data_1VTK
#
_model_server_result.job_id            nmTWWy9onULl8Cboyx-EsQ 
_model_server_result.datetime_utc      '2024-11-13 13:54:29' 
_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          1vtk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    1VTK 
#
_exptl.entry_id    1VTK 
_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    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         90 
_cell.entry_id            1VTK 
_cell.length_a            83.4 
_cell.length_b            83.4 
_cell.length_c            156.7 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1VTK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 41' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 6_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 83.4 0 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 
#
_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 350 n n 
P O2P TMP sing 351 n n 
P O3P TMP sing 352 n n 
P O5' TMP sing 353 n n 
O2P HOP2 TMP sing 354 n n 
O3P HOP3 TMP sing 355 n n 
O5' C5' TMP sing 356 n n 
C5' C4' TMP sing 357 n n 
C5' "H5'1" TMP sing 358 n n 
C5' "H5'2" TMP sing 359 n n 
C4' O4' TMP sing 360 n n 
C4' C3' TMP sing 361 n n 
C4' H4' TMP sing 362 n n 
O4' C1' TMP sing 363 n n 
C3' O3' TMP sing 364 n n 
C3' C2' TMP sing 365 n n 
C3' H3' TMP sing 366 n n 
O3' HO3' TMP sing 367 n n 
C2' C1' TMP sing 368 n n 
C2' "H2'1" TMP sing 369 n n 
C2' "H2'2" TMP sing 370 n n 
C1' N1 TMP sing 371 n n 
C1' H1' TMP sing 372 n n 
N1 C2 TMP sing 373 n n 
N1 C6 TMP sing 374 n n 
C2 O2 TMP doub 375 n n 
C2 N3 TMP sing 376 n n 
N3 C4 TMP sing 377 n n 
N3 HN3 TMP sing 378 n n 
C4 O4 TMP doub 379 n n 
C4 C5 TMP sing 380 n n 
C5 C5M TMP sing 381 n n 
C5 C6 TMP doub 382 n n 
C5M H51 TMP sing 383 n n 
C5M H52 TMP sing 384 n n 
C5M H53 TMP sing 385 n n 
C6 H6 TMP sing 386 n n 
#
_atom_sites.entry_id                     1VTK 
_atom_sites.fract_transf_matrix[1][1]    0.01199 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01199 
_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]    0.006382 
_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 ADP A 1 400 400 ADP ADP . 
C 3 TMP A 1 500 500 TMP TMP . 
D 4 HOH A 1 601 601 HOH HOH . 
D 4 HOH A 2 602 602 HOH HOH . 
D 4 HOH A 3 603 603 HOH HOH . 
D 4 HOH A 4 604 604 HOH HOH . 
D 4 HOH A 5 605 605 HOH HOH . 
D 4 HOH A 6 606 606 HOH HOH . 
D 4 HOH A 7 607 607 HOH HOH . 
D 4 HOH A 8 608 608 HOH HOH . 
D 4 HOH A 9 609 609 HOH HOH . 
D 4 HOH A 10 610 610 HOH HOH . 
D 4 HOH A 11 611 611 HOH HOH . 
D 4 HOH A 12 612 612 HOH HOH . 
D 4 HOH A 13 613 613 HOH HOH . 
D 4 HOH A 14 614 614 HOH HOH . 
D 4 HOH A 15 615 615 HOH HOH . 
D 4 HOH A 16 616 616 HOH HOH . 
D 4 HOH A 17 617 617 HOH HOH . 
D 4 HOH A 18 618 618 HOH HOH . 
D 4 HOH A 19 619 619 HOH HOH . 
D 4 HOH A 20 620 620 HOH HOH . 
D 4 HOH A 21 621 621 HOH HOH . 
D 4 HOH A 22 622 622 HOH HOH . 
D 4 HOH A 23 623 623 HOH HOH . 
D 4 HOH A 24 624 624 HOH HOH . 
D 4 HOH A 25 625 625 HOH HOH . 
D 4 HOH A 26 626 626 HOH HOH . 
D 4 HOH A 27 627 627 HOH HOH . 
D 4 HOH A 28 628 628 HOH HOH . 
D 4 HOH A 29 629 629 HOH HOH . 
