data_7T3B
#
_model_server_result.job_id            IbDh7HfE-YprhX4YQjZTWg 
_model_server_result.datetime_utc      '2025-03-05 22:18:46' 
_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          7t3b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":501}' 
#
_entry.id    7T3B 
#
_exptl.entry_id    7T3B 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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            7T3B 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7T3B 
_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,N 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 11 K N N 
? 11 M N N 
#
_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 86 n n 
PB O2B GDP sing 87 n n 
PB O3B GDP sing 88 n n 
PB O3A GDP sing 89 n n 
O2B HOB2 GDP sing 90 n n 
O3B HOB3 GDP sing 91 n n 
O3A PA GDP sing 92 n n 
PA O1A GDP doub 93 n n 
PA O2A GDP sing 94 n n 
PA O5' GDP sing 95 n n 
O2A HOA2 GDP sing 96 n n 
O5' C5' GDP sing 97 n n 
C5' C4' GDP sing 98 n n 
C5' H5' GDP sing 99 n n 
C5' "H5''" GDP sing 100 n n 
C4' O4' GDP sing 101 n n 
C4' C3' GDP sing 102 n n 
C4' H4' GDP sing 103 n n 
O4' C1' GDP sing 104 n n 
C3' O3' GDP sing 105 n n 
C3' C2' GDP sing 106 n n 
C3' H3' GDP sing 107 n n 
O3' HO3' GDP sing 108 n n 
C2' O2' GDP sing 109 n n 
C2' C1' GDP sing 110 n n 
C2' H2' GDP sing 111 n n 
O2' HO2' GDP sing 112 n n 
C1' N9 GDP sing 113 n n 
C1' H1' GDP sing 114 n n 
N9 C8 GDP sing 115 n y 
N9 C4 GDP sing 116 n y 
C8 N7 GDP doub 117 n y 
C8 H8 GDP sing 118 n n 
N7 C5 GDP sing 119 n y 
C5 C6 GDP sing 120 n n 
C5 C4 GDP doub 121 n y 
C6 O6 GDP doub 122 n n 
C6 N1 GDP sing 123 n n 
N1 C2 GDP sing 124 n n 
N1 HN1 GDP sing 125 n n 
C2 N2 GDP sing 126 n n 
C2 N3 GDP doub 127 n n 
N2 HN21 GDP sing 128 n n 
N2 HN22 GDP sing 129 n n 
N3 C4 GDP sing 130 n n 
#
_atom_sites.entry_id                     7T3B 
_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 GDP E 1 501 501 GDP GDP . 
L 12 AF3 E 1 502 601 AF3 AF3 . 
M 11 GDP B 1 501 501 GDP GDP . 
N 12 AF3 D 1 601 601 AF3 AF3 . 
#
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 . . . K 11 183.884 150.015 186.655 1 268.08 ? PB GDP 501 E 1 
HETATM 2 O O1B GDP . . . K 11 183.852 148.567 186.231 1 268.08 ? O1B GDP 501 E 1 
HETATM 3 O O2B GDP . . . K 11 185.158 150.292 187.405 1 268.08 ? O2B GDP 501 E 1 
HETATM 4 O O3B GDP . . . K 11 182.692 150.312 187.525 1 268.08 ? O3B GDP 501 E 1 
HETATM 5 O O3A GDP . . . K 11 183.783 150.953 185.36 1 268.08 ? O3A GDP 501 E 1 
HETATM 6 P PA GDP . . . K 11 182.322 151.09 184.719 1 268.08 ? PA GDP 501 E 1 
HETATM 7 O O1A GDP . . . K 11 181.6 149.772 184.832 1 268.08 ? O1A GDP 501 E 1 
HETATM 8 O O2A GDP . . . K 11 181.555 152.186 185.415 1 268.08 ? O2A GDP 501 E 1 
HETATM 9 O O5' GDP . . . K 11 182.591 151.463 183.182 1 268.08 ? O5' GDP 501 E 1 
HETATM 10 C C5' GDP . . . K 11 181.67 151.004 182.201 1 268.08 ? C5' GDP 501 E 1 
HETATM 11 C C4' GDP . . . K 11 181.861 151.798 180.923 1 268.08 ? C4' GDP 501 E 1 
HETATM 12 O O4' GDP . . . K 11 180.727 151.58 180.087 1 268.08 ? O4' GDP 501 E 1 
HETATM 13 C C3' GDP . . . K 11 181.937 153.279 181.231 1 268.08 ? C3' GDP 501 E 1 
HETATM 14 O O3' GDP . . . K 11 183.184 153.811 180.779 1 268.08 ? O3' GDP 501 E 1 
HETATM 15 C C2' GDP . . . K 11 180.792 153.92 180.477 1 268.08 ? C2' GDP 501 E 1 
HETATM 16 O O2' GDP . . . K 11 181.289 154.937 179.606 1 268.08 ? O2' GDP 501 E 1 
HETATM 17 C C1' GDP . . . K 11 180.14 152.812 179.672 1 268.08 ? C1' GDP 501 E 1 
HETATM 18 N N9 GDP . . . K 11 178.7 152.774 179.999 1 268.08 ? N9 GDP 501 E 1 
HETATM 19 C C8 GDP . . . K 11 178.201 152.315 181.156 1 268.08 ? C8 GDP 501 E 1 
HETATM 20 N N7 GDP . . . K 11 176.852 152.396 181.17 1 268.08 ? N7 GDP 501 E 1 
HETATM 21 C C5 GDP . . . K 11 176.47 152.926 179.997 1 268.08 ? C5 GDP 501 E 1 
HETATM 22 C C6 GDP . . . K 11 175.183 153.281 179.369 1 268.08 ? C6 GDP 501 E 1 
HETATM 23 O O6 GDP . . . K 11 174.11 153.095 179.974 1 268.08 ? O6 GDP 501 E 1 
HETATM 24 N N1 GDP . . . K 11 175.201 153.799 178.139 1 268.08 ? N1 GDP 501 E 1 
HETATM 25 C C2 GDP . . . K 11 176.35 154.004 177.474 1 268.08 ? C2 GDP 501 E 1 
HETATM 26 N N2 GDP . . . K 11 176.283 154.536 176.233 1 268.08 ? N2 GDP 501 E 1 
HETATM 27 N N3 GDP . . . K 11 177.57 153.703 177.989 1 268.08 ? N3 GDP 501 E 1 
HETATM 28 C C4 GDP . . . K 11 177.69 153.171 179.224 1 268.08 ? C4 GDP 501 E 1 
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_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#