data_5XB2
#
_model_server_result.job_id            70O47Dqdne1rPIQOTnr81A 
_model_server_result.datetime_utc      '2024-11-05 11:02:07' 
_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          5xb2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":202}' 
#
_entry.id    5XB2 
#
_exptl.entry_id    5XB2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              322.208 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-5'-PHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         88.9 
_cell.angle_beta          90.83 
_cell.angle_gamma         70.53 
_cell.entry_id            5XB2 
_cell.length_a            42.62 
_cell.length_b            52.99 
_cell.length_c            54.019 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XB2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,F,G,H,I,J,K,L 
_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 
#
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 J N 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 OG1 THR 14 B THR 14 1_555 E MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc2 D O1P TMP . B TMP 202 1_555 E MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? 
metalc ? metalc3 D O2P TMP . B TMP 202 1_555 E MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? 
#
_chem_comp.formula           'C10 H15 N2 O8 P' 
_chem_comp.formula_weight    322.208 
_chem_comp.id                TMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-5'-PHOSPHATE" 
_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
P O1P TMP doub 316 n n 
P O2P TMP sing 317 n n 
P O3P TMP sing 318 n n 
P O5' TMP sing 319 n n 
O2P HOP2 TMP sing 320 n n 
O3P HOP3 TMP sing 321 n n 
O5' C5' TMP sing 322 n n 
C5' C4' TMP sing 323 n n 
C5' "H5'1" TMP sing 324 n n 
C5' "H5'2" TMP sing 325 n n 
C4' O4' TMP sing 326 n n 
C4' C3' TMP sing 327 n n 
C4' H4' TMP sing 328 n n 
O4' C1' TMP sing 329 n n 
C3' O3' TMP sing 330 n n 
C3' C2' TMP sing 331 n n 
C3' H3' TMP sing 332 n n 
O3' HO3' TMP sing 333 n n 
C2' C1' TMP sing 334 n n 
C2' "H2'1" TMP sing 335 n n 
C2' "H2'2" TMP sing 336 n n 
C1' N1 TMP sing 337 n n 
C1' H1' TMP sing 338 n n 
N1 C2 TMP sing 339 n n 
N1 C6 TMP sing 340 n n 
C2 O2 TMP doub 341 n n 
C2 N3 TMP sing 342 n n 
N3 C4 TMP sing 343 n n 
N3 HN3 TMP sing 344 n n 
C4 O4 TMP doub 345 n n 
C4 C5 TMP sing 346 n n 
C5 C5M TMP sing 347 n n 
C5 C6 TMP doub 348 n n 
C5M H51 TMP sing 349 n n 
C5M H52 TMP sing 350 n n 
C5M H53 TMP sing 351 n n 
C6 H6 TMP sing 352 n n 
#
_atom_sites.entry_id                     5XB2 
_atom_sites.fract_transf_matrix[1][1]    0.023463 
_atom_sites.fract_transf_matrix[1][2]    -0.008295 
_atom_sites.fract_transf_matrix[1][3]    0.000551 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020016 
_atom_sites.fract_transf_matrix[2][3]    -0.00051 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.01852 
_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 ADP B 1 201 1 ADP ADP . 
D 3 TMP B 1 202 1 TMP TMP . 
E 4 MG B 1 203 3 MG MG . 
F 5 F B 1 204 1 F F . 
G 5 F B 1 205 4 F F . 
H 5 F B 1 206 5 F F . 
I 2 ADP A 1 201 2 ADP ADP . 
J 3 TMP A 1 202 2 TMP TMP . 
K 6 HOH B 1 301 91 HOH HOH . 
K 6 HOH B 2 302 133 HOH HOH . 
K 6 HOH B 3 303 39 HOH HOH . 
K 6 HOH B 4 304 16 HOH HOH . 
K 6 HOH B 5 305 49 HOH HOH . 
K 6 HOH B 6 306 132 HOH HOH . 
K 6 HOH B 7 307 45 HOH HOH . 
K 6 HOH B 8 308 145 HOH HOH . 
K 6 HOH B 9 309 61 HOH HOH . 
K 6 HOH B 10 310 62 HOH HOH . 
K 6 HOH B 11 311 68 HOH HOH . 
K 6 HOH B 12 312 54 HOH HOH . 
K 6 HOH B 13 313 135 HOH HOH . 
K 6 HOH B 14 314 15 HOH HOH . 
K 6 HOH B 15 315 88 HOH HOH . 
K 6 HOH B 16 316 46 HOH HOH . 
K 6 HOH B 17 317 48 HOH HOH . 
K 6 HOH B 18 318 52 HOH HOH . 
K 6 HOH B 19 319 33 HOH HOH . 
K 6 HOH B 20 320 37 HOH HOH . 
K 6 HOH B 21 321 44 HOH HOH . 
K 6 HOH B 22 322 105 HOH HOH . 
K 6 HOH B 23 323 75 HOH HOH . 
K 6 HOH B 24 324 136 HOH HOH . 
K 6 HOH B 25 325 41 HOH HOH . 
