATM 19 C C8 GDP . . . C 3 15.085 37.748 -37.092 1 24.63 ? C8 GDP 302 A 1 
HETATM 20 N N7 GDP . . . C 3 14.133 37.484 -36.163 1 24.5 ? N7 GDP 302 A 1 
HETATM 21 C C5 GDP . . . C 3 13.719 36.281 -36.425 1 22.75 ? C5 GDP 302 A 1 
HETATM 22 C C6 GDP . . . C 3 12.747 35.449 -35.781 1 24.43 ? C6 GDP 302 A 1 
HETATM 23 O O6 GDP . . . C 3 12.08 35.942 -34.836 1 23.31 ? O6 GDP 302 A 1 
HETATM 24 N N1 GDP . . . C 3 12.631 34.196 -36.263 1 26.56 ? N1 GDP 302 A 1 
HETATM 25 C C2 GDP . . . C 3 13.376 33.806 -37.347 1 25.72 ? C2 GDP 302 A 1 
HETATM 26 N N2 GDP . . . C 3 13.239 32.61 -37.845 1 23.85 ? N2 GDP 302 A 1 
HETATM 27 N N3 GDP . . . C 3 14.316 34.522 -37.927 1 23.45 ? N3 GDP 302 A 1 
HETATM 28 C C4 GDP . . . C 3 14.511 35.758 -37.523 1 23.48 ? C4 GDP 302 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           659 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#