data_1DKU
#
_model_server_result.job_id            1ewVwxX2NVtiV3eYqh3z_A 
_model_server_result.datetime_utc      '2024-11-26 18:07:02' 
_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          1dku 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1004}' 
#
_entry.id    1DKU 
#
_exptl.entry_id    1DKU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              345.248 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'METHYL PHOSPHONIC ACID ADENOSINE 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         120 
_cell.entry_id            1DKU 
_cell.length_a            115.65 
_cell.length_b            115.65 
_cell.length_c            106.41 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DKU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 63' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA hexameric 6 software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1 
A,B,C,D,E,F,G,H 2 1,2,3 
A,C,D,G 3 1 
B,E,F,H 3 2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 57.825 100.155838 0 
3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -57.825 100.155838 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F N N 
#
_chem_comp.formula           'C11 H16 N5 O6 P' 
_chem_comp.formula_weight    345.248 
_chem_comp.id                ABM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'METHYL PHOSPHONIC ACID ADENOSINE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ALPHA-METHYLENE ADENOSINE MONOPHOSPHATE' 
#
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
P CM ABM sing 1 n n 
P O2P ABM doub 2 n n 
P O3P ABM sing 3 n n 
P O5' ABM sing 4 n n 
CM HM1 ABM sing 5 n n 
CM HM2 ABM sing 6 n n 
CM HM3 ABM sing 7 n n 
O3P HOP3 ABM sing 8 n n 
O5' C5' ABM sing 9 n n 
C5' C4' ABM sing 10 n n 
C5' "H5'1" ABM sing 11 n n 
C5' "H5'2" ABM sing 12 n n 
C4' O4' ABM sing 13 n n 
C4' C3' ABM sing 14 n n 
C4' H4' ABM sing 15 n n 
O4' C1' ABM sing 16 n n 
C3' O3' ABM sing 17 n n 
C3' C2' ABM sing 18 n n 
C3' H3' ABM sing 19 n n 
O3' HO3' ABM sing 20 n n 
C2' O2' ABM sing 21 n n 
C2' C1' ABM sing 22 n n 
C2' H2' ABM sing 23 n n 
O2' HO2' ABM sing 24 n n 
C1' N9 ABM sing 25 n n 
C1' H1' ABM sing 26 n n 
N9 C8 ABM sing 27 n y 
N9 C4 ABM sing 28 n y 
C8 N7 ABM doub 29 n y 
C8 H8 ABM sing 30 n n 
N7 C5 ABM sing 31 n y 
C5 C6 ABM sing 32 n y 
C5 C4 ABM doub 33 n y 
C6 N6 ABM sing 34 n n 
C6 N1 ABM doub 35 n y 
N6 HN61 ABM sing 36 n n 
N6 HN62 ABM sing 37 n n 
N1 C2 ABM sing 38 n y 
C2 N3 ABM doub 39 n y 
C2 H2 ABM sing 40 n n 
N3 C4 ABM sing 41 n y 
#
_atom_sites.entry_id                     1DKU 
_atom_sites.fract_transf_matrix[1][1]    0.00865 
_atom_sites.fract_transf_matrix[1][2]    0.00499 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00998 
_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]    0.0094 
_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 AP2 A 1 1002 1002 AP2 AP2 . 
D 3 ABM A 1 1003 1003 ABM ABM . 
E 2 AP2 B 1 1001 1001 AP2 AP2 . 
F 3 ABM B 1 1004 1004 ABM ABM . 
G 4 HOH A 1 1004 1 HOH HOH . 
G 4 HOH A 2 1005 2 HOH HOH . 
G 4 HOH A 3 1006 3 HOH HOH . 
G 4 HOH A 4 1007 4 HOH HOH . 
G 4 HOH A 5 1008 5 HOH HOH . 
G 4 HOH A 6 1009 6 HOH HOH . 
G 4 HOH A 7 1010 7 HOH HOH . 
G 4 HOH A 8 1011 15 HOH HOH . 
G 4 HOH A 9 1012 21 HOH HOH . 
G 4 HOH A 10 1013 22 HOH HOH . 
G 4 HOH A 11 1014 23 HOH HOH . 
G 4 HOH A 12 1015 24 HOH HOH . 
G 4 HOH A 13 1016 25 HOH HOH . 
G 4 HOH A 14 1017 26 HOH HOH . 
G 4 HOH A 15 1018 27 HOH HOH . 
G 4 HOH A 16 1019 28 HOH HOH . 
