data_3TPS
#
_model_server_result.job_id            skpda-UE4Gipy5Z3V5vBRg 
_model_server_result.datetime_utc      '2024-11-27 00:50:26' 
_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          3tps 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":777}' 
#
_entry.id    3TPS 
#
_exptl.entry_id    3TPS 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            3TPS 
_cell.length_a            60.708 
_cell.length_b            60.708 
_cell.length_c            64.363 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TPS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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    1,2,3 
#
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_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 60.708 105.14934 0 
3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -60.708 105.14934 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 A C LEU 43 A LEU 43 1_555 A N CSO 44 A CSO 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale2 A C CSO 44 A CSO 44 1_555 A N SER 45 A SER 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
metalc ? metalc1 B MG MG . A MG 153 1_555 E O HOH . A HOH 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc2 B MG MG . A MG 153 1_555 E O HOH . A HOH 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc3 B MG MG . A MG 153 1_555 E O HOH . A HOH 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc4 B MG MG . A MG 153 1_555 C O2G DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc5 B MG MG . A MG 153 1_555 C O1A DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc6 B MG MG . A MG 153 1_555 C O1B DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
#
_chem_comp.formula           'C9 H16 N3 O13 P3' 
_chem_comp.formula_weight    467.157 
_chem_comp.id                DUP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
O4 C4 DUP doub 97 n n 
C4 C5 DUP sing 98 n y 
C4 N3 DUP sing 99 n y 
C5 C6 DUP doub 100 n y 
C5 H5 DUP sing 101 n n 
C6 N1 DUP sing 102 n y 
C6 H6 DUP sing 103 n n 
N3 C2 DUP sing 104 n y 
N3 HN3 DUP sing 105 n n 
C2 O2 DUP doub 106 n n 
C2 N1 DUP sing 107 n y 
N1 C1' DUP sing 108 n n 
C1' C2' DUP sing 109 n n 
C1' O4' DUP sing 110 n n 
C1' H1' DUP sing 111 n n 
C2' C3' DUP sing 112 n n 
C2' "H2'1" DUP sing 113 n n 
C2' "H2'2" DUP sing 114 n n 
C3' O3' DUP sing 115 n n 
C3' C4' DUP sing 116 n n 
C3' H1 DUP sing 117 n n 
O3' H3' DUP sing 118 n n 
O4' C4' DUP sing 119 n n 
C4' C5' DUP sing 120 n n 
C4' H4' DUP sing 121 n n 
C5' O5' DUP sing 122 n n 
C5' "H5'1" DUP sing 123 n n 
C5' "H5'2" DUP sing 124 n n 
O5' PA DUP sing 125 n n 
PA O1A DUP doub 126 n n 
PA O2A DUP sing 127 n n 
PA N3A DUP sing 128 n n 
O2A H2A DUP sing 129 n n 
N3A PB DUP sing 130 n n 
N3A H3A DUP sing 131 n n 
PB O1B DUP doub 132 n n 
PB O2B DUP sing 133 n n 
PB O3B DUP sing 134 n n 
O2B H2B DUP sing 135 n n 
O3B PG DUP sing 136 n n 
PG O2G DUP doub 137 n n 
PG O1G DUP sing 138 n n 
PG O3G DUP sing 139 n n 
O1G H1G DUP sing 140 n n 
O3G H3G DUP sing 141 n n 
#
_atom_sites.entry_id                     3TPS 
_atom_sites.fract_transf_matrix[1][1]    0.016472 
_atom_sites.fract_transf_matrix[1][2]    0.00951 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019021 
_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]    0.015537 
_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
B 2 MG A 1 153 1 MG MG . 
C 3 DUP A 1 777 777 DUP DUP . 
D 4 TRS A 1 154 1 TRS TRS . 
E 5 HOH A 1 155 1 HOH HOH . 
E 5 HOH A 2 156 2 HOH HOH . 
E 5 HOH A 3 157 4 HOH HOH . 
