data_3TPW
#
_model_server_result.job_id            bPRinmEU8xnTf5CR2K0sJg 
_model_server_result.datetime_utc      '2024-11-06 21:32:31' 
_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          3tpw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":777}' 
#
_entry.id    3TPW 
#
_exptl.entry_id    3TPW 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.157 
_entity.id                          2 
_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            3TPW 
_cell.length_a            60.619 
_cell.length_b            60.619 
_cell.length_c            63.731 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TPW 
_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 60.619 104.995188 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 -60.619 104.995188 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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
metalc ? metalc1 C MG MG . A MG 153 1_555 E O HOH . A HOH 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc2 C MG MG . A MG 153 1_555 E O HOH . A HOH 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc3 C MG MG . A MG 153 1_555 E O HOH . A HOH 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc4 C MG MG . A MG 153 1_555 B O2G DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc5 C MG MG . A MG 153 1_555 B O1B DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc6 C MG MG . A MG 153 1_555 B O1A DUP . A DUP 777 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
#
_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 83 n n 
C4 C5 DUP sing 84 n y 
C4 N3 DUP sing 85 n y 
C5 C6 DUP doub 86 n y 
C5 H5 DUP sing 87 n n 
C6 N1 DUP sing 88 n y 
C6 H6 DUP sing 89 n n 
N3 C2 DUP sing 90 n y 
N3 HN3 DUP sing 91 n n 
C2 O2 DUP doub 92 n n 
C2 N1 DUP sing 93 n y 
N1 C1' DUP sing 94 n n 
C1' C2' DUP sing 95 n n 
C1' O4' DUP sing 96 n n 
C1' H1' DUP sing 97 n n 
C2' C3' DUP sing 98 n n 
C2' "H2'1" DUP sing 99 n n 
C2' "H2'2" DUP sing 100 n n 
C3' O3' DUP sing 101 n n 
C3' C4' DUP sing 102 n n 
C3' H1 DUP sing 103 n n 
O3' H3' DUP sing 104 n n 
O4' C4' DUP sing 105 n n 
C4' C5' DUP sing 106 n n 
C4' H4' DUP sing 107 n n 
C5' O5' DUP sing 108 n n 
C5' "H5'1" DUP sing 109 n n 
C5' "H5'2" DUP sing 110 n n 
O5' PA DUP sing 111 n n 
PA O1A DUP doub 112 n n 
PA O2A DUP sing 113 n n 
PA N3A DUP sing 114 n n 
O2A H2A DUP sing 115 n n 
N3A PB DUP sing 116 n n 
N3A H3A DUP sing 117 n n 
PB O1B DUP doub 118 n n 
PB O2B DUP sing 119 n n 
PB O3B DUP sing 120 n n 
O2B H2B DUP sing 121 n n 
O3B PG DUP sing 122 n n 
PG O2G DUP doub 123 n n 
PG O1G DUP sing 124 n n 
PG O3G DUP sing 125 n n 
O1G H1G DUP sing 126 n n 
O3G H3G DUP sing 127 n n 
#
_atom_sites.entry_id                     3TPW 
_atom_sites.fract_transf_matrix[1][1]    0.016496 
_atom_sites.fract_transf_matrix[1][2]    0.009524 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019048 
_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]    0.015691 
_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 DUP A 1 777 777 DUP DUP . 
C 3 MG A 1 153 1 MG MG . 
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 3 HOH HOH . 
E 5 HOH A 4 158 4 HOH HOH . 
E 5 HOH A 5 159 5 HOH HOH . 
E 5 HOH A 6 160 6 HOH HOH . 
E 5 HOH A 7 161 7 HOH HOH . 
E 5 HOH A 8 162 8 HOH HOH . 
E 5 HOH A 9 163 9 HOH HOH . 
E 5 HOH A 10 164 10 HOH HOH . 
E 5 HOH A 11 165 11 HOH HOH . 
E 5 HOH A 12 166 12 HOH HOH . 
E 5 HOH A 13 167 13 HOH HOH . 
E 5 HOH A 14 168 14 HOH HOH . 
