data_3OY7
#
_model_server_result.job_id            U5NdBCwCiGhdB5JHOoLNnw 
_model_server_result.datetime_utc      '2025-02-18 09:22:36' 
_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          3oy7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":414}' 
#
_entry.id    3OY7 
#
_exptl.entry_id    3OY7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              605.341 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" 
_entity.pdbx_number_of_molecules    2 
_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            3OY7 
_cell.length_a            154.248 
_cell.length_b            243.189 
_cell.length_c            67.402 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3OY7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C16 H25 N5 O16 P2' 
_chem_comp.formula_weight    605.341 
_chem_comp.id                GDD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" 
_chem_comp.type              non-polymer 
_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
N2 C2 GDD sing 83 n n 
N2 H2N1 GDD sing 84 n n 
N2 H2N2 GDD sing 85 n n 
C2 N1 GDD sing 86 n n 
C2 N3 GDD doub 87 n n 
N1 C6 GDD sing 88 n n 
N1 H1 GDD sing 89 n n 
N3 C4 GDD sing 90 n n 
C4 C5 GDD doub 91 n y 
C4 N9 GDD sing 92 n y 
C5 C6 GDD sing 93 n n 
C5 N7 GDD sing 94 n y 
C6 O6 GDD doub 95 n n 
N7 C8 GDD doub 96 n y 
C8 N9 GDD sing 97 n y 
C8 H8 GDD sing 98 n n 
N9 C1' GDD sing 99 n n 
C1' C2' GDD sing 100 n n 
C1' O4' GDD sing 101 n n 
C1' H1' GDD sing 102 n n 
C2' O2' GDD sing 103 n n 
C2' C3' GDD sing 104 n n 
C2' H2' GDD sing 105 n n 
O2' HA GDD sing 106 n n 
C3' O3' GDD sing 107 n n 
C3' C4' GDD sing 108 n n 
C3' H3' GDD sing 109 n n 
O3' HB GDD sing 110 n n 
C4' O4' GDD sing 111 n n 
C4' C5' GDD sing 112 n n 
C4' H4' GDD sing 113 n n 
C5' O5' GDD sing 114 n n 
C5' "H5'1" GDD sing 115 n n 
C5' "H5'2" GDD sing 116 n n 
O5' PA GDD sing 117 n n 
PA O1A GDD doub 118 n n 
PA O2A GDD sing 119 n n 
PA O3A GDD sing 120 n n 
O2A HO2A GDD sing 121 n n 
O3A PB GDD sing 122 n n 
PB O2B GDD sing 123 n n 
PB O3B GDD doub 124 n n 
PB O1B GDD sing 125 n n 
O2B HO2B GDD sing 126 n n 
O1B C11 GDD sing 127 n n 
C11 O51 GDD sing 128 n n 
C11 C21 GDD sing 129 n n 
C11 H11 GDD sing 130 n n 
O51 C51 GDD sing 131 n n 
C51 C61 GDD sing 132 n n 
C51 C41 GDD sing 133 n n 
C51 H51 GDD sing 134 n n 
C61 O6A GDD sing 135 n n 
C61 H611 GDD sing 136 n n 
C61 H612 GDD sing 137 n n 
O6A H6A GDD sing 138 n n 
C21 O21 GDD sing 139 n n 
C21 C31 GDD sing 140 n n 
C21 H21 GDD sing 141 n n 
O21 HC GDD sing 142 n n 
C31 O31 GDD sing 143 n n 
C31 C41 GDD sing 144 n n 
C31 H31 GDD sing 145 n n 
O31 HD GDD sing 146 n n 
C41 O41 GDD sing 147 n n 
C41 H41 GDD sing 148 n n 
O41 HE GDD sing 149 n n 
#
_atom_sites.entry_id                     3OY7 
_atom_sites.fract_transf_matrix[1][1]    0.006483 
_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]    0.004112 
_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]    0.014836 
_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
C 2 GDD A 1 414 301 GDD GDD . 
D 2 GDD B 1 414 301 GDD GDD . 
E 3 HOH A 1 415 2 HOH HOH . 
E 3 HOH A 2 416 4 HOH HOH . 
E 3 HOH A 3 417 5 HOH HOH . 
E 3 HOH A 4 418 6 HOH HOH . 
E 3 HOH A 5 419 9 HOH HOH . 
F 3 HOH B 1 415 1 HOH HOH . 
F 3 HOH B 2 416 3 HOH HOH . 
F 3 HOH B 3 417 7 HOH HOH . 
