data_5Y0Q
#
_model_server_result.job_id            1MdUUaTjBcsWGC4426wIiQ 
_model_server_result.datetime_utc      '2024-12-01 20:44:53' 
_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          5y0q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1001}' 
#
_entry.id    5Y0Q 
#
_exptl.entry_id    5Y0Q 
_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            5Y0Q 
_cell.length_a            67.995 
_cell.length_b            68.013 
_cell.length_c            211.672 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y0Q 
_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,F 
_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 D 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                     5Y0Q 
_atom_sites.fract_transf_matrix[1][1]    0.014707 
_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]    0.014703 
_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]    0.004724 
_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 A 1 1001 1001 APC APC . 
D 2 APC B 1 1001 1001 APC APC . 
E 3 HOH A 1 1101 88 HOH HOH . 
E 3 HOH A 2 1102 116 HOH HOH . 
E 3 HOH A 3 1103 58 HOH HOH . 
E 3 HOH A 4 1104 21 HOH HOH . 
E 3 HOH A 5 1105 32 HOH HOH . 
E 3 HOH A 6 1106 38 HOH HOH . 
E 3 HOH A 7 1107 146 HOH HOH . 
E 3 HOH A 8 1108 9 HOH HOH . 
E 3 HOH A 9 1109 73 HOH HOH . 
E 3 HOH A 10 1110 2 HOH HOH . 
E 3 HOH A 11 1111 17 HOH HOH . 
E 3 HOH A 12 1112 44 HOH HOH . 
E 3 HOH A 13 1113 143 HOH HOH . 
E 3 HOH A 14 1114 24 HOH HOH . 
E 3 HOH A 15 1115 129 HOH HOH . 
E 3 HOH A 16 1116 41 HOH HOH . 
E 3 HOH A 17 1117 20 HOH HOH . 
E 3 HOH A 18 1118 52 HOH HOH . 
E 3 HOH A 19 1119 72 HOH HOH . 
E 3 HOH A 20 1120 40 HOH HOH . 
E 3 HOH A 21 1121 5 HOH HOH . 
E 3 HOH A 22 1122 99 HOH HOH . 
E 3 HOH A 23 1123 12 HOH HOH . 
E 3 HOH A 24 1124 97 HOH HOH . 
E 3 HOH A 25 1125 27 HOH HOH . 
E 3 HOH A 26 1126 117 HOH HOH . 
E 3 HOH A 27 1127 29 HOH HOH . 
E 3 HOH A 28 1128 28 HOH HOH . 
E 3 HOH A 29 1129 134 HOH HOH . 
E 3 HOH A 30 1130 37 HOH HOH . 
E 3 HOH A 31 1131 108 HOH HOH . 
E 3 HOH A 32 1132 92 HOH HOH . 
E 3 HOH A 33 1133 15 HOH HOH . 
E 3 HOH A 34 1134 14 HOH HOH . 
E 3 HOH A 35 1135 55 HOH HOH . 
E 3 HOH A 36 1136 64 HOH HOH . 
E 3 HOH A 37 1137 109 HOH HOH . 
E 3 HOH A 38 1138 80 HOH HOH . 
E 3 HOH A 39 1139 110 HOH HOH . 
F 3 HOH B 1 1101 90 HOH HOH . 
F 3 HOH B 2 1102 43 HOH HOH . 
F 3 HOH B 3 1103 4 HOH HOH . 
F 3 HOH B 4 1104 23 HOH HOH . 
F 3 HOH B 5 1105 1 HOH HOH . 
F 3 HOH B 6 1106 33 HOH HOH . 
F 3 HOH B 7 1107 3 HOH HOH . 
F 3 HOH B 8 1108 118 HOH HOH . 
F 3 HOH B 9 1109 82 HOH HOH . 
F 3 HOH B 10 1110 67 HOH HOH . 
F 3 HOH B 11 1111 19 HOH HOH . 
F 3 HOH B 12 1112 16 HOH HOH . 
F 3 HOH B 13 1113 65 HOH HOH . 
F 3 HOH B 14 1114 74 HOH HOH . 
F 3 HOH B 15 1115 6 HOH HOH . 
F 3 HOH B 16 1116 34 HOH HOH . 
F 3 HOH B 17 1117 128 HOH HOH . 
F 3 HOH B 18 1118 130 HOH HOH . 
F 3 HOH B 19 1119 105 HOH HOH . 
F 3 HOH B 20 1120 8 HOH HOH . 
F 3 HOH B 21 1121 78 HOH HOH . 
F 3 HOH B 22 1122 138 HOH HOH . 