E 5 HOH A 15 169 15 HOH HOH . 
E 5 HOH A 16 170 17 HOH HOH . 
E 5 HOH A 17 171 18 HOH HOH . 
E 5 HOH A 18 172 19 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 47 HOH HOH . 
E 5 HOH A 46 200 48 HOH HOH . 
E 5 HOH A 47 201 49 HOH HOH . 
E 5 HOH A 48 202 50 HOH HOH . 
E 5 HOH A 49 203 51 HOH HOH . 
E 5 HOH A 50 204 52 HOH HOH . 
E 5 HOH A 51 205 53 HOH HOH . 
E 5 HOH A 52 206 54 HOH HOH . 
E 5 HOH A 53 207 55 HOH HOH . 
E 5 HOH A 54 208 56 HOH HOH . 
E 5 HOH A 55 209 57 HOH HOH . 
E 5 HOH A 56 210 58 HOH HOH . 
E 5 HOH A 57 211 59 HOH HOH . 
E 5 HOH A 58 212 60 HOH HOH . 
E 5 HOH A 59 213 61 HOH HOH . 
E 5 HOH A 60 214 62 HOH HOH . 
E 5 HOH A 61 215 63 HOH HOH . 
E 5 HOH A 62 216 64 HOH HOH . 
E 5 HOH A 63 217 65 HOH HOH . 
E 5 HOH A 64 218 66 HOH HOH . 
E 5 HOH A 65 219 67 HOH HOH . 
E 5 HOH A 66 220 68 HOH HOH . 
E 5 HOH A 67 221 69 HOH HOH . 
E 5 HOH A 68 222 70 HOH HOH . 
E 5 HOH A 69 223 71 HOH HOH . 
E 5 HOH A 70 224 72 HOH HOH . 
E 5 HOH A 71 225 73 HOH HOH . 
E 5 HOH A 72 226 74 HOH HOH . 
E 5 HOH A 73 227 75 HOH HOH . 
E 5 HOH A 74 228 76 HOH HOH . 
E 5 HOH A 75 229 77 HOH HOH . 
E 5 HOH A 76 230 78 HOH HOH . 
E 5 HOH A 77 231 79 HOH HOH . 
E 5 HOH A 78 232 80 HOH HOH . 
E 5 HOH A 79 233 81 HOH HOH . 
E 5 HOH A 80 234 82 HOH HOH . 
E 5 HOH A 81 235 83 HOH HOH . 
E 5 HOH A 82 236 84 HOH HOH . 
E 5 HOH A 83 237 85 HOH HOH . 
E 5 HOH A 84 238 86 HOH HOH . 
E 5 HOH A 85 239 87 HOH HOH . 
E 5 HOH A 86 240 88 HOH HOH . 
E 5 HOH A 87 241 89 HOH HOH . 
E 5 HOH A 88 242 90 HOH HOH . 
E 5 HOH A 89 243 91 HOH HOH . 
E 5 HOH A 90 244 92 HOH HOH . 
E 5 HOH A 91 245 93 HOH HOH . 
E 5 HOH A 92 246 95 HOH HOH . 
E 5 HOH A 93 247 96 HOH HOH . 
E 5 HOH A 94 248 97 HOH HOH . 
E 5 HOH A 95 249 98 HOH HOH . 
E 5 HOH A 96 250 99 HOH HOH . 
E 5 HOH A 97 251 100 HOH HOH . 
E 5 HOH A 98 252 101 HOH HOH . 
E 5 HOH A 99 253 102 HOH HOH . 
E 5 HOH A 100 254 103 HOH HOH . 
E 5 HOH A 101 255 104 HOH HOH . 
E 5 HOH A 102 256 105 HOH HOH . 
E 5 HOH A 103 257 107 HOH HOH . 
E 5 HOH A 104 258 108 HOH HOH . 
E 5 HOH A 105 259 109 HOH HOH . 
E 5 HOH A 106 260 110 HOH HOH . 
E 5 HOH A 107 261 111 HOH HOH . 
E 5 HOH A 108 262 112 HOH HOH . 
E 5 HOH A 109 263 113 HOH HOH . 