E 5 HOH A 4 158 5 HOH HOH . 
E 5 HOH A 5 159 6 HOH HOH . 
E 5 HOH A 6 160 7 HOH HOH . 
E 5 HOH A 7 161 8 HOH HOH . 
E 5 HOH A 8 162 9 HOH HOH . 
E 5 HOH A 9 163 10 HOH HOH . 
E 5 HOH A 10 164 11 HOH HOH . 
E 5 HOH A 11 165 12 HOH HOH . 
E 5 HOH A 12 166 14 HOH HOH . 
E 5 HOH A 13 167 15 HOH HOH . 
E 5 HOH A 14 168 16 HOH HOH . 
E 5 HOH A 15 169 17 HOH HOH . 
E 5 HOH A 16 170 18 HOH HOH . 
E 5 HOH A 17 171 19 HOH HOH . 
E 5 HOH A 18 172 20 HOH HOH . 
E 5 HOH A 19 173 21 HOH HOH . 
E 5 HOH A 20 174 22 HOH HOH . 
E 5 HOH A 21 175 23 HOH HOH . 
E 5 HOH A 22 176 24 HOH HOH . 
E 5 HOH A 23 177 25 HOH HOH . 
E 5 HOH A 24 178 26 HOH HOH . 
E 5 HOH A 25 179 27 HOH HOH . 
E 5 HOH A 26 180 28 HOH HOH . 
E 5 HOH A 27 181 29 HOH HOH . 
E 5 HOH A 28 182 30 HOH HOH . 
E 5 HOH A 29 183 31 HOH HOH . 
E 5 HOH A 30 184 32 HOH HOH . 
E 5 HOH A 31 185 33 HOH HOH . 
E 5 HOH A 32 186 34 HOH HOH . 
E 5 HOH A 33 187 35 HOH HOH . 
E 5 HOH A 34 188 36 HOH HOH . 
E 5 HOH A 35 189 37 HOH HOH . 
E 5 HOH A 36 190 38 HOH HOH . 
E 5 HOH A 37 191 39 HOH HOH . 
E 5 HOH A 38 192 40 HOH HOH . 
E 5 HOH A 39 193 41 HOH HOH . 
E 5 HOH A 40 194 42 HOH HOH . 
E 5 HOH A 41 195 43 HOH HOH . 
E 5 HOH A 42 196 44 HOH HOH . 
E 5 HOH A 43 197 45 HOH HOH . 
E 5 HOH A 44 198 46 HOH HOH . 
E 5 HOH A 45 199 48 HOH HOH . 
E 5 HOH A 46 200 49 HOH HOH . 
E 5 HOH A 47 201 50 HOH HOH . 
E 5 HOH A 48 202 51 HOH HOH . 
E 5 HOH A 49 203 52 HOH HOH . 
E 5 HOH A 50 204 53 HOH HOH . 
E 5 HOH A 51 205 54 HOH HOH . 
E 5 HOH A 52 206 55 HOH HOH . 
E 5 HOH A 53 207 56 HOH HOH . 
E 5 HOH A 54 208 57 HOH HOH . 
E 5 HOH A 55 209 58 HOH HOH . 
E 5 HOH A 56 210 59 HOH HOH . 
E 5 HOH A 57 211 60 HOH HOH . 
E 5 HOH A 58 212 61 HOH HOH . 
E 5 HOH A 59 213 62 HOH HOH . 
E 5 HOH A 60 214 63 HOH HOH . 
E 5 HOH A 61 215 64 HOH HOH . 
E 5 HOH A 62 216 65 HOH HOH . 
E 5 HOH A 63 217 66 HOH HOH . 
E 5 HOH A 64 218 67 HOH HOH . 
E 5 HOH A 65 219 68 HOH HOH . 
E 5 HOH A 66 220 69 HOH HOH . 
E 5 HOH A 67 221 70 HOH HOH . 
E 5 HOH A 68 222 71 HOH HOH . 
E 5 HOH A 69 223 72 HOH HOH . 
