data_9J1N
#
_model_server_result.job_id            -6X4glme2owOgZoWs_PeNg 
_model_server_result.datetime_utc      '2025-07-07 03:07:31' 
_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          9j1n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":101}' 
#
_entry.id    9J1N 
#
_exptl.entry_id    9J1N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              242.229 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            THYMIDINE 
_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            9J1N 
_cell.length_a            33.29 
_cell.length_b            53.81 
_cell.length_c            100.25 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9J1N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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                      5 
_struct_asym.id                             E 
_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
covale ? covale1 A P DT 1 A DT 2 1_555 D O3' 3D1 . A 3D1 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? 
covale ? covale2 B P DC 1 B DC 2 1_555 E O3' THM . B THM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? 
hydrog WATSON-CRICK hydrog1 A N3 DT 1 A DT 2 1_555 B N1 DA 15 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A O4 DT 1 A DT 2 1_555 B N6 DA 15 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N1 DG 2 A DG 3 1_555 B N3 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N2 DG 2 A DG 3 1_555 B O2 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A O6 DG 2 A DG 3 1_555 B N4 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N1 DA 3 A DA 4 1_555 B N3 DT 13 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N6 DA 3 A DA 4 1_555 B O4 DT 13 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N1 DA 4 A DA 5 1_555 B N3 DT 12 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N6 DA 4 A DA 5 1_555 B O4 DT 12 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DA 5 A DA 6 1_555 B N3 DT 11 B DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N6 DA 5 A DA 6 1_555 B O4 DT 11 B DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N1 DA 6 A DA 7 1_555 B N3 DT 10 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N6 DA 6 A DA 7 1_555 B O4 DT 10 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N1 DG 7 A DG 8 1_555 B N3 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N2 DG 7 A DG 8 1_555 B O2 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A O6 DG 7 A DG 8 1_555 B N4 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N1 DA 8 A DA 9 1_555 B N3 DT 8 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A N6 DA 8 A DA 9 1_555 B O4 DT 8 B DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A N1 DG 9 A DG 10 1_555 B N3 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A N2 DG 9 A DG 10 1_555 B O2 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A O6 DG 9 A DG 10 1_555 B N4 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A N1 DA 10 A DA 11 1_555 B N3 DT 6 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A N6 DA 10 A DA 11 1_555 B O4 DT 6 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 A N1 DA 11 A DA 12 1_555 B N3 DT 5 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog25 A N6 DA 11 A DA 12 1_555 B O4 DT 5 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog26 A N3 DT 12 A DT 13 1_555 B N1 DA 4 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog27 A O4 DT 12 A DT 13 1_555 B N6 DA 4 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog28 A N3 DT 13 A DT 14 1_555 B N1 DA 3 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog29 A O4 DT 13 A DT 14 1_555 B N6 DA 3 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog30 A N1 DG 14 A DG 15 1_555 B N3 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog31 A N2 DG 14 A DG 15 1_555 B O2 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog32 A O6 DG 14 A DG 15 1_555 B N4 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog33 A N1 DG 15 A DG 16 1_555 B N3 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog34 A N2 DG 15 A DG 16 1_555 B O2 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog35 A O6 DG 15 A DG 16 1_555 B N4 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 472 n n 
O5' HO5' THM sing 473 n n 
C5' C4' THM sing 474 n n 
C5' "H5'1" THM sing 475 n n 
C5' "H5'2" THM sing 476 n n 
C4' O4' THM sing 477 n n 
C4' C3' THM sing 478 n n 
C4' H4' THM sing 479 n n 
O4' C1' THM sing 480 n n 
C3' O3' THM sing 481 n n 
C3' C2' THM sing 482 n n 
C3' H3' THM sing 483 n n 
O3' HO3' THM sing 484 n n 
C2' C1' THM sing 485 n n 
C2' "H2'1" THM sing 486 n n 
C2' "H2'2" THM sing 487 n n 
C1' N1 THM sing 488 n n 
C1' H1' THM sing 489 n n 
N1 C2 THM sing 490 n n 
N1 C6 THM sing 491 n n 
C2 O2 THM doub 492 n n 
C2 N3 THM sing 493 n n 
N3 C4 THM sing 494 n n 
N3 HN3 THM sing 495 n n 
C4 O4 THM doub 496 n n 
C4 C5 THM sing 497 n n 
C5 C5M THM sing 498 n n 
C5 C6 THM doub 499 n n 
C5M HM51 THM sing 500 n n 
C5M HM52 THM sing 501 n n 
C5M HM53 THM sing 502 n n 
C6 H6 THM sing 503 n n 
#
_atom_sites.entry_id                     9J1N 
_atom_sites.fract_transf_matrix[1][1]    0.030039 
_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]    0.018584 
_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]    0.009975 
_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
D 4 3D1 A 1 101 1 3D1 3D1 . 
E 5 THM B 1 101 1 THM THM . 
F 6 HOH A 1 201 28 HOH HOH . 
F 6 HOH A 2 202 44 HOH HOH . 
F 6 HOH A 3 203 17 HOH HOH . 
F 6 HOH A 4 204 26 HOH HOH . 
F 6 HOH A 5 205 15 HOH HOH . 
F 6 HOH A 6 206 45 HOH HOH . 
