data_4YEK
#
_model_server_result.job_id            ufmXnD7HbH2MJ-ptLU2VNg 
_model_server_result.datetime_utc      '2025-01-10 12:48:09' 
_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          4yek 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"T","auth_seq_id":506}' 
#
_entry.id    4YEK 
#
_exptl.entry_id    4YEK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              242.229 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            THYMIDINE 
_entity.pdbx_number_of_molecules    4 
_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            4YEK 
_cell.length_a            190.919 
_cell.length_b            190.919 
_cell.length_c            57.718 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YEK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
_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,M,N,O,P,Q,R,S,T,U,V,W 
_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 I N N 
? 3 J N N 
? 3 S N N 
? 3 T N N 
#
_chem_comp.formula           'C10 H14 N2 O5' 
_chem_comp.formula_weight    242.229 
_chem_comp.id                THM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              THYMIDINE 
_chem_comp.type              'dna oh 5 prime terminus' 
_chem_comp.pdbx_synonyms     "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" 
#
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
O5' C5' THM sing 339 n n 
O5' HO5' THM sing 340 n n 
C5' C4' THM sing 341 n n 
C5' "H5'1" THM sing 342 n n 
C5' "H5'2" THM sing 343 n n 
C4' O4' THM sing 344 n n 
C4' C3' THM sing 345 n n 
C4' H4' THM sing 346 n n 
O4' C1' THM sing 347 n n 
C3' O3' THM sing 348 n n 
C3' C2' THM sing 349 n n 
C3' H3' THM sing 350 n n 
O3' HO3' THM sing 351 n n 
C2' C1' THM sing 352 n n 
C2' "H2'1" THM sing 353 n n 
C2' "H2'2" THM sing 354 n n 
C1' N1 THM sing 355 n n 
C1' H1' THM sing 356 n n 
N1 C2 THM sing 357 n n 
N1 C6 THM sing 358 n n 
C2 O2 THM doub 359 n n 
C2 N3 THM sing 360 n n 
N3 C4 THM sing 361 n n 
N3 HN3 THM sing 362 n n 
C4 O4 THM doub 363 n n 
C4 C5 THM sing 364 n n 
C5 C5M THM sing 365 n n 
C5 C6 THM doub 366 n n 
C5M HM51 THM sing 367 n n 
C5M HM52 THM sing 368 n n 
C5M HM53 THM sing 369 n n 
C6 H6 THM sing 370 n n 
#
_atom_sites.entry_id                     4YEK 
_atom_sites.fract_transf_matrix[1][1]    0.005238 
_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]    0.005238 
_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]    0.017326 
_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 SO4 A 1 501 1 SO4 SO4 . 
D 2 SO4 A 1 502 2 SO4 SO4 . 
E 2 SO4 A 1 503 4 SO4 SO4 . 
F 2 SO4 A 1 504 5 SO4 SO4 . 
G 2 SO4 A 1 505 6 SO4 SO4 . 
H 2 SO4 A 1 506 10 SO4 SO4 . 
I 3 THM A 1 507 1 THM THM . 
J 3 THM A 1 508 4 THM THM . 
K 4 PGE A 1 509 1 PGE PGE . 
L 5 EDO A 1 510 4 EDO EDO . 
M 5 EDO A 1 511 5 EDO EDO . 
N 6 GOL A 1 512 1 GOL GOL . 
O 2 SO4 B 1 501 3 SO4 SO4 . 
P 2 SO4 B 1 502 7 SO4 SO4 . 
Q 2 SO4 B 1 503 8 SO4 SO4 . 
R 2 SO4 B 1 504 9 SO4 SO4 . 
S 3 THM B 1 505 2 THM THM . 
T 3 THM B 1 506 3 THM THM . 
U 5 EDO B 1 507 6 EDO EDO . 
V 7 HOH A 1 601 138 HOH HOH . 
V 7 HOH A 2 602 114 HOH HOH . 
V 7 HOH A 3 603 83 HOH HOH . 
V 7 HOH A 4 604 26 HOH HOH . 
V 7 HOH A 5 605 90 HOH HOH . 
V 7 HOH A 6 606 140 HOH HOH . 
V 7 HOH A 7 607 120 HOH HOH . 
V 7 HOH A 8 608 12 HOH HOH . 
V 7 HOH A 9 609 34 HOH HOH . 
V 7 HOH A 10 610 139 HOH HOH . 
V 7 HOH A 11 611 113 HOH HOH . 
V 7 HOH A 12 612 21 HOH HOH . 
V 7 HOH A 13 613 72 HOH HOH . 
V 7 HOH A 14 614 130 HOH HOH . 
V 7 HOH A 15 615 36 HOH HOH . 
V 7 HOH A 16 616 17 HOH HOH . 
V 7 HOH A 17 617 78 HOH HOH . 
V 7 HOH A 18 618 35 HOH HOH . 
V 7 HOH A 19 619 106 HOH HOH . 
V 7 HOH A 20 620 37 HOH HOH . 
V 7 HOH A 21 621 47 HOH HOH . 
V 7 HOH A 22 622 76 HOH HOH . 
V 7 HOH A 23 623 108 HOH HOH . 
V 7 HOH A 24 624 23 HOH HOH . 
V 7 HOH A 25 625 8 HOH HOH . 
V 7 HOH A 26 626 66 HOH HOH . 
V 7 HOH A 27 627 91 HOH HOH . 
V 7 HOH A 28 628 22 HOH HOH . 
V 7 HOH A 29 629 9 HOH HOH . 
V 7 HOH A 30 630 116 HOH HOH . 