G 4 HOH A 17 1020 29 HOH HOH . 
G 4 HOH A 18 1021 30 HOH HOH . 
G 4 HOH A 19 1022 37 HOH HOH . 
G 4 HOH A 20 1023 41 HOH HOH . 
G 4 HOH A 21 1024 42 HOH HOH . 
G 4 HOH A 22 1025 43 HOH HOH . 
G 4 HOH A 23 1026 44 HOH HOH . 
G 4 HOH A 24 1027 45 HOH HOH . 
G 4 HOH A 25 1028 46 HOH HOH . 
G 4 HOH A 26 1029 47 HOH HOH . 
G 4 HOH A 27 1030 48 HOH HOH . 
G 4 HOH A 28 1031 49 HOH HOH . 
G 4 HOH A 29 1032 51 HOH HOH . 
G 4 HOH A 30 1033 53 HOH HOH . 
G 4 HOH A 31 1034 54 HOH HOH . 
G 4 HOH A 32 1035 55 HOH HOH . 
G 4 HOH A 33 1036 70 HOH HOH . 
G 4 HOH A 34 1037 71 HOH HOH . 
G 4 HOH A 35 1038 72 HOH HOH . 
G 4 HOH A 36 1039 74 HOH HOH . 
G 4 HOH A 37 1040 75 HOH HOH . 
G 4 HOH A 38 1041 76 HOH HOH . 
G 4 HOH A 39 1042 77 HOH HOH . 
G 4 HOH A 40 1043 79 HOH HOH . 
G 4 HOH A 41 1044 81 HOH HOH . 
G 4 HOH A 42 1045 82 HOH HOH . 
G 4 HOH A 43 1046 84 HOH HOH . 
G 4 HOH A 44 1047 86 HOH HOH . 
G 4 HOH A 45 1048 87 HOH HOH . 
G 4 HOH A 46 1049 88 HOH HOH . 
G 4 HOH A 47 1050 89 HOH HOH . 
G 4 HOH A 48 1051 95 HOH HOH . 
G 4 HOH A 49 1052 98 HOH HOH . 
G 4 HOH A 50 1053 99 HOH HOH . 
G 4 HOH A 51 1054 100 HOH HOH . 
G 4 HOH A 52 1055 101 HOH HOH . 
G 4 HOH A 53 1056 102 HOH HOH . 
G 4 HOH A 54 1057 103 HOH HOH . 
G 4 HOH A 55 1058 111 HOH HOH . 
G 4 HOH A 56 1059 115 HOH HOH . 
G 4 HOH A 57 1060 119 HOH HOH . 
G 4 HOH A 58 1061 120 HOH HOH . 
G 4 HOH A 59 1062 121 HOH HOH . 
G 4 HOH A 60 1063 122 HOH HOH . 
G 4 HOH A 61 1064 123 HOH HOH . 
G 4 HOH A 62 1065 124 HOH HOH . 
G 4 HOH A 63 1066 125 HOH HOH . 
G 4 HOH A 64 1067 126 HOH HOH . 
G 4 HOH A 65 1068 128 HOH HOH . 
G 4 HOH A 66 1069 129 HOH HOH . 
G 4 HOH A 67 1070 131 HOH HOH . 
G 4 HOH A 68 1071 138 HOH HOH . 
G 4 HOH A 69 1072 140 HOH HOH . 
G 4 HOH A 70 1073 141 HOH HOH . 
G 4 HOH A 71 1074 142 HOH HOH . 
G 4 HOH A 72 1075 143 HOH HOH . 
G 4 HOH A 73 1076 144 HOH HOH . 
G 4 HOH A 74 1077 145 HOH HOH . 
G 4 HOH A 75 1078 146 HOH HOH . 
G 4 HOH A 76 1079 149 HOH HOH . 
G 4 HOH A 77 1080 150 HOH HOH . 
G 4 HOH A 78 1081 151 HOH HOH . 
G 4 HOH A 79 1082 152 HOH HOH . 
G 4 HOH A 80 1083 153 HOH HOH . 
G 4 HOH A 81 1084 154 HOH HOH . 
G 4 HOH A 82 1085 157 HOH HOH . 
G 4 HOH A 83 1086 158 HOH HOH . 
G 4 HOH A 84 1087 161 HOH HOH . 
G 4 HOH A 85 1088 162 HOH HOH . 
G 4 HOH A 86 1089 164 HOH HOH . 
G 4 HOH A 87 1090 166 HOH HOH . 
G 4 HOH A 88 1091 167 HOH HOH . 