D 4 HOH A 30 630 630 HOH HOH . 
D 4 HOH A 31 631 631 HOH HOH . 
D 4 HOH A 32 632 632 HOH HOH . 
D 4 HOH A 33 633 633 HOH HOH . 
D 4 HOH A 34 634 634 HOH HOH . 
D 4 HOH A 35 635 635 HOH HOH . 
D 4 HOH A 36 636 636 HOH HOH . 
D 4 HOH A 37 637 637 HOH HOH . 
D 4 HOH A 38 638 638 HOH HOH . 
D 4 HOH A 39 639 639 HOH HOH . 
D 4 HOH A 40 640 640 HOH HOH . 
D 4 HOH A 41 641 641 HOH HOH . 
D 4 HOH A 42 642 642 HOH HOH . 
D 4 HOH A 43 643 643 HOH HOH . 
D 4 HOH A 44 644 644 HOH HOH . 
D 4 HOH A 45 645 645 HOH HOH . 
D 4 HOH A 46 646 646 HOH HOH . 
D 4 HOH A 47 647 647 HOH HOH . 
D 4 HOH A 48 648 648 HOH HOH . 
D 4 HOH A 49 649 649 HOH HOH . 
D 4 HOH A 50 650 650 HOH HOH . 
D 4 HOH A 51 651 651 HOH HOH . 
D 4 HOH A 52 652 652 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 . . . C 3 39.914 20.657 33.304 1 37.52 ? P TMP 500 A 1 
HETATM 2 O O1P TMP . . . C 3 38.994 20.458 34.43 1 39.12 ? O1P TMP 500 A 1 
HETATM 3 O O2P TMP . . . C 3 39.391 21.72 32.418 1 38.41 ? O2P TMP 500 A 1 
HETATM 4 O O3P TMP . . . C 3 41.261 20.994 33.795 1 28.61 ? O3P TMP 500 A 1 
HETATM 5 O O5' TMP . . . C 3 39.996 19.281 32.47 1 33.74 ? O5' TMP 500 A 1 
HETATM 6 C C5' TMP . . . C 3 41.022 19.021 31.503 1 26.1 ? C5' TMP 500 A 1 
HETATM 7 C C4' TMP . . . C 3 40.415 18.203 30.408 1 15.9 ? C4' TMP 500 A 1 
HETATM 8 O O4' TMP . . . C 3 40.505 16.827 30.759 1 13.03 ? O4' TMP 500 A 1 
HETATM 9 C C3' TMP . . . C 3 38.968 18.502 30.148 1 18.39 ? C3' TMP 500 A 1 
HETATM 10 O O3' TMP . . . C 3 38.768 18.664 28.742 1 25.79 ? O3' TMP 500 A 1 
HETATM 11 C C2' TMP . . . C 3 38.262 17.307 30.751 1 11.56 ? C2' TMP 500 A 1 
HETATM 12 C C1' TMP . . . C 3 39.258 16.216 30.469 1 14.29 ? C1' TMP 500 A 1 
HETATM 13 N N1 TMP . . . C 3 39.199 15.057 31.39 1 18.58 ? N1 TMP 500 A 1 
HETATM 14 C C2 TMP . . . C 3 38.849 13.851 30.873 1 20.27 ? C2 TMP 500 A 1 
HETATM 15 O O2 TMP . . . C 3 38.532 13.725 29.687 1 22.16 ? O2 TMP 500 A 1 
HETATM 16 N N3 TMP . . . C 3 38.847 12.763 31.707 1 25.52 ? N3 TMP 500 A 1 
HETATM 17 C C4 TMP . . . C 3 39.185 12.839 33.029 1 23.6 ? C4 TMP 500 A 1 
HETATM 18 O O4 TMP . . . C 3 39.153 11.817 33.712 1 21.3 ? O4 TMP 500 A 1 
HETATM 19 C C5 TMP . . . C 3 39.549 14.079 33.55 1 20.22 ? C5 TMP 500 A 1 
HETATM 20 C C5M TMP . . . C 3 39.914 14.175 34.986 1 15.96 ? C5M TMP 500 A 1 
HETATM 21 C C6 TMP . . . C 3 39.559 15.199 32.699 1 22.38 ? C6 TMP 500 A 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           21 
#