data_4OGK
#
_model_server_result.job_id            K1P1qh6c3YEPcqsUMSdJcw 
_model_server_result.datetime_utc      '2025-06-30 12:32:09' 
_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          4ogk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":301}' 
#
_entry.id    4OGK 
#
_exptl.entry_id    4OGK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              242.229 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            THYMIDINE 
_entity.pdbx_number_of_molecules    5 
_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         120 
_cell.entry_id            4OGK 
_cell.length_a            89.97 
_cell.length_b            89.97 
_cell.length_c            256.56 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4OGK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,X,Y 
_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
? 2 G N N 
? 2 J N N 
? 2 L N N 
? 2 N N N 
? 2 Q 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 E OE2 GLU 49 E GLU 49 1_555 R K K . F K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? 
metalc ? metalc2 E O ILE 69 E ILE 69 1_555 R K K . F K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.224 ? 
metalc ? metalc3 F OE1 GLU 49 F GLU 49 1_555 R K K . F K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc4 F OE2 GLU 49 F GLU 49 1_555 R K K . F K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.293 ? 
metalc ? metalc5 F O ILE 69 F ILE 69 1_555 R K K . F K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? 
metalc ? metalc6 F OG SER 73 F SER 73 1_555 R K K . F K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.301 ? 
#
_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 356 n n 
O5' HO5' THM sing 357 n n 
C5' C4' THM sing 358 n n 
C5' "H5'1" THM sing 359 n n 
C5' "H5'2" THM sing 360 n n 
C4' O4' THM sing 361 n n 
C4' C3' THM sing 362 n n 
C4' H4' THM sing 363 n n 
O4' C1' THM sing 364 n n 
C3' O3' THM sing 365 n n 
C3' C2' THM sing 366 n n 
C3' H3' THM sing 367 n n 
O3' HO3' THM sing 368 n n 
C2' C1' THM sing 369 n n 
C2' "H2'1" THM sing 370 n n 
C2' "H2'2" THM sing 371 n n 
C1' N1 THM sing 372 n n 
C1' H1' THM sing 373 n n 
N1 C2 THM sing 374 n n 
N1 C6 THM sing 375 n n 
C2 O2 THM doub 376 n n 
C2 N3 THM sing 377 n n 
N3 C4 THM sing 378 n n 
N3 HN3 THM sing 379 n n 
C4 O4 THM doub 380 n n 
C4 C5 THM sing 381 n n 
C5 C5M THM sing 382 n n 
C5 C6 THM doub 383 n n 
C5M HM51 THM sing 384 n n 
C5M HM52 THM sing 385 n n 
C5M HM53 THM sing 386 n n 
C6 H6 THM sing 387 n n 
#
_atom_sites.entry_id                     4OGK 
_atom_sites.fract_transf_matrix[1][1]    0.011115 
_atom_sites.fract_transf_matrix[1][2]    0.006417 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012834 
_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]    0.003898 
_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
G 2 THM A 1 301 301 THM THM . 
H 3 IPA A 1 302 6 IPA IPA . 
I 4 EDO A 1 303 1 EDO EDO . 
J 2 THM B 1 301 301 THM THM . 
K 4 EDO C 1 301 4 EDO EDO . 
L 2 THM D 1 301 301 THM THM . 
M 5 PEG D 1 302 1 PEG PEG . 
N 2 THM E 1 301 301 THM THM . 
O 6 PG4 E 1 302 2 PG4 PG4 . 
P 4 EDO E 1 303 5 EDO EDO . 
Q 2 THM F 1 301 301 THM THM . 
R 7 K F 1 302 302 K K . 
S 4 EDO F 1 303 3 EDO EDO . 
T 8 HOH A 1 401 10 HOH HOH . 
T 8 HOH A 2 402 53 HOH HOH . 
T 8 HOH A 3 403 169 HOH HOH . 
T 8 HOH A 4 404 16 HOH HOH . 
T 8 HOH A 5 405 203 HOH HOH . 
T 8 HOH A 6 406 300 HOH HOH . 
T 8 HOH A 7 407 308 HOH HOH . 
T 8 HOH A 8 408 544 HOH HOH . 
T 8 HOH A 9 409 856 HOH HOH . 
T 8 HOH A 10 410 863 HOH HOH . 
U 8 HOH B 1 401 108 HOH HOH . 
U 8 HOH B 2 402 114 HOH HOH . 
U 8 HOH B 3 403 123 HOH HOH . 
U 8 HOH B 4 404 168 HOH HOH . 
U 8 HOH B 5 405 91 HOH HOH . 
U 8 HOH B 6 406 181 HOH HOH . 
U 8 HOH B 7 407 362 HOH HOH . 