K 6 HOH B 26 326 60 HOH HOH . 
K 6 HOH B 27 327 31 HOH HOH . 
K 6 HOH B 28 328 32 HOH HOH . 
K 6 HOH B 29 329 66 HOH HOH . 
K 6 HOH B 30 330 36 HOH HOH . 
K 6 HOH B 31 331 92 HOH HOH . 
K 6 HOH B 32 332 38 HOH HOH . 
K 6 HOH B 33 333 35 HOH HOH . 
K 6 HOH B 34 334 51 HOH HOH . 
K 6 HOH B 35 335 87 HOH HOH . 
K 6 HOH B 36 336 138 HOH HOH . 
K 6 HOH B 37 337 40 HOH HOH . 
K 6 HOH B 38 338 139 HOH HOH . 
K 6 HOH B 39 339 30 HOH HOH . 
K 6 HOH B 40 340 67 HOH HOH . 
K 6 HOH B 41 341 77 HOH HOH . 
K 6 HOH B 42 342 89 HOH HOH . 
K 6 HOH B 43 343 95 HOH HOH . 
K 6 HOH B 44 344 71 HOH HOH . 
K 6 HOH B 45 345 74 HOH HOH . 
K 6 HOH B 46 346 81 HOH HOH . 
K 6 HOH B 47 347 82 HOH HOH . 
K 6 HOH B 48 348 43 HOH HOH . 
K 6 HOH B 49 349 59 HOH HOH . 
K 6 HOH B 50 350 93 HOH HOH . 
K 6 HOH B 51 351 79 HOH HOH . 
K 6 HOH B 52 352 72 HOH HOH . 
K 6 HOH B 53 353 78 HOH HOH . 
K 6 HOH B 54 354 134 HOH HOH . 
K 6 HOH B 55 355 96 HOH HOH . 
K 6 HOH B 56 356 104 HOH HOH . 
K 6 HOH B 57 357 57 HOH HOH . 
K 6 HOH B 58 358 119 HOH HOH . 
K 6 HOH B 59 359 53 HOH HOH . 
K 6 HOH B 60 360 63 HOH HOH . 
K 6 HOH B 61 361 103 HOH HOH . 
K 6 HOH B 62 362 14 HOH HOH . 
K 6 HOH B 63 363 55 HOH HOH . 
K 6 HOH B 64 364 64 HOH HOH . 
K 6 HOH B 65 365 58 HOH HOH . 
K 6 HOH B 66 366 101 HOH HOH . 
K 6 HOH B 67 367 29 HOH HOH . 
K 6 HOH B 68 368 90 HOH HOH . 
K 6 HOH B 69 369 69 HOH HOH . 
K 6 HOH B 70 370 94 HOH HOH . 
K 6 HOH B 71 371 50 HOH HOH . 
K 6 HOH B 72 372 73 HOH HOH . 
K 6 HOH B 73 373 21 HOH HOH . 
K 6 HOH B 74 374 42 HOH HOH . 
K 6 HOH B 75 375 76 HOH HOH . 
K 6 HOH B 76 376 102 HOH HOH . 
K 6 HOH B 77 377 17 HOH HOH . 
K 6 HOH B 78 378 70 HOH HOH . 
K 6 HOH B 79 379 56 HOH HOH . 
K 6 HOH B 80 380 80 HOH HOH . 
K 6 HOH B 81 381 137 HOH HOH . 
L 6 HOH A 1 301 117 HOH HOH . 
L 6 HOH A 2 302 99 HOH HOH . 
L 6 HOH A 3 303 11 HOH HOH . 
L 6 HOH A 4 304 98 HOH HOH . 
L 6 HOH A 5 305 115 HOH HOH . 
L 6 HOH A 6 306 8 HOH HOH . 
L 6 HOH A 7 307 24 HOH HOH . 
L 6 HOH A 8 308 20 HOH HOH . 
L 6 HOH A 9 309 106 HOH HOH . 
L 6 HOH A 10 310 141 HOH HOH . 
L 6 HOH A 11 311 118 HOH HOH . 
L 6 HOH A 12 312 114 HOH HOH . 
L 6 HOH A 13 313 143 HOH HOH . 
L 6 HOH A 14 314 121 HOH HOH . 
L 6 HOH A 15 315 127 HOH HOH . 
L 6 HOH A 16 316 107 HOH HOH . 
L 6 HOH A 17 317 10 HOH HOH . 
L 6 HOH A 18 318 4 HOH HOH . 
L 6 HOH A 19 319 13 HOH HOH . 
L 6 HOH A 20 320 83 HOH HOH . 
L 6 HOH A 21 321 9 HOH HOH . 
L 6 HOH A 22 322 126 HOH HOH . 
L 6 HOH A 23 323 125 HOH HOH . 
L 6 HOH A 24 324 12 HOH HOH . 
L 6 HOH A 25 325 97 HOH HOH . 
L 6 HOH A 26 326 129 HOH HOH . 
L 6 HOH A 27 327 28 HOH HOH . 
