data_2QQE
#
_model_server_result.job_id            98vbI6RJLqlrFLioVdhdGw 
_model_server_result.datetime_utc      '2024-10-19 13:17:55' 
_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          2qqe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":502}' 
#
_entry.id    2QQE 
#
_exptl.entry_id    2QQE 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          107.9 
_cell.angle_gamma         90 
_cell.entry_id            2QQE 
_cell.length_a            111.59 
_cell.length_b            52.82 
_cell.length_c            59.31 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2QQE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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    1,2 
#
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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 111.59 0 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 F 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 SG CYS 140 A CYS 140 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc2 A SG CYS 143 A CYS 143 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc3 A SG CYS 173 A CYS 173 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? 
metalc ? metalc4 A SG CYS 176 A CYS 176 1_555 C ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc5 B SG CYS 140 B CYS 140 1_555 E ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc6 B SG CYS 143 B CYS 143 1_555 E ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc7 B SG CYS 173 B CYS 173 1_555 E ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc8 B SG CYS 176 B CYS 176 1_555 E ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
#
_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 290 n n 
O5' HO5' THM sing 291 n n 
C5' C4' THM sing 292 n n 
C5' "H5'1" THM sing 293 n n 
C5' "H5'2" THM sing 294 n n 
C4' O4' THM sing 295 n n 
C4' C3' THM sing 296 n n 
C4' H4' THM sing 297 n n 
O4' C1' THM sing 298 n n 
C3' O3' THM sing 299 n n 
C3' C2' THM sing 300 n n 
C3' H3' THM sing 301 n n 
O3' HO3' THM sing 302 n n 
C2' C1' THM sing 303 n n 
C2' "H2'1" THM sing 304 n n 
C2' "H2'2" THM sing 305 n n 
C1' N1 THM sing 306 n n 
C1' H1' THM sing 307 n n 
N1 C2 THM sing 308 n n 
N1 C6 THM sing 309 n n 
C2 O2 THM doub 310 n n 
C2 N3 THM sing 311 n n 
N3 C4 THM sing 312 n n 
N3 HN3 THM sing 313 n n 
C4 O4 THM doub 314 n n 
C4 C5 THM sing 315 n n 
C5 C5M THM sing 316 n n 
C5 C6 THM doub 317 n n 
C5M HM51 THM sing 318 n n 
C5M HM52 THM sing 319 n n 
C5M HM53 THM sing 320 n n 
C6 H6 THM sing 321 n n 
#
_atom_sites.entry_id                     2QQE 
_atom_sites.fract_transf_matrix[1][1]    0.008961 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002895 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018932 
_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]    0.017719 
_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 ZN A 1 400 400 ZN ZN . 
D 3 THM A 1 501 501 THM THY . 
E 2 ZN B 1 402 402 ZN ZN . 
F 3 THM B 1 502 502 THM THY . 
G 4 HOH A 1 502 2 HOH HOH . 
G 4 HOH A 2 503 3 HOH HOH . 
G 4 HOH A 3 504 4 HOH HOH . 
G 4 HOH A 4 505 8 HOH HOH . 
G 4 HOH A 5 506 11 HOH HOH . 
G 4 HOH A 6 507 12 HOH HOH . 
G 4 HOH A 7 508 14 HOH HOH . 
G 4 HOH A 8 509 17 HOH HOH . 
G 4 HOH A 9 510 19 HOH HOH . 
G 4 HOH A 10 511 22 HOH HOH . 
G 4 HOH A 11 512 25 HOH HOH . 
G 4 HOH A 12 513 26 HOH HOH . 
G 4 HOH A 13 514 29 HOH HOH . 
G 4 HOH A 14 515 31 HOH HOH . 
G 4 HOH A 15 516 33 HOH HOH . 
G 4 HOH A 16 517 35 HOH HOH . 
G 4 HOH A 17 518 37 HOH HOH . 
G 4 HOH A 18 519 38 HOH HOH . 
G 4 HOH A 19 520 40 HOH HOH . 
G 4 HOH A 20 521 41 HOH HOH . 