E 5 HOH A 70 224 73 HOH HOH . 
E 5 HOH A 71 225 74 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 O O4 DUP . . . C 3 10.095 73.151 29.101 1 22.6 ? O4 DUP 777 A 1 
HETATM 2 C C4 DUP . . . C 3 11.124 72.799 29.725 1 23.36 ? C4 DUP 777 A 1 
HETATM 3 C C5 DUP . . . C 3 11.315 71.473 30.177 1 21.2 ? C5 DUP 777 A 1 
HETATM 4 C C6 DUP . . . C 3 12.51 71.175 30.854 1 18.24 ? C6 DUP 777 A 1 
HETATM 5 N N3 DUP . . . C 3 12.111 73.725 29.892 1 23.94 ? N3 DUP 777 A 1 
HETATM 6 C C2 DUP . . . C 3 13.293 73.431 30.571 1 21.49 ? C2 DUP 777 A 1 
HETATM 7 O O2 DUP . . . C 3 14.116 74.333 30.721 1 25.49 ? O2 DUP 777 A 1 
HETATM 8 N N1 DUP . . . C 3 13.491 72.15 31.026 1 23.68 ? N1 DUP 777 A 1 
HETATM 9 C C1' DUP . . . C 3 14.705 71.754 31.768 1 25.92 ? C1' DUP 777 A 1 
HETATM 10 C C2' DUP . . . C 3 14.427 71.761 33.297 1 19.85 ? C2' DUP 777 A 1 
HETATM 11 C C3' DUP . . . C 3 14.255 70.282 33.585 1 24.41 ? C3' DUP 777 A 1 
HETATM 12 O O3' DUP . . . C 3 14.63 69.994 34.911 1 25.97 ? O3' DUP 777 A 1 
HETATM 13 O O4' DUP . . . C 3 15.131 70.434 31.418 1 25.93 ? O4' DUP 777 A 1 
HETATM 14 C C4' DUP . . . C 3 15.228 69.668 32.613 1 22.55 ? C4' DUP 777 A 1 
HETATM 15 C C5' DUP . . . C 3 14.957 68.196 32.332 1 26.39 ? C5' DUP 777 A 1 
HETATM 16 O O5' DUP . . . C 3 13.714 68.075 31.68 1 32.63 ? O5' DUP 777 A 1 
HETATM 17 P PA DUP . . . C 3 12.915 66.712 31.603 1 25.79 ? PA DUP 777 A 1 
HETATM 18 O O1A DUP . . . C 3 13.228 65.657 32.547 1 34.13 ? O1A DUP 777 A 1 
HETATM 19 O O2A DUP . . . C 3 11.568 66.907 31.1 1 28.15 ? O2A DUP 777 A 1 
HETATM 20 N N3A DUP . . . C 3 13.829 66.3 30.349 1 30.25 ? N3A DUP 777 A 1 
HETATM 21 P PB DUP . . . C 3 14.675 64.884 29.901 1 34.26 ? PB DUP 777 A 1 
HETATM 22 O O1B DUP . . . C 3 14.093 63.685 30.625 1 41.39 ? O1B DUP 777 A 1 
HETATM 23 O O2B DUP . . . C 3 14.839 64.775 28.407 1 30.85 ? O2B DUP 777 A 1 
HETATM 24 O O3B DUP . . . C 3 16.178 65.074 30.457 1 46.29 ? O3B DUP 777 A 1 
HETATM 25 P PG DUP . . . C 3 16.795 64.423 31.83 1 52.42 ? PG DUP 777 A 1 
HETATM 26 O O2G DUP . . . C 3 15.786 64.354 32.975 1 37.89 ? O2G DUP 777 A 1 
HETATM 27 O O1G DUP . . . C 3 17.223 63.004 31.5 1 50.49 ? O1G DUP 777 A 1 
HETATM 28 O O3G DUP . . . C 3 17.968 65.332 32.177 1 45.19 ? O3G DUP 777 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           28 
#