data_7M2X
#
_model_server_result.job_id            66O_8zs5IHdLfMm0drzqng 
_model_server_result.datetime_utc      '2025-08-31 00:33:33' 
_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          7m2x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1400}' 
#
_entry.id    7M2X 
#
_exptl.entry_id    7M2X 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_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                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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
? 5 F N N 
? 5 G 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 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                     7M2X 
_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
F 5 GDP A 1 1400 1400 GDP GDP . 
G 5 GDP B 1 501 1626 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 . . . F 5 307.098 422.452 364.329 1 20 ? PB GDP 1400 A 1 
HETATM 2 O O1B GDP . . . F 5 307.468 423.69 363.624 1 20 ? O1B GDP 1400 A 1 
HETATM 3 O O2B GDP . . . F 5 307.122 422.673 365.887 1 20 ? O2B GDP 1400 A 1 
HETATM 4 O O3B GDP . . . F 5 308.114 421.321 363.973 1 20 ? O3B GDP 1400 A 1 
HETATM 5 O O3A GDP . . . F 5 305.677 421.989 363.89 1 20 ? O3A GDP 1400 A 1 
HETATM 6 P PA GDP . . . F 5 305.151 421.806 362.414 1 20 ? PA GDP 1400 A 1 
HETATM 7 O O1A GDP . . . F 5 306.275 421.447 361.502 1 20 ? O1A GDP 1400 A 1 
HETATM 8 O O2A GDP . . . F 5 304.08 420.678 362.375 1 20 ? O2A GDP 1400 A 1 
HETATM 9 O O5' GDP . . . F 5 304.387 423.168 361.964 1 20 ? O5' GDP 1400 A 1 
HETATM 10 C C5' GDP . . . F 5 303.04 423.602 362.365 1 20 ? C5' GDP 1400 A 1 
HETATM 11 C C4' GDP . . . F 5 301.877 422.911 361.56 1 20 ? C4' GDP 1400 A 1 
HETATM 12 O O4' GDP . . . F 5 302.351 421.763 360.817 1 20 ? O4' GDP 1400 A 1 
HETATM 13 C C3' GDP . . . F 5 300.732 422.326 362.448 1 20 ? C3' GDP 1400 A 1 
HETATM 14 O O3' GDP . . . F 5 299.603 423.195 362.527 1 20 ? O3' GDP 1400 A 1 
HETATM 15 C C2' GDP . . . F 5 300.269 421.033 361.712 1 20 ? C2' GDP 1400 A 1 
HETATM 16 O O2' GDP . . . F 5 298.881 421.138 361.337 1 20 ? O2' GDP 1400 A 1 
HETATM 17 C C1' GDP . . . F 5 301.188 420.961 360.445 1 20 ? C1' GDP 1400 A 1 
HETATM 18 N N9 GDP . . . F 5 301.569 419.553 360.104 1 20 ? N9 GDP 1400 A 1 
HETATM 19 C C8 GDP . . . F 5 302.513 418.784 360.763 1 20 ? C8 GDP 1400 A 1 
HETATM 20 N N7 GDP . . . F 5 303.024 417.882 359.998 1 20 ? N7 GDP 1400 A 1 
HETATM 21 C C5 GDP . . . F 5 302.414 417.939 358.792 1 20 ? C5 GDP 1400 A 1 
HETATM 22 C C6 GDP . . . F 5 302.496 417.179 357.548 1 20 ? C6 GDP 1400 A 1 
HETATM 23 O O6 GDP . . . F 5 303.307 416.292 357.389 1 20 ? O6 GDP 1400 A 1 
HETATM 24 N N1 GDP . . . F 5 301.628 417.464 356.521 1 20 ? N1 GDP 1400 A 1 
HETATM 25 C C2 GDP . . . F 5 300.645 418.434 356.661 1 20 ? C2 GDP 1400 A 1 
HETATM 26 N N2 GDP . . . F 5 299.76 418.539 355.659 1 20 ? N2 GDP 1400 A 1 
HETATM 27 N N3 GDP . . . F 5 300.556 419.197 357.775 1 20 ? N3 GDP 1400 A 1 
HETATM 28 C C4 GDP . . . F 5 301.42 418.988 358.861 1 20 ? C4 GDP 1400 A 1 
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_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    57 
_model_server_stats.query_time_ms           533 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#