G 4 HOH A 89 1092 168 HOH HOH . 
G 4 HOH A 90 1093 169 HOH HOH . 
G 4 HOH A 91 1094 173 HOH HOH . 
G 4 HOH A 92 1095 176 HOH HOH . 
G 4 HOH A 93 1096 177 HOH HOH . 
G 4 HOH A 94 1097 178 HOH HOH . 
G 4 HOH A 95 1098 179 HOH HOH . 
G 4 HOH A 96 1099 180 HOH HOH . 
H 4 HOH B 1 1005 8 HOH HOH . 
H 4 HOH B 2 1006 9 HOH HOH . 
H 4 HOH B 3 1007 10 HOH HOH . 
H 4 HOH B 4 1008 11 HOH HOH . 
H 4 HOH B 5 1009 12 HOH HOH . 
H 4 HOH B 6 1010 13 HOH HOH . 
H 4 HOH B 7 1011 14 HOH HOH . 
H 4 HOH B 8 1012 16 HOH HOH . 
H 4 HOH B 9 1013 17 HOH HOH . 
H 4 HOH B 10 1014 18 HOH HOH . 
H 4 HOH B 11 1015 19 HOH HOH . 
H 4 HOH B 12 1016 20 HOH HOH . 
H 4 HOH B 13 1017 31 HOH HOH . 
H 4 HOH B 14 1018 32 HOH HOH . 
H 4 HOH B 15 1019 33 HOH HOH . 
H 4 HOH B 16 1020 34 HOH HOH . 
H 4 HOH B 17 1021 35 HOH HOH . 
H 4 HOH B 18 1022 36 HOH HOH . 
H 4 HOH B 19 1023 38 HOH HOH . 
H 4 HOH B 20 1024 39 HOH HOH . 
H 4 HOH B 21 1025 40 HOH HOH . 
H 4 HOH B 22 1026 50 HOH HOH . 
H 4 HOH B 23 1027 52 HOH HOH . 
H 4 HOH B 24 1028 56 HOH HOH . 
H 4 HOH B 25 1029 57 HOH HOH . 
H 4 HOH B 26 1030 58 HOH HOH . 
H 4 HOH B 27 1031 59 HOH HOH . 
H 4 HOH B 28 1032 60 HOH HOH . 
H 4 HOH B 29 1033 61 HOH HOH . 
H 4 HOH B 30 1034 62 HOH HOH . 
H 4 HOH B 31 1035 63 HOH HOH . 
H 4 HOH B 32 1036 64 HOH HOH . 
H 4 HOH B 33 1037 65 HOH HOH . 
H 4 HOH B 34 1038 66 HOH HOH . 
H 4 HOH B 35 1039 67 HOH HOH . 
H 4 HOH B 36 1040 68 HOH HOH . 
H 4 HOH B 37 1041 69 HOH HOH . 
H 4 HOH B 38 1042 73 HOH HOH . 
H 4 HOH B 39 1043 78 HOH HOH . 
H 4 HOH B 40 1044 80 HOH HOH . 
H 4 HOH B 41 1045 83 HOH HOH . 
H 4 HOH B 42 1046 85 HOH HOH . 
H 4 HOH B 43 1047 90 HOH HOH . 
H 4 HOH B 44 1048 91 HOH HOH . 
H 4 HOH B 45 1049 92 HOH HOH . 
H 4 HOH B 46 1050 93 HOH HOH . 
H 4 HOH B 47 1051 94 HOH HOH . 
H 4 HOH B 48 1052 96 HOH HOH . 
H 4 HOH B 49 1053 97 HOH HOH . 
H 4 HOH B 50 1054 104 HOH HOH . 
H 4 HOH B 51 1055 105 HOH HOH . 
H 4 HOH B 52 1056 106 HOH HOH . 
H 4 HOH B 53 1057 107 HOH HOH . 
H 4 HOH B 54 1058 108 HOH HOH . 
H 4 HOH B 55 1059 109 HOH HOH . 
H 4 HOH B 56 1060 110 HOH HOH . 
H 4 HOH B 57 1061 112 HOH HOH . 
H 4 HOH B 58 1062 113 HOH HOH . 
H 4 HOH B 59 1063 114 HOH HOH . 
H 4 HOH B 60 1064 116 HOH HOH . 
H 4 HOH B 61 1065 117 HOH HOH . 
H 4 HOH B 62 1066 118 HOH HOH . 
H 4 HOH B 63 1067 127 HOH HOH . 