G 4 HOH A 21 522 44 HOH HOH . 
G 4 HOH A 22 523 45 HOH HOH . 
G 4 HOH A 23 524 46 HOH HOH . 
G 4 HOH A 24 525 48 HOH HOH . 
G 4 HOH A 25 526 50 HOH HOH . 
G 4 HOH A 26 527 51 HOH HOH . 
G 4 HOH A 27 528 52 HOH HOH . 
H 4 HOH B 1 503 1 HOH HOH . 
H 4 HOH B 2 504 6 HOH HOH . 
H 4 HOH B 3 505 7 HOH HOH . 
H 4 HOH B 4 506 9 HOH HOH . 
H 4 HOH B 5 507 10 HOH HOH . 
H 4 HOH B 6 508 15 HOH HOH . 
H 4 HOH B 7 509 16 HOH HOH . 
H 4 HOH B 8 510 18 HOH HOH . 
H 4 HOH B 9 511 20 HOH HOH . 
H 4 HOH B 10 512 21 HOH HOH . 
H 4 HOH B 11 513 23 HOH HOH . 
H 4 HOH B 12 514 24 HOH HOH . 
H 4 HOH B 13 515 27 HOH HOH . 
H 4 HOH B 14 516 28 HOH HOH . 
H 4 HOH B 15 517 30 HOH HOH . 
H 4 HOH B 16 518 32 HOH HOH . 
H 4 HOH B 17 519 34 HOH HOH . 
H 4 HOH B 18 520 36 HOH HOH . 
H 4 HOH B 19 521 39 HOH HOH . 
H 4 HOH B 20 522 43 HOH HOH . 
H 4 HOH B 21 523 47 HOH HOH . 
H 4 HOH B 22 524 53 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 . . . F 3 70.826 -0.915 16.598 1 29.55 ? O5' THM 502 B 1 
HETATM 2 C C5' THM . . . F 3 69.785 -1.197 17.52 1 26.52 ? C5' THM 502 B 1 
HETATM 3 C C4' THM . . . F 3 70.319 -1.221 18.937 1 26.97 ? C4' THM 502 B 1 
HETATM 4 O O4' THM . . . F 3 69.183 -1.398 19.812 1 24.44 ? O4' THM 502 B 1 
HETATM 5 C C3' THM . . . F 3 71.305 -2.365 19.216 1 28.26 ? C3' THM 502 B 1 
HETATM 6 O O3' THM . . . F 3 72.492 -1.907 19.928 1 30.37 ? O3' THM 502 B 1 
HETATM 7 C C2' THM . . . F 3 70.493 -3.331 20.062 1 25.96 ? C2' THM 502 B 1 
HETATM 8 C C1' THM . . . F 3 69.452 -2.438 20.73 1 24.21 ? C1' THM 502 B 1 
HETATM 9 N N1 THM . . . F 3 68.178 -3.145 21.005 1 24.97 ? N1 THM 502 B 1 
HETATM 10 C C2 THM . . . F 3 67.629 -3.176 22.289 1 23.03 ? C2 THM 502 B 1 
HETATM 11 O O2 THM . . . F 3 68.093 -2.633 23.249 1 24.69 ? O2 THM 502 B 1 
HETATM 12 N N3 THM . . . F 3 66.462 -3.849 22.417 1 20.17 ? N3 THM 502 B 1 
HETATM 13 C C4 THM . . . F 3 65.769 -4.514 21.437 1 23.68 ? C4 THM 502 B 1 
HETATM 14 O O4 THM . . . F 3 64.724 -5.111 21.699 1 23.77 ? O4 THM 502 B 1 
HETATM 15 C C5 THM . . . F 3 66.369 -4.439 20.122 1 20.8 ? C5 THM 502 B 1 
HETATM 16 C C5M THM . . . F 3 65.759 -5.094 18.957 1 19.25 ? C5M THM 502 B 1 
HETATM 17 C C6 THM . . . F 3 67.525 -3.795 19.974 1 22.47 ? C6 THM 502 B 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           17 
#