data_6GYX
#
_model_server_result.job_id            n8ntMGQ7vTkYqf2r30jXIA 
_model_server_result.datetime_utc      '2025-02-27 07:22:47' 
_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":"C","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 . . . C 2 -17.471 -7.562 21.584 1 209.7 ? PG APC 301 B 1 
HETATM 2 O O1G APC . . . C 2 -16.461 -6.694 20.878 1 209.66 ? O1G APC 301 B 1 
HETATM 3 O O2G APC . . . C 2 -18.68 -6.84 22.12 1 211.9 ? O2G APC 301 B 1 
HETATM 4 O O3G APC . . . C 2 -16.885 -8.556 22.519 1 212.42 ? O3G APC 301 B 1 
HETATM 5 P PB APC . . . C 2 -19.518 -8.721 20.28 1 197.4 ? PB APC 301 B 1 
HETATM 6 O O1B APC . . . C 2 -20.321 -7.481 19.659 1 199.81 ? O1B APC 301 B 1 
HETATM 7 O O2B APC . . . C 2 -20.101 -8.894 21.604 1 194.08 ? O2B APC 301 B 1 
HETATM 8 O O3B APC . . . C 2 -17.966 -8.516 20.447 1 208.08 ? O3B APC 301 B 1 
HETATM 9 P PA APC . . . C 2 -20.098 -9.388 17.662 1 149.6 ? PA APC 301 B 1 
HETATM 10 O O1A APC . . . C 2 -20.974 -10.351 16.803 1 164.93 ? O1A APC 301 B 1 
HETATM 11 O O2A APC . . . C 2 -20.806 -8.173 17.897 1 143.06 ? O2A APC 301 B 1 
HETATM 12 C C3A APC . . . C 2 -19.64 -10.148 19.191 1 188.89 ? C3A APC 301 B 1 
HETATM 13 O O5' APC . . . C 2 -18.828 -9.106 16.868 1 141.74 ? O5' APC 301 B 1 
HETATM 14 C C5' APC . . . C 2 -18.093 -8.033 17.265 1 136.95 ? C5' APC 301 B 1 
HETATM 15 C C4' APC . . . C 2 -17.634 -7.42 16.009 1 115.81 ? C4' APC 301 B 1 
HETATM 16 O O4' APC . . . C 2 -18.737 -7.169 15.209 1 115.37 ? O4' APC 301 B 1 
HETATM 17 C C3' APC . . . C 2 -17.104 -6.079 16.282 1 112.23 ? C3' APC 301 B 1 
HETATM 18 O O3' APC . . . C 2 -15.752 -6.053 16.047 1 109.9 ? O3' APC 301 B 1 
HETATM 19 C C2' APC . . . C 2 -17.591 -5.218 15.202 1 102.46 ? C2' APC 301 B 1 
HETATM 20 O O2' APC . . . C 2 -16.432 -5.044 14.466 1 98.58 ? O2' APC 301 B 1 
HETATM 21 C C1' APC . . . C 2 -18.536 -6.02 14.422 1 100.51 ? C1' APC 301 B 1 
HETATM 22 N N9 APC . . . C 2 -19.805 -5.401 14.159 1 88.65 ? N9 APC 301 B 1 
HETATM 23 C C8 APC . . . C 2 -20.857 -5.545 14.873 1 94.21 ? C8 APC 301 B 1 
HETATM 24 N N7 APC . . . C 2 -21.9 -4.918 14.351 1 92.07 ? N7 APC 301 B 1 
HETATM 25 C C5 APC . . . C 2 -21.499 -4.36 13.251 1 89.55 ? C5 APC 301 B 1 
HETATM 26 C C6 APC . . . C 2 -22.076 -3.553 12.213 1 86.79 ? C6 APC 301 B 1 
HETATM 27 N N6 APC . . . C 2 -23.31 -3.162 12.183 1 87.72 ? N6 APC 301 B 1 
HETATM 28 N N1 APC . . . C 2 -21.355 -3.168 11.246 1 82.54 ? N1 APC 301 B 1 
HETATM 29 C C2 APC . . . C 2 -20.118 -3.522 11.245 1 84.8 ? C2 APC 301 B 1 
HETATM 30 N N3 APC . . . C 2 -19.523 -4.257 12.141 1 89.33 ? N3 APC 301 B 1 
HETATM 31 C C4 APC . . . C 2 -20.14 -4.707 13.157 1 88.34 ? C4 APC 301 B 1 
HETATM 32 H H3A1 APC . . . C 2 -20.397 -10.858 19.526 1 226.78 ? H3A1 APC 301 B 1 
HETATM 33 H H3A2 APC . . . C 2 -18.679 -10.654 19.098 1 226.78 ? H3A2 APC 301 B 1 
HETATM 34 H "H5'1" APC . . . C 2 -17.249 -8.358 17.865 1 164.45 ? "H5'1" APC 301 B 1 
HETATM 35 H "H5'2" APC . . . C 2 -18.69 -7.317 17.823 1 164.45 ? "H5'2" APC 301 B 1 
HETATM 36 H H4' APC . . . C 2 -16.895 -8.043 15.506 1 139.08 ? H4' APC 301 B 1 
HETATM 37 H H3' APC . . . C 2 -17.374 -5.707 17.273 1 134.78 ? H3' APC 301 B 1 
HETATM 38 H HO3' APC . . . C 2 -15.393 -5.276 16.485 1 131.99 ? HO3' APC 301 B 1 
HETATM 39 H H2' APC . . . C 2 -18.028 -4.287 15.564 1 123.07 ? H2' APC 301 B 1 
HETATM 40 H HO2' APC . . . C 2 -16.023 -4.211 14.725 1 118.41 ? HO2' APC 301 B 1 
HETATM 41 H H1' APC . . . C 2 -18.067 -6.291 13.477 1 120.72 ? H1' APC 301 B 1 
HETATM 42 H H8 APC . . . C 2 -20.873 -6.114 15.785 1 113.17 ? H8 APC 301 B 1 
HETATM 43 H HN61 APC . . . C 2 -23.934 -3.426 12.924 1 105.38 ? HN61 APC 301 B 1 
HETATM 44 H HN62 APC . . . C 2 -23.624 -2.586 11.417 1 105.38 ? HN62 APC 301 B 1 
HETATM 45 H H2 APC . . . C 2 -19.522 -3.197 10.416 1 101.86 ? H2 APC 301 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           45 
#