data_5MJS
#
_model_server_result.job_id            vsO6969-YtY7L3w9RKb2PQ 
_model_server_result.datetime_utc      '2025-03-06 01:09:23' 
_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          5mjs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":500}' 
#
_entry.id    5MJS 
#
_exptl.entry_id    5MJS 
_exptl.method      'ELECTRON MICROSCOPY' 
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_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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            5MJS 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5MJS 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_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,J,K,L,M,N,O,P,Q 
_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
? 4 J N N 
? 4 O N N 
? 4 P N N 
? 4 Q 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     ? 
#
_atom_sites.entry_id                     5MJS 
_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
J 4 GDP A 1 500 500 GDP GDP . 
K 5 GTP E 1 500 500 GTP GTP . 
L 5 GTP F 1 500 500 GTP GTP . 
M 5 GTP G 1 500 500 GTP GTP . 
N 5 GTP H 1 500 500 GTP GTP . 
O 4 GDP J 1 500 500 GDP GDP . 
P 4 GDP B 1 500 500 GDP GDP . 
Q 4 GDP C 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 . . . P 4 70.206 95.664 224.631 1 48.7 ? PB GDP 500 B 1 
HETATM 2 O O1B GDP . . . P 4 70.752 95.058 223.372 1 48.7 ? O1B GDP 500 B 1 
HETATM 3 O O2B GDP . . . P 4 70.828 94.936 225.792 1 48.7 ? O2B GDP 500 B 1 
HETATM 4 O O3B GDP . . . P 4 68.709 95.531 224.698 1 48.7 ? O3B GDP 500 B 1 
HETATM 5 O O3A GDP . . . P 4 70.61 97.19 224.637 1 48.7 ? O3A GDP 500 B 1 
HETATM 6 P PA GDP . . . P 4 69.438 98.193 224.963 1 48.7 ? PA GDP 500 B 1 
HETATM 7 O O1A GDP . . . P 4 68.425 98.221 223.849 1 48.7 ? O1A GDP 500 B 1 
HETATM 8 O O2A GDP . . . P 4 68.869 97.888 226.317 1 48.7 ? O2A GDP 500 B 1 
HETATM 9 O O5' GDP . . . P 4 70.273 99.538 224.977 1 48.7 ? O5' GDP 500 B 1 
HETATM 10 C C5' GDP . . . P 4 69.802 100.536 224.109 1 48.7 ? C5' GDP 500 B 1 
HETATM 11 C C4' GDP . . . P 4 70.97 100.77 223.201 1 48.7 ? C4' GDP 500 B 1 
HETATM 12 O O4' GDP . . . P 4 70.517 101.625 222.175 1 48.7 ? O4' GDP 500 B 1 
HETATM 13 C C3' GDP . . . P 4 72.036 101.48 223.987 1 48.7 ? C3' GDP 500 B 1 
HETATM 14 O O3' GDP . . . P 4 73.302 100.967 223.58 1 48.7 ? O3' GDP 500 B 1 
HETATM 15 C C2' GDP . . . P 4 71.912 102.919 223.578 1 48.7 ? C2' GDP 500 B 1 
HETATM 16 O O2' GDP . . . P 4 73.211 103.44 223.344 1 48.7 ? O2' GDP 500 B 1 
HETATM 17 C C1' GDP . . . P 4 71.177 102.873 222.266 1 48.7 ? C1' GDP 500 B 1 
HETATM 18 N N9 GDP . . . P 4 70.11 103.867 222.267 1 48.7 ? N9 GDP 500 B 1 
HETATM 19 C C8 GDP . . . P 4 69.783 104.751 223.217 1 48.7 ? C8 GDP 500 B 1 
HETATM 20 N N7 GDP . . . P 4 68.707 105.472 222.813 1 48.7 ? N7 GDP 500 B 1 
HETATM 21 C C5 GDP . . . P 4 68.338 105.027 221.603 1 48.7 ? C5 GDP 500 B 1 
HETATM 22 C C6 GDP . . . P 4 67.297 105.324 220.614 1 48.7 ? C6 GDP 500 B 1 
HETATM 23 O O6 GDP . . . P 4 66.481 106.211 220.83 1 48.7 ? O6 GDP 500 B 1 
HETATM 24 N N1 GDP . . . P 4 67.262 104.626 219.486 1 48.7 ? N1 GDP 500 B 1 
HETATM 25 C C2 GDP . . . P 4 68.156 103.665 219.241 1 48.7 ? C2 GDP 500 B 1 
HETATM 26 N N2 GDP . . . P 4 68.07 102.989 218.082 1 48.7 ? N2 GDP 500 B 1 
HETATM 27 N N3 GDP . . . P 4 69.143 103.328 220.094 1 48.7 ? N3 GDP 500 B 1 
HETATM 28 C C4 GDP . . . P 4 69.266 103.963 221.266 1 48.7 ? C4 GDP 500 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    134 
_model_server_stats.query_time_ms           414 
_model_server_stats.encode_time_ms          45 
_model_server_stats.element_count           28 
#