data_1ZMX
#
_model_server_result.job_id            rDMNqBQm0kkxlv2qqFps-Q 
_model_server_result.datetime_utc      '2024-12-02 22:58:56' 
_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          1zmx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":1400}' 
#
_entry.id    1ZMX 
#
_exptl.entry_id    1ZMX 
_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.69 
_cell.angle_gamma         90 
_cell.entry_id            1ZMX 
_cell.length_a            69.712 
_cell.length_b            70.34 
_cell.length_c            224.528 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ZMX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,K,L 1 1 
C,D,M,N,O,P 2 1 
E,F,Q,R,S,T 3 1 
G,H,U,V,W,X 4 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 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 R N N 
? 3 T N N 
? 3 V N N 
? 3 X 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 292 n n 
O5' HO5' THM sing 293 n n 
C5' C4' THM sing 294 n n 
C5' "H5'1" THM sing 295 n n 
C5' "H5'2" THM sing 296 n n 
C4' O4' THM sing 297 n n 
C4' C3' THM sing 298 n n 
C4' H4' THM sing 299 n n 
O4' C1' THM sing 300 n n 
C3' O3' THM sing 301 n n 
C3' C2' THM sing 302 n n 
C3' H3' THM sing 303 n n 
O3' HO3' THM sing 304 n n 
C2' C1' THM sing 305 n n 
C2' "H2'1" THM sing 306 n n 
C2' "H2'2" THM sing 307 n n 
C1' N1 THM sing 308 n n 
C1' H1' THM sing 309 n n 
N1 C2 THM sing 310 n n 
N1 C6 THM sing 311 n n 
C2 O2 THM doub 312 n n 
C2 N3 THM sing 313 n n 
N3 C4 THM sing 314 n n 
N3 HN3 THM sing 315 n n 
C4 O4 THM doub 316 n n 
C4 C5 THM sing 317 n n 
C5 C5M THM sing 318 n n 
C5 C6 THM doub 319 n n 
C5M HM51 THM sing 320 n n 
C5M HM52 THM sing 321 n n 
C5M HM53 THM sing 322 n n 
C6 H6 THM sing 323 n n 
#
_atom_sites.entry_id                     1ZMX 
_atom_sites.fract_transf_matrix[1][1]    0.014345 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000173 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014217 
_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]    0.004454 
_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
I 2 SO4 A 1 1300 1300 SO4 SO4 . 
J 3 THM A 1 1400 1400 THM THM . 
K 2 SO4 B 1 1301 1301 SO4 SO4 . 
L 3 THM B 1 1401 1401 THM THM . 
M 2 SO4 C 1 1306 1306 SO4 SO4 . 
N 3 THM C 1 1406 1406 THM THM . 
O 2 SO4 D 1 1307 1307 SO4 SO4 . 
P 3 THM D 1 1407 1407 THM THM . 
Q 2 SO4 E 1 1304 1304 SO4 SO4 . 
R 3 THM E 1 1404 1404 THM THM . 
S 2 SO4 F 1 1305 1305 SO4 SO4 . 
T 3 THM F 1 1405 1405 THM THM . 
U 2 SO4 G 1 1302 1302 SO4 SO4 . 
V 3 THM G 1 1402 1402 THM THM . 
W 2 SO4 H 1 1303 1303 SO4 SO4 . 
X 3 THM H 1 1403 1403 THM THM . 
#
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 3 14.52 -8.557 3.966 1 14.22 ? O5' THM 1400 A 1 
HETATM 2 C C5' THM . . . J 3 13.512 -9.379 4.507 1 12.13 ? C5' THM 1400 A 1 
HETATM 3 C C4' THM . . . J 3 12.425 -8.438 4.971 1 12.44 ? C4' THM 1400 A 1 
HETATM 4 O O4' THM . . . J 3 12.801 -7.703 6.139 1 13.38 ? O4' THM 1400 A 1 
HETATM 5 C C3' THM . . . J 3 12.045 -7.41 3.924 1 13.28 ? C3' THM 1400 A 1 
HETATM 6 O O3' THM . . . J 3 10.657 -7.616 3.756 1 15.52 ? O3' THM 1400 A 1 
HETATM 7 C C2' THM . . . J 3 12.206 -6.024 4.517 1 11.94 ? C2' THM 1400 A 1 
HETATM 8 C C1' THM . . . J 3 12.591 -6.296 5.961 1 10.87 ? C1' THM 1400 A 1 
HETATM 9 N N1 THM . . . J 3 13.502 -5.367 6.647 1 8.24 ? N1 THM 1400 A 1 
HETATM 10 C C2 THM . . . J 3 12.884 -4.33 7.399 1 6.63 ? C2 THM 1400 A 1 
HETATM 11 O O2 THM . . . J 3 11.642 -4.229 7.428 1 6.65 ? O2 THM 1400 A 1 
HETATM 12 N N3 THM . . . J 3 13.592 -3.433 8.081 1 5.64 ? N3 THM 1400 A 1 
HETATM 13 C C4 THM . . . J 3 14.926 -3.474 8.086 1 4.16 ? C4 THM 1400 A 1 
HETATM 14 O O4 THM . . . J 3 15.572 -2.606 8.728 1 3.79 ? O4 THM 1400 A 1 
HETATM 15 C C5 THM . . . J 3 15.602 -4.549 7.324 1 3.96 ? C5 THM 1400 A 1 
HETATM 16 C C5M THM . . . J 3 17.1 -4.584 7.298 1 6.93 ? C5M THM 1400 A 1 
HETATM 17 C C6 THM . . . J 3 14.838 -5.487 6.617 1 6.99 ? C6 THM 1400 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           402 
_model_server_stats.encode_time_ms          22 
_model_server_stats.element_count           17 
#