data_3MZ5
#
_model_server_result.job_id            3ms_7oZlDmE_bcWK4ngUuA 
_model_server_result.datetime_utc      '2024-10-20 03:32:37' 
_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          3mz5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":150}' 
#
_entry.id    3MZ5 
#
_exptl.entry_id    3MZ5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-3',5'-DIPHOSPHATE" 
_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          93.65 
_cell.angle_gamma         90 
_cell.entry_id            3MZ5 
_cell.length_a            31.068 
_cell.length_b            60.504 
_cell.length_c            38.032 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3MZ5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_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 A OD2 ASP 21 A ASP 21 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? 
metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.053 ? 
metalc ? metalc5 B O6P THP . A THP 150 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.05 ? 
metalc ? metalc6 C CA CA . A CA 151 1_555 D O HOH . A HOH 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? 
metalc ? metalc7 C CA CA . A CA 151 1_555 D O HOH . A HOH 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                THP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-3',5'-DIPHOSPHATE" 
_chem_comp.type              'dna linking' 
_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
P2 O4P THP doub 277 n n 
P2 O5P THP sing 278 n n 
P2 O6P THP sing 279 n n 
P2 O5' THP sing 280 n n 
O5P HOP5 THP sing 281 n n 
O6P HOP6 THP sing 282 n n 
P1 O1P THP doub 283 n n 
P1 O2P THP sing 284 n n 
P1 O3P THP sing 285 n n 
P1 O3' THP sing 286 n n 
O2P HOP2 THP sing 287 n n 
O3P HOP3 THP sing 288 n n 
O5' C5' THP sing 289 n n 
C5' C4' THP sing 290 n n 
C5' "H5'1" THP sing 291 n n 
C5' "H5'2" THP sing 292 n n 
C4' O4' THP sing 293 n n 
C4' C3' THP sing 294 n n 
C4' H4' THP sing 295 n n 
O4' C1' THP sing 296 n n 
C3' O3' THP sing 297 n n 
C3' C2' THP sing 298 n n 
C3' H3' THP sing 299 n n 
C2' C1' THP sing 300 n n 
C2' "H2'1" THP sing 301 n n 
C2' "H2'2" THP sing 302 n n 
C1' N1 THP sing 303 n n 
C1' H1' THP sing 304 n n 
N1 C2 THP sing 305 n n 
N1 C6 THP sing 306 n n 
C2 O2 THP doub 307 n n 
C2 N3 THP sing 308 n n 
N3 C4 THP sing 309 n n 
N3 H3 THP sing 310 n n 
C4 O4 THP doub 311 n n 
C4 C5 THP sing 312 n n 
C5 C5M THP sing 313 n n 
C5 C6 THP doub 314 n n 
C5M H51 THP sing 315 n n 
C5M H52 THP sing 316 n n 
C5M H53 THP sing 317 n n 
C6 H6 THP sing 318 n n 
#
_atom_sites.entry_id                     3MZ5 
_atom_sites.fract_transf_matrix[1][1]    0.032187 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002053 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016528 
_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]    0.026347 
_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 THP A 1 150 150 THP THP . 
C 3 CA A 1 151 151 CA CA . 
D 4 HOH A 1 152 152 HOH HOH . 
D 4 HOH A 2 153 153 HOH HOH . 
D 4 HOH A 3 154 154 HOH HOH . 
D 4 HOH A 4 155 155 HOH HOH . 
D 4 HOH A 5 156 156 HOH HOH . 
D 4 HOH A 6 157 157 HOH HOH . 
D 4 HOH A 7 158 158 HOH HOH . 
D 4 HOH A 8 159 159 HOH HOH . 
D 4 HOH A 9 160 160 HOH HOH . 
D 4 HOH A 10 161 161 HOH HOH . 
D 4 HOH A 11 162 162 HOH HOH . 
D 4 HOH A 12 163 163 HOH HOH . 
D 4 HOH A 13 164 164 HOH HOH . 
D 4 HOH A 14 165 165 HOH HOH . 
D 4 HOH A 15 166 166 HOH HOH . 
D 4 HOH A 16 167 167 HOH HOH . 
D 4 HOH A 17 168 168 HOH HOH . 
D 4 HOH A 18 169 169 HOH HOH . 
D 4 HOH A 19 170 170 HOH HOH . 
D 4 HOH A 20 171 171 HOH HOH . 
D 4 HOH A 21 172 172 HOH HOH . 
D 4 HOH A 22 173 173 HOH HOH . 
D 4 HOH A 23 174 174 HOH HOH . 
D 4 HOH A 24 175 175 HOH HOH . 
D 4 HOH A 25 176 176 HOH HOH . 
D 4 HOH A 26 177 177 HOH HOH . 
D 4 HOH A 27 178 178 HOH HOH . 
D 4 HOH A 28 179 179 HOH HOH . 
D 4 HOH A 29 180 180 HOH HOH . 
D 4 HOH A 30 181 181 HOH HOH . 
D 4 HOH A 31 182 182 HOH HOH . 
D 4 HOH A 32 183 183 HOH HOH . 
D 4 HOH A 33 184 184 HOH HOH . 
D 4 HOH A 34 185 185 HOH HOH . 
D 4 HOH A 35 186 186 HOH HOH . 
D 4 HOH A 36 187 187 HOH HOH . 
D 4 HOH A 37 188 188 HOH HOH . 
D 4 HOH A 38 189 189 HOH HOH . 
D 4 HOH A 39 190 190 HOH HOH . 