F 3 HOH B 4 418 8 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 N N2 GDD . . . D 2 -34.285 -18.862 1.836 1 101.39 ? N2 GDD 414 B 1 
HETATM 2 C C2 GDD . . . D 2 -33.638 -19.964 1.476 1 101.23 ? C2 GDD 414 B 1 
HETATM 3 N N1 GDD . . . D 2 -34.124 -21.223 1.866 1 101.23 ? N1 GDD 414 B 1 
HETATM 4 N N3 GDD . . . D 2 -32.518 -19.864 0.74 1 101.26 ? N3 GDD 414 B 1 
HETATM 5 C C4 GDD . . . D 2 -31.832 -20.959 0.355 1 101.23 ? C4 GDD 414 B 1 
HETATM 6 C C5 GDD . . . D 2 -32.269 -22.229 0.712 1 101.18 ? C5 GDD 414 B 1 
HETATM 7 C C6 GDD . . . D 2 -33.427 -22.374 1.475 1 101.23 ? C6 GDD 414 B 1 
HETATM 8 O O6 GDD . . . D 2 -33.837 -23.487 1.803 1 101.03 ? O6 GDD 414 B 1 
HETATM 9 N N7 GDD . . . D 2 -31.404 -23.097 0.196 1 101.39 ? N7 GDD 414 B 1 
HETATM 10 C C8 GDD . . . D 2 -30.462 -22.416 -0.456 1 101.19 ? C8 GDD 414 B 1 
HETATM 11 N N9 GDD . . . D 2 -30.719 -21.11 -0.358 1 101.3 ? N9 GDD 414 B 1 
HETATM 12 C C1' GDD . . . D 2 -29.919 -20.001 -0.951 1 101.42 ? C1' GDD 414 B 1 
HETATM 13 C C2' GDD . . . D 2 -28.422 -20.158 -0.72 1 101.44 ? C2' GDD 414 B 1 
HETATM 14 O O2' GDD . . . D 2 -28.06 -19.601 0.548 1 101.3 ? O2' GDD 414 B 1 
HETATM 15 C C3' GDD . . . D 2 -27.833 -19.329 -1.865 1 101.65 ? C3' GDD 414 B 1 
HETATM 16 O O3' GDD . . . D 2 -27.563 -17.989 -1.44 1 101.77 ? O3' GDD 414 B 1 
HETATM 17 C C4' GDD . . . D 2 -28.948 -19.291 -2.925 1 101.64 ? C4' GDD 414 B 1 
HETATM 18 O O4' GDD . . . D 2 -30.042 -20.076 -2.383 1 101.48 ? O4' GDD 414 B 1 
HETATM 19 C C5' GDD . . . D 2 -28.521 -19.919 -4.272 1 101.58 ? C5' GDD 414 B 1 
HETATM 20 O O5' GDD . . . D 2 -27.106 -19.797 -4.528 1 101.29 ? O5' GDD 414 B 1 
HETATM 21 P PA GDD . . . D 2 -26.409 -20.757 -5.631 1 100.84 ? PA GDD 414 B 1 
HETATM 22 O O1A GDD . . . D 2 -26.668 -22.193 -5.343 1 101.18 ? O1A GDD 414 B 1 
HETATM 23 O O2A GDD . . . D 2 -24.824 -20.417 -5.587 1 100.65 ? O2A GDD 414 B 1 
HETATM 24 O O3A GDD . . . D 2 -26.977 -20.272 -7.06 1 100.51 ? O3A GDD 414 B 1 
HETATM 25 P PB GDD . . . D 2 -27.33 -21.341 -8.225 1 99.99 ? PB GDD 414 B 1 
HETATM 26 O O2B GDD . . . D 2 -26.04 -22.307 -8.267 1 99.96 ? O2B GDD 414 B 1 
HETATM 27 O O3B GDD . . . D 2 -28.575 -22.085 -7.911 1 99.69 ? O3B GDD 414 B 1 
HETATM 28 O O1B GDD . . . D 2 -27.378 -20.565 -9.668 1 99.97 ? O1B GDD 414 B 1 
HETATM 29 C C11 GDD . . . D 2 -26.488 -19.463 -10.062 1 99.75 ? C11 GDD 414 B 1 
HETATM 30 O O51 GDD . . . D 2 -26.527 -18.41 -9.039 1 99.7 ? O51 GDD 414 B 1 
HETATM 31 C C51 GDD . . . D 2 -25.324 -17.601 -8.768 1 99.72 ? C51 GDD 414 B 1 
HETATM 32 C C61 GDD . . . D 2 -25.323 -16.347 -9.68 1 100.15 ? C61 GDD 414 B 1 
HETATM 33 O O6A GDD . . . D 2 -26.414 -15.484 -9.327 1 100.32 ? O6A GDD 414 B 1 
HETATM 34 C C21 GDD . . . D 2 -25.08 -19.979 -10.445 1 99.71 ? C21 GDD 414 B 1 
HETATM 35 O O21 GDD . . . D 2 -24.61 -19.297 -11.615 1 99.73 ? O21 GDD 414 B 1 
HETATM 36 C C31 GDD . . . D 2 -24.067 -19.796 -9.306 1 99.65 ? C31 GDD 414 B 1 
HETATM 37 O O31 GDD . . . D 2 -22.784 -20.271 -9.735 1 99.34 ? O31 GDD 414 B 1 
HETATM 38 C C41 GDD . . . D 2 -23.955 -18.329 -8.846 1 99.6 ? C41 GDD 414 B 1 
HETATM 39 O O41 GDD . . . D 2 -23.315 -18.288 -7.564 1 99.19 ? O41 GDD 414 B 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           39 
#