data_5EKK
#
_model_server_result.job_id            cE7mCVtbTQzkAX88DjcAPg 
_model_server_result.datetime_utc      '2024-11-22 16:33:39' 
_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          5ekk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    5EKK 
#
_exptl.entry_id    5EKK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          3 
_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          93.52 
_cell.angle_gamma         90 
_cell.entry_id            5EKK 
_cell.length_a            31.178 
_cell.length_b            60.353 
_cell.length_c            38.425 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EKK 
_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                      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
metalc ? metalc1 A OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? 
metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.136 ? 
metalc ? metalc5 B CA CA . A CA 201 1_555 D O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? 
metalc ? metalc6 B CA CA . A CA 201 1_555 D O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
#
_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                     5EKK 
_atom_sites.fract_transf_matrix[1][1]    0.032074 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001973 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016569 
_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]    0.026074 
_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 CA A 1 201 1 CA CA . 
C 3 THP A 1 202 1 THP THP . 
D 4 HOH A 1 301 30 HOH HOH . 
D 4 HOH A 2 302 27 HOH HOH . 
D 4 HOH A 3 303 20 HOH HOH . 
D 4 HOH A 4 304 1 HOH HOH . 
D 4 HOH A 5 305 3 HOH HOH . 
D 4 HOH A 6 306 12 HOH HOH . 
D 4 HOH A 7 307 6 HOH HOH . 
D 4 HOH A 8 308 2 HOH HOH . 
D 4 HOH A 9 309 28 HOH HOH . 
D 4 HOH A 10 310 9 HOH HOH . 
D 4 HOH A 11 311 22 HOH HOH . 
D 4 HOH A 12 312 46 HOH HOH . 
D 4 HOH A 13 313 7 HOH HOH . 
D 4 HOH A 14 314 39 HOH HOH . 
D 4 HOH A 15 315 23 HOH HOH . 
D 4 HOH A 16 316 8 HOH HOH . 
D 4 HOH A 17 317 31 HOH HOH . 
D 4 HOH A 18 318 25 HOH HOH . 
D 4 HOH A 19 319 40 HOH HOH . 
D 4 HOH A 20 320 5 HOH HOH . 
D 4 HOH A 21 321 42 HOH HOH . 
D 4 HOH A 22 322 21 HOH HOH . 
D 4 HOH A 23 323 32 HOH HOH . 
D 4 HOH A 24 324 10 HOH HOH . 
D 4 HOH A 25 325 17 HOH HOH . 
D 4 HOH A 26 326 26 HOH HOH . 
D 4 HOH A 27 327 34 HOH HOH . 
D 4 HOH A 28 328 44 HOH HOH . 
D 4 HOH A 29 329 35 HOH HOH . 
D 4 HOH A 30 330 14 HOH HOH . 
D 4 HOH A 31 331 18 HOH HOH . 
D 4 HOH A 32 332 13 HOH HOH . 
D 4 HOH A 33 333 47 HOH HOH . 
D 4 HOH A 34 334 4 HOH HOH . 
D 4 HOH A 35 335 11 HOH HOH . 
D 4 HOH A 36 336 45 HOH HOH . 
D 4 HOH A 37 337 37 HOH HOH . 
D 4 HOH A 38 338 41 HOH HOH . 
D 4 HOH A 39 339 19 HOH HOH . 
D 4 HOH A 40 340 33 HOH HOH . 
D 4 HOH A 41 341 36 HOH HOH . 
D 4 HOH A 42 342 29 HOH HOH . 
D 4 HOH A 43 343 16 HOH HOH . 
D 4 HOH A 44 344 15 HOH HOH . 
D 4 HOH A 45 345 43 HOH HOH . 
D 4 HOH A 46 346 38 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 . . . C 3 18.056 10.645 4.934 1 21.17 ? P2 THP 202 A 1 
HETATM 2 O O4P THP . . . C 3 18.023 9.146 5.209 1 19.82 ? O4P THP 202 A 1 
HETATM 3 O O5P THP . . . C 3 19.292 11.37 5.304 1 20.83 ? O5P THP 202 A 1 
HETATM 4 O O6P THP . . . C 3 16.821 11.398 5.354 1 21.06 ? O6P THP 202 A 1 
HETATM 5 P P1 THP . . . C 3 21.254 14.044 0.666 1 26.76 ? P1 THP 202 A 1 
HETATM 6 O O1P THP . . . C 3 22.118 14.482 -0.462 1 32.23 ? O1P THP 202 A 1 
HETATM 7 O O2P THP . . . C 3 21.829 12.921 1.497 1 33.99 ? O2P THP 202 A 1 
HETATM 8 O O3P THP . . . C 3 20.709 15.119 1.545 1 25.77 ? O3P THP 202 A 1 
HETATM 9 O O5' THP . . . C 3 18.092 10.657 3.328 1 20.92 ? O5' THP 202 A 1 
HETATM 10 C C5' THP . . . C 3 18.039 11.877 2.596 1 20.27 ? C5' THP 202 A 1 
HETATM 11 C C4' THP . . . C 3 18.921 11.794 1.357 1 21.77 ? C4' THP 202 A 1 
HETATM 12 O O4' THP . . . C 3 18.527 10.686 0.566 1 21.54 ? O4' THP 202 A 1 
HETATM 13 C C3' THP . . . C 3 18.829 13.03 0.456 1 23.86 ? C3' THP 202 A 1 
HETATM 14 O O3' THP . . . C 3 20.061 13.414 -0.175 1 28.07 ? O3' THP 202 A 1 
HETATM 15 C C2' THP . . . C 3 17.93 12.595 -0.67 1 23.2 ? C2' THP 202 A 1 
HETATM 16 C C1' THP . . . C 3 18.045 11.085 -0.698 1 22.4 ? C1' THP 202 A 1 
HETATM 17 N N1 THP . . . C 3 16.73 10.519 -1.033 1 22.69 ? N1 THP 202 A 1 
HETATM 18 C C2 THP . . . C 3 16.407 10.339 -2.399 1 23.71 ? C2 THP 202 A 1 
HETATM 19 O O2 THP . . . C 3 17.256 10.642 -3.245 1 23.48 ? O2 THP 202 A 1 
HETATM 20 N N3 THP . . . C 3 15.208 9.864 -2.799 1 22.18 ? N3 THP 202 A 1 
HETATM 21 C C4 THP . . . C 3 14.255 9.551 -1.904 1 20.6 ? C4 THP 202 A 1 
HETATM 22 O O4 THP . . . C 3 13.149 9.144 -2.312 1 19.77 ? O4 THP 202 A 1 
HETATM 23 C C5 THP . . . C 3 14.556 9.74 -0.463 1 20.72 ? C5 THP 202 A 1 
HETATM 24 C C5M THP . . . C 3 13.579 9.415 0.628 1 20.95 ? C5M THP 202 A 1 
HETATM 25 C C6 THP . . . C 3 15.797 10.247 -0.109 1 22.14 ? C6 THP 202 A 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#