data_6GYX
#
_model_server_result.job_id            DVV3qbBjNQjhFpEzQ_jo9g 
_model_server_result.datetime_utc      '2025-02-27 07:17:24' 
_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          6gyx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":301}' 
#
_entry.id    6GYX 
#
_exptl.entry_id    6GYX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' 
_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            6GYX 
_cell.length_a            44.092 
_cell.length_b            80.424 
_cell.length_c            96.195 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GYX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 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 
_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 E N N 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                APC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" 
#
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
PG O1G APC doub 13 n n 
PG O2G APC sing 14 n n 
PG O3G APC sing 15 n n 
PG O3B APC sing 16 n n 
O2G HOG2 APC sing 17 n n 
O3G HOG3 APC sing 18 n n 
PB O1B APC doub 19 n n 
PB O2B APC sing 20 n n 
PB O3B APC sing 21 n n 
PB C3A APC sing 22 n n 
O2B HOB2 APC sing 23 n n 
PA O1A APC doub 24 n n 
PA O2A APC sing 25 n n 
PA C3A APC sing 26 n n 
PA O5' APC sing 27 n n 
O2A HOA2 APC sing 28 n n 
C3A H3A1 APC sing 29 n n 
C3A H3A2 APC sing 30 n n 
O5' C5' APC sing 31 n n 
C5' C4' APC sing 32 n n 
C5' "H5'1" APC sing 33 n n 
C5' "H5'2" APC sing 34 n n 
C4' O4' APC sing 35 n n 
C4' C3' APC sing 36 n n 
C4' H4' APC sing 37 n n 
O4' C1' APC sing 38 n n 
C3' O3' APC sing 39 n n 
C3' C2' APC sing 40 n n 
C3' H3' APC sing 41 n n 
O3' HO3' APC sing 42 n n 
C2' O2' APC sing 43 n n 
C2' C1' APC sing 44 n n 
C2' H2' APC sing 45 n n 
O2' HO2' APC sing 46 n n 
C1' N9 APC sing 47 n n 
C1' H1' APC sing 48 n n 
N9 C8 APC sing 49 n y 
N9 C4 APC sing 50 n y 
C8 N7 APC doub 51 n y 
C8 H8 APC sing 52 n n 
N7 C5 APC sing 53 n y 
C5 C6 APC sing 54 n y 
C5 C4 APC doub 55 n y 
C6 N6 APC sing 56 n n 
C6 N1 APC doub 57 n y 
N6 HN61 APC sing 58 n n 
N6 HN62 APC sing 59 n n 
N1 C2 APC sing 60 n y 
C2 N3 APC doub 61 n y 
C2 H2 APC sing 62 n n 
N3 C4 APC sing 63 n y 
#
_atom_sites.entry_id                     6GYX 
_atom_sites.fract_transf_matrix[1][1]    0.02268 
_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]    0.012434 
_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]    0.010396 
_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 APC B 1 301 1668 APC APC . 
D 3 MN B 1 302 76 MN MN . 
E 2 APC A 1 301 1669 APC APC . 
#
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 PG APC . . . E 2 11.816 3.86 28.384 1 175.91 ? PG APC 301 A 1 
HETATM 2 O O1G APC . . . E 2 11.188 5.17 28.051 1 146.24 ? O1G APC 301 A 1 
HETATM 3 O O2G APC . . . E 2 13.041 4.021 29.231 1 149.11 ? O2G APC 301 A 1 
HETATM 4 O O3G APC . . . E 2 10.842 2.815 28.856 1 147.55 ? O3G APC 301 A 1 
HETATM 5 P PB APC . . . E 2 13.169 4.506 26.229 1 191.8 ? PB APC 301 A 1 
HETATM 6 O O1B APC . . . E 2 12.212 5.481 25.742 1 158.2 ? O1B APC 301 A 1 