H 4 HOH B 64 1068 130 HOH HOH . 
H 4 HOH B 65 1069 132 HOH HOH . 
H 4 HOH B 66 1070 133 HOH HOH . 
H 4 HOH B 67 1071 134 HOH HOH . 
H 4 HOH B 68 1072 135 HOH HOH . 
H 4 HOH B 69 1073 136 HOH HOH . 
H 4 HOH B 70 1074 137 HOH HOH . 
H 4 HOH B 71 1075 139 HOH HOH . 
H 4 HOH B 72 1076 147 HOH HOH . 
H 4 HOH B 73 1077 148 HOH HOH . 
H 4 HOH B 74 1078 155 HOH HOH . 
H 4 HOH B 75 1079 156 HOH HOH . 
H 4 HOH B 76 1080 159 HOH HOH . 
H 4 HOH B 77 1081 160 HOH HOH . 
H 4 HOH B 78 1082 163 HOH HOH . 
H 4 HOH B 79 1083 165 HOH HOH . 
H 4 HOH B 80 1084 170 HOH HOH . 
H 4 HOH B 81 1085 171 HOH HOH . 
H 4 HOH B 82 1086 172 HOH HOH . 
H 4 HOH B 83 1087 174 HOH HOH . 
H 4 HOH B 84 1088 175 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 P ABM . . . F 3 27.599 50.279 49.75 1 57.01 ? P ABM 1004 B 1 
HETATM 2 C CM ABM . . . F 3 29.108 49.287 49.619 1 55.46 ? CM ABM 1004 B 1 
HETATM 3 O O2P ABM . . . F 3 27.85 51.49 48.808 1 56.3 ? O2P ABM 1004 B 1 
HETATM 4 O O3P ABM . . . F 3 27.425 50.533 51.247 1 56.31 ? O3P ABM 1004 B 1 
HETATM 5 O O5' ABM . . . F 3 26.445 49.271 49.202 1 55.51 ? O5' ABM 1004 B 1 
HETATM 6 C C5' ABM . . . F 3 25.249 49.714 48.448 1 50.91 ? C5' ABM 1004 B 1 
HETATM 7 C C4' ABM . . . F 3 24.893 48.793 47.239 1 48.11 ? C4' ABM 1004 B 1 
HETATM 8 O O4' ABM . . . F 3 24.399 47.467 47.661 1 46.07 ? O4' ABM 1004 B 1 
HETATM 9 C C3' ABM . . . F 3 23.819 49.413 46.279 1 46.66 ? C3' ABM 1004 B 1 
HETATM 10 O O3' ABM . . . F 3 24.328 49.418 44.92 1 47.41 ? O3' ABM 1004 B 1 
HETATM 11 C C2' ABM . . . F 3 22.611 48.468 46.339 1 45.8 ? C2' ABM 1004 B 1 
HETATM 12 O O2' ABM . . . F 3 22.046 48.269 45.004 1 46.32 ? O2' ABM 1004 B 1 
HETATM 13 C C1' ABM . . . F 3 23.134 47.148 46.982 1 42.42 ? C1' ABM 1004 B 1 
HETATM 14 N N9 ABM . . . F 3 22.174 46.573 47.983 1 37.03 ? N9 ABM 1004 B 1 
HETATM 15 C C8 ABM . . . F 3 20.935 47.026 48.375 1 35.39 ? C8 ABM 1004 B 1 
HETATM 16 N N7 ABM . . . F 3 20.27 46.194 49.155 1 34.02 ? N7 ABM 1004 B 1 
HETATM 17 C C5 ABM . . . F 3 21.11 45.089 49.208 1 33.6 ? C5 ABM 1004 B 1 
HETATM 18 C C6 ABM . . . F 3 21.054 43.88 49.948 1 33.59 ? C6 ABM 1004 B 1 
HETATM 19 N N6 ABM . . . F 3 20.066 43.565 50.771 1 33.14 ? N6 ABM 1004 B 1 
HETATM 20 N N1 ABM . . . F 3 21.95 42.938 49.634 1 33.17 ? N1 ABM 1004 B 1 
HETATM 21 C C2 ABM . . . F 3 22.967 43.278 48.819 1 33.59 ? C2 ABM 1004 B 1 
HETATM 22 N N3 ABM . . . F 3 23.284 44.49 48.305 1 34.15 ? N3 ABM 1004 B 1 
HETATM 23 C C4 ABM . . . F 3 22.279 45.345 48.526 1 34.33 ? C4 ABM 1004 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           23 
#