data_3N2I
#
_model_server_result.job_id            cOs4lvUzm08tWlTXzeF-VQ 
_model_server_result.datetime_utc      '2024-12-21 17:22:17' 
_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          3n2i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":214}' 
#
_entry.id    3N2I 
#
_exptl.entry_id    3N2I 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            3N2I 
_cell.length_a            92.6 
_cell.length_b            92.6 
_cell.length_c            231.538 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3N2I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        98 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41 2 2' 
#
_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 
_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 D N N 
? 3 F 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 277 n n 
O5' HO5' THM sing 278 n n 
C5' C4' THM sing 279 n n 
C5' "H5'1" THM sing 280 n n 
C5' "H5'2" THM sing 281 n n 
C4' O4' THM sing 282 n n 
C4' C3' THM sing 283 n n 
C4' H4' THM sing 284 n n 
O4' C1' THM sing 285 n n 
C3' O3' THM sing 286 n n 
C3' C2' THM sing 287 n n 
C3' H3' THM sing 288 n n 
O3' HO3' THM sing 289 n n 
C2' C1' THM sing 290 n n 
C2' "H2'1" THM sing 291 n n 
C2' "H2'2" THM sing 292 n n 
C1' N1 THM sing 293 n n 
C1' H1' THM sing 294 n n 
N1 C2 THM sing 295 n n 
N1 C6 THM sing 296 n n 
C2 O2 THM doub 297 n n 
C2 N3 THM sing 298 n n 
N3 C4 THM sing 299 n n 
N3 HN3 THM sing 300 n n 
C4 O4 THM doub 301 n n 
C4 C5 THM sing 302 n n 
C5 C5M THM sing 303 n n 
C5 C6 THM doub 304 n n 
C5M HM51 THM sing 305 n n 
C5M HM52 THM sing 306 n n 
C5M HM53 THM sing 307 n n 
C6 H6 THM sing 308 n n 
#
_atom_sites.entry_id                     3N2I 
_atom_sites.fract_transf_matrix[1][1]    0.010799 
_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]    0.010799 
_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]    0.004319 
_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 CL A 1 213 1 CL CL . 
D 3 THM A 1 214 3 THM THM . 
E 2 CL B 1 213 2 CL CL . 
F 3 THM B 1 214 4 THM THM . 
G 4 HOH A 1 215 7 HOH HOH . 
G 4 HOH A 2 216 8 HOH HOH . 
G 4 HOH A 3 217 9 HOH HOH . 
G 4 HOH A 4 218 10 HOH HOH . 
G 4 HOH A 5 219 11 HOH HOH . 
G 4 HOH A 6 220 14 HOH HOH . 
G 4 HOH A 7 221 16 HOH HOH . 
G 4 HOH A 8 222 17 HOH HOH . 
G 4 HOH A 9 223 22 HOH HOH . 
G 4 HOH A 10 224 30 HOH HOH . 
G 4 HOH A 11 225 31 HOH HOH . 
G 4 HOH A 12 226 32 HOH HOH . 
G 4 HOH A 13 227 33 HOH HOH . 
G 4 HOH A 14 228 34 HOH HOH . 
G 4 HOH A 15 229 35 HOH HOH . 
G 4 HOH A 16 230 37 HOH HOH . 
G 4 HOH A 17 231 38 HOH HOH . 
G 4 HOH A 18 232 39 HOH HOH . 
G 4 HOH A 19 233 40 HOH HOH . 
G 4 HOH A 20 234 41 HOH HOH . 
G 4 HOH A 21 235 42 HOH HOH . 
G 4 HOH A 22 236 44 HOH HOH . 
G 4 HOH A 23 237 45 HOH HOH . 
G 4 HOH A 24 238 46 HOH HOH . 
G 4 HOH A 25 239 48 HOH HOH . 
G 4 HOH A 26 240 49 HOH HOH . 
G 4 HOH A 27 241 53 HOH HOH . 
G 4 HOH A 28 242 54 HOH HOH . 
G 4 HOH A 29 243 56 HOH HOH . 
G 4 HOH A 30 244 60 HOH HOH . 
G 4 HOH A 31 245 61 HOH HOH . 
G 4 HOH A 32 246 62 HOH HOH . 
G 4 HOH A 33 247 68 HOH HOH . 
G 4 HOH A 34 248 73 HOH HOH . 
G 4 HOH A 35 249 74 HOH HOH . 
G 4 HOH A 36 250 75 HOH HOH . 
G 4 HOH A 37 251 80 HOH HOH . 
G 4 HOH A 38 252 81 HOH HOH . 