HETATM 7 O O2B APC . . . E 2 14.051 5.175 27.371 1 187.31 ? O2B APC 301 A 1 
HETATM 8 O O3B APC . . . E 2 12.385 3.363 26.983 1 178.62 ? O3B APC 301 A 1 
HETATM 9 P PA APC . . . E 2 13.392 3.213 23.626 1 191.04 ? PA APC 301 A 1 
HETATM 10 O O1A APC . . . E 2 14.186 2.632 22.537 1 171.76 ? O1A APC 301 A 1 
HETATM 11 O O2A APC . . . E 2 12.415 2.094 24.197 1 162.64 ? O2A APC 301 A 1 
HETATM 12 C C3A APC . . . E 2 14.311 3.977 24.948 1 165.46 ? C3A APC 301 A 1 
HETATM 13 O O5' APC . . . E 2 12.517 4.365 23.062 1 154.87 ? O5' APC 301 A 1 
HETATM 14 C C5' APC . . . E 2 11.507 3.859 22.276 1 152.9 ? C5' APC 301 A 1 
HETATM 15 C C4' APC . . . E 2 10.722 4.996 21.746 1 141.77 ? C4' APC 301 A 1 
HETATM 16 O O4' APC . . . E 2 11.502 6.054 21.316 1 131.9 ? O4' APC 301 A 1 
HETATM 17 C C3' APC . . . E 2 10.087 4.508 20.526 1 134.5 ? C3' APC 301 A 1 
HETATM 18 O O3' APC . . . E 2 8.92 3.906 21.014 1 129.97 ? O3' APC 301 A 1 
HETATM 19 C C2' APC . . . E 2 9.902 5.733 19.722 1 125.81 ? C2' APC 301 A 1 
HETATM 20 O O2' APC . . . E 2 8.577 6.152 19.928 1 113.97 ? O2' APC 301 A 1 
HETATM 21 C C1' APC . . . E 2 10.853 6.728 20.285 1 125.53 ? C1' APC 301 A 1 
HETATM 22 N N9 APC . . . E 2 11.852 7.143 19.316 1 125.75 ? N9 APC 301 A 1 
HETATM 23 C C8 APC . . . E 2 12.815 6.387 18.871 1 128.47 ? C8 APC 301 A 1 
HETATM 24 N N7 APC . . . E 2 13.581 7.073 18.006 1 134.09 ? N7 APC 301 A 1 
HETATM 25 C C5 APC . . . E 2 13.113 8.298 17.895 1 121.28 ? C5 APC 301 A 1 
HETATM 26 C C6 APC . . . E 2 13.43 9.506 17.155 1 113.73 ? C6 APC 301 A 1 
HETATM 27 N N6 APC . . . E 2 14.414 9.678 16.303 1 116.82 ? N6 APC 301 A 1 
HETATM 28 N N1 APC . . . E 2 12.694 10.536 17.318 1 112.79 ? N1 APC 301 A 1 
HETATM 29 C C2 APC . . . E 2 11.684 10.476 18.133 1 114.24 ? C2 APC 301 A 1 
HETATM 30 N N3 APC . . . E 2 11.327 9.42 18.827 1 116.94 ? N3 APC 301 A 1 
HETATM 31 C C4 APC . . . E 2 11.981 8.308 18.762 1 123.2 ? C4 APC 301 A 1 
HETATM 32 H H3A1 APC . . . E 2 14.844 4.846 24.561 1 198.66 ? H3A1 APC 301 A 1 
HETATM 33 H H3A2 APC . . . E 2 15.033 3.275 25.362 1 198.66 ? H3A2 APC 301 A 1 
HETATM 34 H "H5'1" APC . . . E 2 11.954 3.274 21.471 1 183.59 ? "H5'1" APC 301 A 1 
HETATM 35 H "H5'2" APC . . . E 2 10.869 3.209 22.87 1 183.59 ? "H5'2" APC 301 A 1 
HETATM 36 H H4' APC . . . E 2 9.97 5.317 22.471 1 170.24 ? H4' APC 301 A 1 
HETATM 37 H H3' APC . . . E 2 10.726 3.805 19.979 1 161.51 ? H3' APC 301 A 1 
HETATM 38 H HO3' APC . . . E 2 8.754 3.093 20.525 1 156.07 ? HO3' APC 301 A 1 
HETATM 39 H H2' APC . . . E 2 10.13 5.542 18.672 1 151.09 ? H2' APC 301 A 1 
HETATM 40 H HO2' APC . . . E 2 7.982 5.586 19.423 1 136.87 ? HO2' APC 301 A 1 
HETATM 41 H H1' APC . . . E 2 10.3 7.587 20.668 1 150.75 ? H1' APC 301 A 1 
HETATM 42 H H8 APC . . . E 2 12.97 5.36 19.162 1 154.27 ? H8 APC 301 A 1 
HETATM 43 H HN61 APC . . . E 2 14.523 10.579 15.864 1 140.29 ? HN61 APC 301 A 1 
HETATM 44 H HN62 APC . . . E 2 15.056 8.929 16.103 1 140.29 ? HN62 APC 301 A 1 
HETATM 45 H H2 APC . . . E 2 11.091 11.368 18.243 1 137.2 ? H2 APC 301 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           45 
#