F 3 HOH B 23 1123 93 HOH HOH . 
F 3 HOH B 24 1124 69 HOH HOH . 
F 3 HOH B 25 1125 81 HOH HOH . 
F 3 HOH B 26 1126 131 HOH HOH . 
F 3 HOH B 27 1127 76 HOH HOH . 
F 3 HOH B 28 1128 46 HOH HOH . 
#
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 . . . D 2 12.435 -3.418 3.59 1 176.3 ? PG APC 1001 B 1 
HETATM 2 O O1G APC . . . D 2 11.228 -3.128 2.735 1 176.67 ? O1G APC 1001 B 1 
HETATM 3 O O2G APC . . . D 2 12.799 -2.302 4.539 1 175.19 ? O2G APC 1001 B 1 
HETATM 4 O O3G APC . . . D 2 12.458 -4.792 4.218 1 176.23 ? O3G APC 1001 B 1 
HETATM 5 P PB APC . . . D 2 15.088 -3.949 3.005 1 114.53 ? PB APC 1001 B 1 
HETATM 6 O O1B APC . . . D 2 15.383 -5.326 2.463 1 112.1 ? O1B APC 1001 B 1 
HETATM 7 O O2B APC . . . D 2 15.138 -3.732 4.493 1 118.98 ? O2B APC 1001 B 1 
HETATM 8 O O3B APC . . . D 2 13.639 -3.463 2.521 1 85.11 ? O3B APC 1001 B 1 
HETATM 9 P PA APC . . . D 2 17.831 -2.848 2.785 1 52.1 ? PA APC 1001 B 1 
HETATM 10 O O1A APC . . . D 2 18.432 -4.16 2.352 1 53.84 ? O1A APC 1001 B 1 
HETATM 11 O O2A APC . . . D 2 18.503 -1.526 2.512 1 48.58 ? O2A APC 1001 B 1 
HETATM 12 C C3A APC . . . D 2 16.125 -2.712 2.171 1 65.87 ? C3A APC 1001 B 1 
HETATM 13 O O5' APC . . . D 2 17.695 -2.929 4.389 1 62.55 ? O5' APC 1001 B 1 
HETATM 14 C C5' APC . . . D 2 18.808 -2.614 5.231 1 60.48 ? C5' APC 1001 B 1 
HETATM 15 C C4' APC . . . D 2 18.593 -3.182 6.63 1 56.39 ? C4' APC 1001 B 1 
HETATM 16 O O4' APC . . . D 2 17.715 -2.332 7.37 1 49.18 ? O4' APC 1001 B 1 
HETATM 17 C C3' APC . . . D 2 17.959 -4.564 6.546 1 56.91 ? C3' APC 1001 B 1 
HETATM 18 O O3' APC . . . D 2 18.715 -5.505 7.317 1 62.11 ? O3' APC 1001 B 1 
HETATM 19 C C2' APC . . . D 2 16.583 -4.401 7.146 1 52.18 ? C2' APC 1001 B 1 
HETATM 20 O O2' APC . . . D 2 16.241 -5.536 7.945 1 59.4 ? O2' APC 1001 B 1 
HETATM 21 C C1' APC . . . D 2 16.716 -3.145 7.978 1 49.72 ? C1' APC 1001 B 1 
HETATM 22 N N9 APC . . . D 2 15.463 -2.377 8.015 1 56.89 ? N9 APC 1001 B 1 
HETATM 23 C C8 APC . . . D 2 14.934 -1.658 7.013 1 58.92 ? C8 APC 1001 B 1 
HETATM 24 N N7 APC . . . D 2 13.771 -1.074 7.406 1 60.26 ? N7 APC 1001 B 1 
HETATM 25 C C5 APC . . . D 2 13.553 -1.417 8.69 1 62.82 ? C5 APC 1001 B 1 
HETATM 26 C C6 APC . . . D 2 12.523 -1.146 9.723 1 62.39 ? C6 APC 1001 B 1 
HETATM 27 N N6 APC . . . D 2 11.447 -0.365 9.459 1 64.65 ? N6 APC 1001 B 1 
HETATM 28 N N1 APC . . . D 2 12.696 -1.71 10.94 1 59.57 ? N1 APC 1001 B 1 
HETATM 29 C C2 APC . . . D 2 13.752 -2.495 11.225 1 59.08 ? C2 APC 1001 B 1 
HETATM 30 N N3 APC . . . D 2 14.719 -2.781 10.34 1 60.37 ? N3 APC 1001 B 1 
HETATM 31 C C4 APC . . . D 2 14.676 -2.279 9.083 1 61.9 ? C4 APC 1001 B 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#