V 7 HOH A 31 631 93 HOH HOH . 
V 7 HOH A 32 632 115 HOH HOH . 
V 7 HOH A 33 633 105 HOH HOH . 
V 7 HOH A 34 634 50 HOH HOH . 
V 7 HOH A 35 635 62 HOH HOH . 
V 7 HOH A 36 636 107 HOH HOH . 
V 7 HOH A 37 637 75 HOH HOH . 
V 7 HOH A 38 638 132 HOH HOH . 
V 7 HOH A 39 639 58 HOH HOH . 
V 7 HOH A 40 640 57 HOH HOH . 
V 7 HOH A 41 641 112 HOH HOH . 
V 7 HOH A 42 642 134 HOH HOH . 
V 7 HOH A 43 643 48 HOH HOH . 
V 7 HOH A 44 644 85 HOH HOH . 
V 7 HOH A 45 645 40 HOH HOH . 
V 7 HOH A 46 646 80 HOH HOH . 
V 7 HOH A 47 647 11 HOH HOH . 
V 7 HOH A 48 648 43 HOH HOH . 
V 7 HOH A 49 649 68 HOH HOH . 
W 7 HOH B 1 601 18 HOH HOH . 
W 7 HOH B 2 602 55 HOH HOH . 
W 7 HOH B 3 603 141 HOH HOH . 
W 7 HOH B 4 604 70 HOH HOH . 
W 7 HOH B 5 605 56 HOH HOH . 
W 7 HOH B 6 606 77 HOH HOH . 
W 7 HOH B 7 607 5 HOH HOH . 
W 7 HOH B 8 608 136 HOH HOH . 
W 7 HOH B 9 609 15 HOH HOH . 
W 7 HOH B 10 610 99 HOH HOH . 
W 7 HOH B 11 611 98 HOH HOH . 
W 7 HOH B 12 612 42 HOH HOH . 
W 7 HOH B 13 613 39 HOH HOH . 
W 7 HOH B 14 614 127 HOH HOH . 
W 7 HOH B 15 615 44 HOH HOH . 
W 7 HOH B 16 616 25 HOH HOH . 
W 7 HOH B 17 617 27 HOH HOH . 
W 7 HOH B 18 618 125 HOH HOH . 
W 7 HOH B 19 619 33 HOH HOH . 
W 7 HOH B 20 620 10 HOH HOH . 
W 7 HOH B 21 621 16 HOH HOH . 
W 7 HOH B 22 622 14 HOH HOH . 
W 7 HOH B 23 623 137 HOH HOH . 
W 7 HOH B 24 624 13 HOH HOH . 
W 7 HOH B 25 625 97 HOH HOH . 
W 7 HOH B 26 626 60 HOH HOH . 
W 7 HOH B 27 627 24 HOH HOH . 
W 7 HOH B 28 628 121 HOH HOH . 
W 7 HOH B 29 629 88 HOH HOH . 
W 7 HOH B 30 630 128 HOH HOH . 
W 7 HOH B 31 631 135 HOH HOH . 
W 7 HOH B 32 632 46 HOH HOH . 
W 7 HOH B 33 633 84 HOH HOH . 
W 7 HOH B 34 634 82 HOH HOH . 
W 7 HOH B 35 635 69 HOH HOH . 
W 7 HOH B 36 636 74 HOH HOH . 
W 7 HOH B 37 637 133 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 O5' THM . . . T 3 186.902 59.471 -19.664 1 138.43 ? O5' THM 506 B 1 
HETATM 2 C C5' THM . . . T 3 188.046 59.363 -18.782 1 138.09 ? C5' THM 506 B 1 
HETATM 3 C C4' THM . . . T 3 188.796 58.076 -19.046 1 138.5 ? C4' THM 506 B 1 
HETATM 4 O O4' THM . . . T 3 189.571 58.23 -20.046 1 140.07 ? O4' THM 506 B 1 
HETATM 5 C C3' THM . . . T 3 189.754 57.59 -17.783 1 131.92 ? C3' THM 506 B 1 
HETATM 6 O O3' THM . . . T 3 189.286 56.289 -17.247 1 121.12 ? O3' THM 506 B 1 
HETATM 7 C C2' THM . . . T 3 190.899 57.457 -18.217 1 126.8 ? C2' THM 506 B 1 
HETATM 8 C C1' THM . . . T 3 190.655 57.26 -19.756 1 130.09 ? C1' THM 506 B 1 
HETATM 9 N N1 THM . . . T 3 191.771 57.44 -20.46 1 117.49 ? N1 THM 506 B 1 
HETATM 10 C C2 THM . . . T 3 192.209 58.748 -21.063 1 105.79 ? C2 THM 506 B 1 
HETATM 11 O O2 THM . . . T 3 191.548 59.778 -20.956 1 102.96 ? O2 THM 506 B 1 
HETATM 12 N N3 THM . . . T 3 193.463 58.834 -21.808 1 94.47 ? N3 THM 506 B 1 
HETATM 13 C C4 THM . . . T 3 194.252 57.664 -21.944 1 86.57 ? C4 THM 506 B 1 
HETATM 14 O O4 THM . . . T 3 195.291 57.75 -22.563 1 71.88 ? O4 THM 506 B 1 
HETATM 15 C C5 THM . . . T 3 193.821 56.365 -21.342 1 88.62 ? C5 THM 506 B 1 
HETATM 16 C C5M THM . . . T 3 194.637 55.077 -21.46 1 87.25 ? C5M THM 506 B 1 
HETATM 17 C C6 THM . . . T 3 192.582 56.286 -20.609 1 100.9 ? C6 THM 506 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           17 
#