L 6 HOH A 28 328 1 HOH HOH . 
L 6 HOH A 29 329 27 HOH HOH . 
L 6 HOH A 30 330 86 HOH HOH . 
L 6 HOH A 31 331 122 HOH HOH . 
L 6 HOH A 32 332 130 HOH HOH . 
L 6 HOH A 33 333 131 HOH HOH . 
L 6 HOH A 34 334 5 HOH HOH . 
L 6 HOH A 35 335 2 HOH HOH . 
L 6 HOH A 36 336 3 HOH HOH . 
L 6 HOH A 37 337 123 HOH HOH . 
L 6 HOH A 38 338 25 HOH HOH . 
L 6 HOH A 39 339 23 HOH HOH . 
L 6 HOH A 40 340 120 HOH HOH . 
L 6 HOH A 41 341 128 HOH HOH . 
L 6 HOH A 42 342 113 HOH HOH . 
L 6 HOH A 43 343 112 HOH HOH . 
L 6 HOH A 44 344 110 HOH HOH . 
L 6 HOH A 45 345 142 HOH HOH . 
L 6 HOH A 46 346 111 HOH HOH . 
L 6 HOH A 47 347 144 HOH HOH . 
L 6 HOH A 48 348 18 HOH HOH . 
L 6 HOH A 49 349 116 HOH HOH . 
L 6 HOH A 50 350 85 HOH HOH . 
L 6 HOH A 51 351 84 HOH HOH . 
L 6 HOH A 52 352 47 HOH HOH . 
L 6 HOH A 53 353 140 HOH HOH . 
L 6 HOH A 54 354 19 HOH HOH . 
L 6 HOH A 55 355 109 HOH HOH . 
L 6 HOH A 56 356 100 HOH HOH . 
L 6 HOH A 57 357 26 HOH HOH . 
L 6 HOH A 58 358 7 HOH HOH . 
L 6 HOH A 59 359 124 HOH HOH . 
L 6 HOH A 60 360 22 HOH HOH . 
L 6 HOH A 61 361 108 HOH HOH . 
L 6 HOH A 62 362 6 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 TMP . . . D 3 18.977 19.059 -18.265 1 28.1 ? P TMP 202 B 1 
HETATM 2 O O1P TMP . . . D 3 19.635 19.041 -19.594 1 24.22 ? O1P TMP 202 B 1 
HETATM 3 O O2P TMP . . . D 3 19.961 18.786 -17.186 1 27.18 ? O2P TMP 202 B 1 
HETATM 4 O O3P TMP . . . D 3 17.841 18 -18.228 1 32.92 ? O3P TMP 202 B 1 
HETATM 5 O O5' TMP . . . D 3 18.413 20.616 -18.014 1 27.29 ? O5' TMP 202 B 1 
HETATM 6 C C5' TMP . . . D 3 17.472 20.87 -17.05 1 20.41 ? C5' TMP 202 B 1 
HETATM 7 C C4' TMP . . . D 3 16.324 21.641 -17.819 1 33.49 ? C4' TMP 202 B 1 
HETATM 8 O O4' TMP . . . D 3 16.699 23.198 -17.83 1 18.49 ? O4' TMP 202 B 1 
HETATM 9 C C3' TMP . . . D 3 16.254 21.266 -19.056 1 26.65 ? C3' TMP 202 B 1 
HETATM 10 O O3' TMP . . . D 3 14.852 21.037 -19.415 1 24.01 ? O3' TMP 202 B 1 
HETATM 11 C C2' TMP . . . D 3 16.804 22.531 -19.968 1 29.02 ? C2' TMP 202 B 1 
HETATM 12 C C1' TMP . . . D 3 16.407 23.598 -19.268 1 20.57 ? C1' TMP 202 B 1 
HETATM 13 N N1 TMP . . . D 3 17.227 24.815 -19.576 1 17.11 ? N1 TMP 202 B 1 
HETATM 14 C C2 TMP . . . D 3 16.537 26.073 -20.051 1 24.64 ? C2 TMP 202 B 1 
HETATM 15 O O2 TMP . . . D 3 15.37 26.086 -20.181 1 19.56 ? O2 TMP 202 B 1 
HETATM 16 N N3 TMP . . . D 3 17.354 27.296 -20.348 1 21.02 ? N3 TMP 202 B 1 
HETATM 17 C C4 TMP . . . D 3 18.766 27.276 -20.185 1 17.38 ? C4 TMP 202 B 1 
HETATM 18 O O4 TMP . . . D 3 19.42 28.302 -20.439 1 19.4 ? O4 TMP 202 B 1 
HETATM 19 C C5 TMP . . . D 3 19.451 26.002 -19.703 1 19.42 ? C5 TMP 202 B 1 
HETATM 20 C C5M TMP . . . D 3 21.018 25.968 -19.521 1 13.64 ? C5M TMP 202 B 1 
HETATM 21 C C6 TMP . . . D 3 18.653 24.782 -19.408 1 14.24 ? C6 TMP 202 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#