E 5 HOH A 110 264 114 HOH HOH . 
E 5 HOH A 111 265 115 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 . . . B 2 -2.488 59.776 28.866 1 20.05 ? O4 DUP 777 A 1 
HETATM 2 C C4 DUP . . . B 2 -3.31 59.087 29.451 1 20.59 ? C4 DUP 777 A 1 
HETATM 3 C C5 DUP . . . B 2 -4.508 59.592 29.895 1 16.5 ? C5 DUP 777 A 1 
HETATM 4 C C6 DUP . . . B 2 -5.39 58.746 30.536 1 18.18 ? C6 DUP 777 A 1 
HETATM 5 N N3 DUP . . . B 2 -3.02 57.769 29.614 1 12.74 ? N3 DUP 777 A 1 
HETATM 6 C C2 DUP . . . B 2 -3.859 56.938 30.307 1 14.19 ? C2 DUP 777 A 1 
HETATM 7 O O2 DUP . . . B 2 -3.572 55.746 30.468 1 16.97 ? O2 DUP 777 A 1 
HETATM 8 N N1 DUP . . . B 2 -5.053 57.427 30.755 1 18.2 ? N1 DUP 777 A 1 
HETATM 9 C C1' DUP . . . B 2 -5.983 56.549 31.479 1 18.58 ? C1' DUP 777 A 1 
HETATM 10 C C2' DUP . . . B 2 -5.843 56.771 32.999 1 19.29 ? C2' DUP 777 A 1 
HETATM 11 C C3' DUP . . . B 2 -7.066 57.627 33.297 1 18.15 ? C3' DUP 777 A 1 
HETATM 12 O O3' DUP . . . B 2 -7.504 57.454 34.641 1 18.7 ? O3' DUP 777 A 1 
HETATM 13 O O4' DUP . . . B 2 -7.339 56.874 31.115 1 19.64 ? O4' DUP 777 A 1 
HETATM 14 C C4' DUP . . . B 2 -8.083 57.11 32.307 1 17.27 ? C4' DUP 777 A 1 
HETATM 15 C C5' DUP . . . B 2 -9.208 58.121 32.02 1 18.99 ? C5' DUP 777 A 1 
HETATM 16 O O5' DUP . . . B 2 -8.586 59.247 31.466 1 24.68 ? O5' DUP 777 A 1 
HETATM 17 P PA DUP . . . B 2 -9.299 60.632 31.286 1 22.69 ? PA DUP 777 A 1 
HETATM 18 O O1A DUP . . . B 2 -10.469 60.8 31.938 1 24.63 ? O1A DUP 777 A 1 
HETATM 19 O O2A DUP . . . B 2 -8.453 61.712 30.663 1 22.32 ? O2A DUP 777 A 1 
HETATM 20 N N3A DUP . . . B 2 -10.285 60.132 30.158 1 25.38 ? N3A DUP 777 A 1 
HETATM 21 P PB DUP . . . B 2 -11.883 60.05 29.659 1 31.13 ? PB DUP 777 A 1 
HETATM 22 O O1B DUP . . . B 2 -12.651 61.135 30.395 1 31.04 ? O1B DUP 777 A 1 
HETATM 23 O O2B DUP . . . B 2 -11.99 60.161 28.168 1 31.22 ? O2B DUP 777 A 1 
HETATM 24 O O3B DUP . . . B 2 -12.392 58.626 30.247 1 40.62 ? O3B DUP 777 A 1 
HETATM 25 P PG DUP . . . B 2 -13.284 58.514 31.605 1 45.11 ? PG DUP 777 A 1 
HETATM 26 O O2G DUP . . . B 2 -12.65 59.365 32.687 1 34.74 ? O2G DUP 777 A 1 
HETATM 27 O O1G DUP . . . B 2 -14.675 59.042 31.261 1 41.76 ? O1G DUP 777 A 1 
HETATM 28 O O3G DUP . . . B 2 -13.235 57.04 32.001 1 46.31 ? O3G DUP 777 A 1 
#
_model_server_stats.io_time_ms              41 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           28 
#