U 8 HOH B 8 408 445 HOH HOH . 
U 8 HOH B 9 409 585 HOH HOH . 
U 8 HOH B 10 410 970 HOH HOH . 
V 8 HOH C 1 401 12 HOH HOH . 
V 8 HOH C 2 402 82 HOH HOH . 
V 8 HOH C 3 403 2 HOH HOH . 
V 8 HOH C 4 404 4 HOH HOH . 
V 8 HOH C 5 405 5 HOH HOH . 
V 8 HOH C 6 406 69 HOH HOH . 
V 8 HOH C 7 407 266 HOH HOH . 
V 8 HOH C 8 408 496 HOH HOH . 
V 8 HOH C 9 409 567 HOH HOH . 
V 8 HOH C 10 410 663 HOH HOH . 
V 8 HOH C 11 411 859 HOH HOH . 
W 8 HOH D 1 401 14 HOH HOH . 
W 8 HOH D 2 402 101 HOH HOH . 
W 8 HOH D 3 403 1 HOH HOH . 
W 8 HOH D 4 404 147 HOH HOH . 
W 8 HOH D 5 405 156 HOH HOH . 
W 8 HOH D 6 406 306 HOH HOH . 
W 8 HOH D 7 407 609 HOH HOH . 
X 8 HOH E 1 401 67 HOH HOH . 
X 8 HOH E 2 402 92 HOH HOH . 
X 8 HOH E 3 403 95 HOH HOH . 
X 8 HOH E 4 404 141 HOH HOH . 
X 8 HOH E 5 405 155 HOH HOH . 
X 8 HOH E 6 406 6 HOH HOH . 
X 8 HOH E 7 407 309 HOH HOH . 
X 8 HOH E 8 408 583 HOH HOH . 
X 8 HOH E 9 409 603 HOH HOH . 
X 8 HOH E 10 410 678 HOH HOH . 
X 8 HOH E 11 411 701 HOH HOH . 
X 8 HOH E 12 412 853 HOH HOH . 
X 8 HOH E 13 413 969 HOH HOH . 
Y 8 HOH F 1 401 112 HOH HOH . 
Y 8 HOH F 2 402 144 HOH HOH . 
Y 8 HOH F 3 403 3 HOH HOH . 
Y 8 HOH F 4 404 441 HOH HOH . 
Y 8 HOH F 5 405 864 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 . . . J 2 -8.534 37.013 -23.86 1 59.83 ? O5' THM 301 B 1 
HETATM 2 C C5' THM . . . J 2 -7.688 37.135 -22.778 1 60.75 ? C5' THM 301 B 1 
HETATM 3 C C4' THM . . . J 2 -7.574 38.556 -22.359 1 60.8 ? C4' THM 301 B 1 
HETATM 4 O O4' THM . . . J 2 -7.404 39.39 -23.469 1 60.45 ? O4' THM 301 B 1 
HETATM 5 C C3' THM . . . J 2 -8.768 39.027 -21.6 1 60.07 ? C3' THM 301 B 1 
HETATM 6 O O3' THM . . . J 2 -8.373 39.762 -20.516 1 59.55 ? O3' THM 301 B 1 
HETATM 7 C C2' THM . . . J 2 -9.477 39.898 -22.536 1 60.08 ? C2' THM 301 B 1 
HETATM 8 C C1' THM . . . J 2 -8.373 40.382 -23.429 1 60.08 ? C1' THM 301 B 1 
HETATM 9 N N1 THM . . . J 2 -8.853 40.681 -24.762 1 59.83 ? N1 THM 301 B 1 
HETATM 10 C C2 THM . . . J 2 -9.522 41.925 -24.991 1 59.65 ? C2 THM 301 B 1 
HETATM 11 O O2 THM . . . J 2 -9.668 42.706 -24.066 1 59.6 ? O2 THM 301 B 1 
HETATM 12 N N3 THM . . . J 2 -10.007 42.238 -26.287 1 59.63 ? N3 THM 301 B 1 
HETATM 13 C C4 THM . . . J 2 -9.828 41.322 -27.332 1 59.9 ? C4 THM 301 B 1 
HETATM 14 O O4 THM . . . J 2 -10.24 41.581 -28.447 1 60.22 ? O4 THM 301 B 1 
HETATM 15 C C5 THM . . . J 2 -9.141 40.038 -27.098 1 59.74 ? C5 THM 301 B 1 
HETATM 16 C C5M THM . . . J 2 -8.967 39.093 -28.215 1 54.83 ? C5M THM 301 B 1 
HETATM 17 C C6 THM . . . J 2 -8.671 39.737 -25.836 1 60.29 ? C6 THM 301 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           17 
#