F 6 HOH A 7 207 16 HOH HOH . 
F 6 HOH A 8 208 8 HOH HOH . 
F 6 HOH A 9 209 51 HOH HOH . 
G 6 HOH B 1 201 12 HOH HOH . 
G 6 HOH B 2 202 2 HOH HOH . 
G 6 HOH B 3 203 41 HOH HOH . 
G 6 HOH B 4 204 39 HOH HOH . 
G 6 HOH B 5 205 42 HOH HOH . 
G 6 HOH B 6 206 7 HOH HOH . 
G 6 HOH B 7 207 13 HOH HOH . 
G 6 HOH B 8 208 18 HOH HOH . 
G 6 HOH B 9 209 22 HOH HOH . 
G 6 HOH B 10 210 49 HOH HOH . 
H 6 HOH C 1 301 33 HOH HOH . 
H 6 HOH C 2 302 25 HOH HOH . 
H 6 HOH C 3 303 46 HOH HOH . 
H 6 HOH C 4 304 23 HOH HOH . 
H 6 HOH C 5 305 37 HOH HOH . 
H 6 HOH C 6 306 47 HOH HOH . 
H 6 HOH C 7 307 32 HOH HOH . 
H 6 HOH C 8 308 19 HOH HOH . 
H 6 HOH C 9 309 1 HOH HOH . 
H 6 HOH C 10 310 30 HOH HOH . 
H 6 HOH C 11 311 5 HOH HOH . 
H 6 HOH C 12 312 38 HOH HOH . 
H 6 HOH C 13 313 6 HOH HOH . 
H 6 HOH C 14 314 31 HOH HOH . 
H 6 HOH C 15 315 4 HOH HOH . 
H 6 HOH C 16 316 9 HOH HOH . 
H 6 HOH C 17 317 43 HOH HOH . 
H 6 HOH C 18 318 14 HOH HOH . 
H 6 HOH C 19 319 29 HOH HOH . 
H 6 HOH C 20 320 11 HOH HOH . 
H 6 HOH C 21 321 35 HOH HOH . 
H 6 HOH C 22 322 3 HOH HOH . 
H 6 HOH C 23 323 53 HOH HOH . 
H 6 HOH C 24 324 20 HOH HOH . 
H 6 HOH C 25 325 40 HOH HOH . 
H 6 HOH C 26 326 27 HOH HOH . 
H 6 HOH C 27 327 50 HOH HOH . 
H 6 HOH C 28 328 52 HOH HOH . 
H 6 HOH C 29 329 21 HOH HOH . 
H 6 HOH C 30 330 48 HOH HOH . 
H 6 HOH C 31 331 54 HOH HOH . 
H 6 HOH C 32 332 10 HOH HOH . 
H 6 HOH C 33 333 36 HOH HOH . 
H 6 HOH C 34 334 24 HOH HOH . 
H 6 HOH C 35 335 34 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 . . . E 5 -8.775 -1.982 18.545 1 78.13 ? O5' THM 101 B 1 
HETATM 2 C C5' THM . . . E 5 -9.77 -2.472 17.658 1 72.2 ? C5' THM 101 B 1 
HETATM 3 C C4' THM . . . E 5 -9.665 -1.812 16.303 1 67.24 ? C4' THM 101 B 1 
HETATM 4 O O4' THM . . . E 5 -8.311 -1.959 15.811 1 68.12 ? O4' THM 101 B 1 
HETATM 5 C C3' THM . . . E 5 -10.557 -2.442 15.231 1 73.7 ? C3' THM 101 B 1 
HETATM 6 O O3' THM . . . E 5 -10.791 -1.524 14.171 1 70.53 ? O3' THM 101 B 1 
HETATM 7 C C2' THM . . . E 5 -9.609 -3.474 14.644 1 67.2 ? C2' THM 101 B 1 
HETATM 8 C C1' THM . . . E 5 -8.362 -2.613 14.551 1 59.84 ? C1' THM 101 B 1 
HETATM 9 N N1 THM . . . E 5 -7.1 -3.356 14.355 1 59.37 ? N1 THM 101 B 1 
HETATM 10 C C2 THM . . . E 5 -5.947 -2.632 14.135 1 59.67 ? C2 THM 101 B 1 
HETATM 11 O O2 THM . . . E 5 -5.922 -1.408 14.126 1 62.91 ? O2 THM 101 B 1 
HETATM 12 N N3 THM . . . E 5 -4.818 -3.39 13.946 1 57.36 ? N3 THM 101 B 1 
HETATM 13 C C4 THM . . . E 5 -4.733 -4.77 13.941 1 65.75 ? C4 THM 101 B 1 
HETATM 14 O O4 THM . . . E 5 -3.641 -5.317 13.755 1 62.93 ? O4 THM 101 B 1 
HETATM 15 C C5 THM . . . E 5 -5.981 -5.466 14.162 1 64.57 ? C5 THM 101 B 1 
HETATM 16 C C5M THM . . . E 5 -5.977 -6.966 14.172 1 62.37 ? C5M THM 101 B 1 
HETATM 17 C C6 THM . . . E 5 -7.092 -4.736 14.353 1 56.58 ? C6 THM 101 B 1 
#
_model_server_stats.io_time_ms              78 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           259 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           17 
#