H 4 HOH B 1 215 5 HOH HOH . 
H 4 HOH B 2 216 6 HOH HOH . 
H 4 HOH B 3 217 12 HOH HOH . 
H 4 HOH B 4 218 13 HOH HOH . 
H 4 HOH B 5 219 15 HOH HOH . 
H 4 HOH B 6 220 18 HOH HOH . 
H 4 HOH B 7 221 19 HOH HOH . 
H 4 HOH B 8 222 20 HOH HOH . 
H 4 HOH B 9 223 21 HOH HOH . 
H 4 HOH B 10 224 23 HOH HOH . 
H 4 HOH B 11 225 24 HOH HOH . 
H 4 HOH B 12 226 25 HOH HOH . 
H 4 HOH B 13 227 26 HOH HOH . 
H 4 HOH B 14 228 27 HOH HOH . 
H 4 HOH B 15 229 28 HOH HOH . 
H 4 HOH B 16 230 29 HOH HOH . 
H 4 HOH B 17 231 36 HOH HOH . 
H 4 HOH B 18 232 43 HOH HOH . 
H 4 HOH B 19 233 47 HOH HOH . 
H 4 HOH B 20 234 50 HOH HOH . 
H 4 HOH B 21 235 51 HOH HOH . 
H 4 HOH B 22 236 52 HOH HOH . 
H 4 HOH B 23 237 55 HOH HOH . 
H 4 HOH B 24 238 57 HOH HOH . 
H 4 HOH B 25 239 58 HOH HOH . 
H 4 HOH B 26 240 59 HOH HOH . 
H 4 HOH B 27 241 63 HOH HOH . 
H 4 HOH B 28 242 64 HOH HOH . 
H 4 HOH B 29 243 65 HOH HOH . 
H 4 HOH B 30 244 66 HOH HOH . 
H 4 HOH B 31 245 67 HOH HOH . 
H 4 HOH B 32 246 69 HOH HOH . 
H 4 HOH B 33 247 70 HOH HOH . 
H 4 HOH B 34 248 71 HOH HOH . 
H 4 HOH B 35 249 72 HOH HOH . 
H 4 HOH B 36 250 76 HOH HOH . 
H 4 HOH B 37 251 77 HOH HOH . 
H 4 HOH B 38 252 78 HOH HOH . 
H 4 HOH B 39 253 79 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 . . . D 3 32.251 -21.573 4.524 1 73.58 ? O5' THM 214 A 1 
HETATM 2 C C5' THM . . . D 3 31.906 -20.375 3.793 1 70.6 ? C5' THM 214 A 1 
HETATM 3 C C4' THM . . . D 3 33.166 -19.564 3.97 1 70.52 ? C4' THM 214 A 1 
HETATM 4 O O4' THM . . . D 3 33.067 -18.267 4.515 1 66.73 ? O4' THM 214 A 1 
HETATM 5 C C3' THM . . . D 3 34.002 -19.223 2.775 1 70.48 ? C3' THM 214 A 1 
HETATM 6 O O3' THM . . . D 3 34.19 -20.312 1.919 1 72.83 ? O3' THM 214 A 1 
HETATM 7 C C2' THM . . . D 3 35.187 -18.771 3.614 1 68.84 ? C2' THM 214 A 1 
HETATM 8 C C1' THM . . . D 3 34.44 -17.843 4.576 1 64.99 ? C1' THM 214 A 1 
HETATM 9 N N1 THM . . . D 3 34.785 -17.805 6 1 61.56 ? N1 THM 214 A 1 
HETATM 10 C C2 THM . . . D 3 35.308 -16.619 6.472 1 58.85 ? C2 THM 214 A 1 
HETATM 11 O O2 THM . . . D 3 35.541 -15.71 5.662 1 62.58 ? O2 THM 214 A 1 
HETATM 12 N N3 THM . . . D 3 35.609 -16.422 7.745 1 57.83 ? N3 THM 214 A 1 
HETATM 13 C C4 THM . . . D 3 35.39 -17.35 8.637 1 55.73 ? C4 THM 214 A 1 
HETATM 14 O O4 THM . . . D 3 35.67 -17.072 9.798 1 57.9 ? O4 THM 214 A 1 
HETATM 15 C C5 THM . . . D 3 34.781 -18.614 8.236 1 56.59 ? C5 THM 214 A 1 
HETATM 16 C C5M THM . . . D 3 34.489 -19.692 9.244 1 55.73 ? C5M THM 214 A 1 
HETATM 17 C C6 THM . . . D 3 34.501 -18.787 6.883 1 59.98 ? C6 THM 214 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           17 
#