D 4 HOH A 40 191 191 HOH HOH . 
D 4 HOH A 41 192 192 HOH HOH . 
D 4 HOH A 42 193 193 HOH HOH . 
D 4 HOH A 43 194 194 HOH HOH . 
D 4 HOH A 44 195 195 HOH HOH . 
D 4 HOH A 45 196 196 HOH HOH . 
D 4 HOH A 46 197 197 HOH HOH . 
D 4 HOH A 47 198 198 HOH HOH . 
D 4 HOH A 48 199 199 HOH HOH . 
D 4 HOH A 49 200 200 HOH HOH . 
D 4 HOH A 50 201 201 HOH HOH . 
D 4 HOH A 51 202 202 HOH HOH . 
D 4 HOH A 52 203 203 HOH HOH . 
D 4 HOH A 53 204 204 HOH HOH . 
D 4 HOH A 54 205 205 HOH HOH . 
D 4 HOH A 55 206 206 HOH HOH . 
D 4 HOH A 56 207 207 HOH HOH . 
D 4 HOH A 57 208 208 HOH HOH . 
D 4 HOH A 58 209 209 HOH HOH . 
D 4 HOH A 59 210 210 HOH HOH . 
D 4 HOH A 60 211 211 HOH HOH . 
D 4 HOH A 61 212 212 HOH HOH . 
D 4 HOH A 62 213 213 HOH HOH . 
D 4 HOH A 63 214 214 HOH HOH . 
D 4 HOH A 64 215 215 HOH HOH . 
D 4 HOH A 65 216 216 HOH HOH . 
D 4 HOH A 66 217 217 HOH HOH . 
D 4 HOH A 67 218 218 HOH HOH . 
D 4 HOH A 68 219 219 HOH HOH . 
D 4 HOH A 69 220 220 HOH HOH . 
D 4 HOH A 70 221 221 HOH HOH . 
D 4 HOH A 71 222 222 HOH HOH . 
D 4 HOH A 72 223 223 HOH HOH . 
D 4 HOH A 73 224 224 HOH HOH . 
D 4 HOH A 74 225 225 HOH HOH . 
D 4 HOH A 75 226 226 HOH HOH . 
D 4 HOH A 76 227 227 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 P2 THP . . . B 2 17.902 11.091 4.812 1 18.13 ? P2 THP 150 A 1 
HETATM 2 O O4P THP . . . B 2 17.886 9.61 5.07 1 17.42 ? O4P THP 150 A 1 
HETATM 3 O O5P THP . . . B 2 19.197 11.81 5.387 1 20.97 ? O5P THP 150 A 1 
HETATM 4 O O6P THP . . . B 2 16.662 11.866 5.42 1 20.58 ? O6P THP 150 A 1 
HETATM 5 P P1 THP . . . B 2 21.138 14.605 0.974 1 21.46 ? P1 THP 150 A 1 
HETATM 6 O O1P THP . . . B 2 22.133 15.211 0.045 1 25.73 ? O1P THP 150 A 1 
HETATM 7 O O2P THP . . . B 2 20.465 15.634 1.964 1 25.71 ? O2P THP 150 A 1 
HETATM 8 O O3P THP . . . B 2 21.849 13.425 1.776 1 23.34 ? O3P THP 150 A 1 
HETATM 9 O O5' THP . . . B 2 17.864 11.145 3.233 1 18.07 ? O5' THP 150 A 1 
HETATM 10 C C5' THP . . . B 2 17.957 12.478 2.679 1 19.93 ? C5' THP 150 A 1 
HETATM 11 C C4' THP . . . B 2 18.834 12.344 1.411 1 19.25 ? C4' THP 150 A 1 
HETATM 12 O O4' THP . . . B 2 18.504 11.239 0.55 1 20.05 ? O4' THP 150 A 1 
HETATM 13 C C3' THP . . . B 2 18.796 13.62 0.509 1 24.96 ? C3' THP 150 A 1 
HETATM 14 O O3' THP . . . B 2 20.095 13.929 -0.046 1 21.57 ? O3' THP 150 A 1 
HETATM 15 C C2' THP . . . B 2 17.865 13.142 -0.649 1 20.51 ? C2' THP 150 A 1 
HETATM 16 C C1' THP . . . B 2 18.132 11.615 -0.769 1 19.56 ? C1' THP 150 A 1 
HETATM 17 N N1 THP . . . B 2 16.826 10.988 -1.161 1 17.35 ? N1 THP 150 A 1 
HETATM 18 C C2 THP . . . B 2 16.561 10.807 -2.472 1 20.58 ? C2 THP 150 A 1 
HETATM 19 O O2 THP . . . B 2 17.423 11.11 -3.334 1 21.33 ? O2 THP 150 A 1 
HETATM 20 N N3 THP . . . B 2 15.413 10.286 -2.928 1 18.21 ? N3 THP 150 A 1 
HETATM 21 C C4 THP . . . B 2 14.423 9.995 -2.007 1 18.18 ? C4 THP 150 A 1 
HETATM 22 O O4 THP . . . B 2 13.352 9.587 -2.415 1 18.01 ? O4 THP 150 A 1 
HETATM 23 C C5 THP . . . B 2 14.681 10.183 -0.618 1 15.55 ? C5 THP 150 A 1 
HETATM 24 C C5M THP . . . B 2 13.658 9.842 0.492 1 17.22 ? C5M THP 150 A 1 
HETATM 25 C C6 THP . . . B 2 15.878 10.671 -0.189 1 16.88 ? C6 THP 150 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#