data_3MY1
#
_model_server_result.job_id            URoSKVKh-F8l-W3nNfWG-w 
_model_server_result.datetime_utc      '2024-10-25 20:22:44' 
_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          3my1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":336}' 
#
_entry.id    3MY1 
#
_exptl.entry_id    3MY1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              319.141 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole 
_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         120 
_cell.entry_id            3MY1 
_cell.length_a            173.789 
_cell.length_b            173.789 
_cell.length_c            99.221 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3MY1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_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,I,J,K 
_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 C TYR 186 A TYR 185 1_555 A N TPO 187 A TPO 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C TPO 187 A TPO 186 1_555 A N ASN 188 A ASN 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
#
_chem_comp.formula           'C12 H12 Cl2 N2 O4' 
_chem_comp.formula_weight    319.141 
_chem_comp.id                RFZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
O3' C3' RFZ sing 294 n n 
C3' C4' RFZ sing 295 n n 
C3' C2' RFZ sing 296 n n 
C4' C5' RFZ sing 297 n n 
C4' O4' RFZ sing 298 n n 
C5' O5' RFZ sing 299 n n 
O2' C2' RFZ sing 300 n n 
C2' C1' RFZ sing 301 n n 
O4' C1' RFZ sing 302 n n 
C1' N1 RFZ sing 303 n n 
N1 C1 RFZ sing 304 n y 
N1 C6 RFZ sing 305 n y 
C1 N2 RFZ doub 306 n y 
C5 C6 RFZ doub 307 n y 
C5 C4 RFZ sing 308 n y 
C6 C7 RFZ sing 309 n y 
CL2 C4 RFZ sing 310 n n 
C4 C3 RFZ doub 311 n y 
N2 C7 RFZ sing 312 n y 
C7 C2 RFZ doub 313 n y 
C3 C2 RFZ sing 314 n y 
C3 CL1 RFZ sing 315 n n 
C5 H5 RFZ sing 316 n n 
C2 H2 RFZ sing 317 n n 
C1 H1 RFZ sing 318 n n 
C1' H1' RFZ sing 319 n n 
C4' H4' RFZ sing 320 n n 
C5' H5' RFZ sing 321 n n 
C5' "H5'A" RFZ sing 322 n n 
O5' HO5' RFZ sing 323 n n 
C3' H3' RFZ sing 324 n n 
O3' HO3' RFZ sing 325 n n 
C2' H2' RFZ sing 326 n n 
O2' HO2' RFZ sing 327 n n 
#
_atom_sites.entry_id                     3MY1 
_atom_sites.fract_transf_matrix[1][1]    0.005754 
_atom_sites.fract_transf_matrix[1][2]    0.003322 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006644 
_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]    0.010079 
_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 3 PO4 A 1 332 332 PO4 PO4 . 
D 4 GOL A 1 333 333 GOL GOL . 
E 5 RFZ A 1 336 336 RFZ RFZ . 
F 4 GOL B 1 261 261 GOL GOL . 
G 4 GOL B 1 262 262 GOL GOL . 
H 4 GOL B 1 263 263 GOL GOL . 
I 4 GOL B 1 265 265 GOL GOL . 
J 6 HOH A 1 331 331 HOH HOH . 
J 6 HOH A 2 334 334 HOH HOH . 
J 6 HOH A 3 335 335 HOH HOH . 
J 6 HOH A 4 337 337 HOH HOH . 
J 6 HOH A 5 338 338 HOH HOH . 
J 6 HOH A 6 339 339 HOH HOH . 
J 6 HOH A 7 340 340 HOH HOH . 
J 6 HOH A 8 341 341 HOH HOH . 
J 6 HOH A 9 342 342 HOH HOH . 
J 6 HOH A 10 343 343 HOH HOH . 
J 6 HOH A 11 344 344 HOH HOH . 
J 6 HOH A 12 345 345 HOH HOH . 
J 6 HOH A 13 346 346 HOH HOH . 
J 6 HOH A 14 347 347 HOH HOH . 
J 6 HOH A 15 348 348 HOH HOH . 
J 6 HOH A 16 349 349 HOH HOH . 
K 6 HOH B 1 260 260 HOH HOH . 
K 6 HOH B 2 264 264 HOH HOH . 
K 6 HOH B 3 266 266 HOH HOH . 
K 6 HOH B 4 267 267 HOH HOH . 
K 6 HOH B 5 268 268 HOH HOH . 
K 6 HOH B 6 269 269 HOH HOH . 
K 6 HOH B 7 270 270 HOH HOH . 
K 6 HOH B 8 271 271 HOH HOH . 
K 6 HOH B 9 272 272 HOH HOH . 
K 6 HOH B 10 273 273 HOH HOH . 
K 6 HOH B 11 274 274 HOH HOH . 
K 6 HOH B 12 275 275 HOH HOH . 
K 6 HOH B 13 276 276 HOH HOH . 
K 6 HOH B 14 277 277 HOH HOH . 
K 6 HOH B 15 278 278 HOH HOH . 
K 6 HOH B 16 279 279 HOH HOH . 
K 6 HOH B 17 280 280 HOH HOH . 
K 6 HOH B 18 281 281 HOH HOH . 
K 6 HOH B 19 282 282 HOH HOH . 
K 6 HOH B 20 283 283 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 C C6 RFZ . . . E 5 53.139 -15.95 -13.301 1 117.8 ? C6 RFZ 336 A 1 
HETATM 2 C C5 RFZ . . . E 5 54.504 -15.695 -13.343 1 116.88 ? C5 RFZ 336 A 1 
HETATM 3 C C4 RFZ . . . E 5 54.945 -14.382 -13.451 1 110.24 ? C4 RFZ 336 A 1 
HETATM 4 CL CL2 RFZ . . . E 5 56.704 -14.023 -13.506 1 241.54 ? CL2 RFZ 336 A 1 
HETATM 5 C C3 RFZ . . . E 5 54.024 -13.348 -13.514 1 98.96 ? C3 RFZ 336 A 1 
HETATM 6 CL CL1 RFZ . . . E 5 54.614 -11.669 -13.653 1 114.2 ? CL1 RFZ 336 A 1 
HETATM 7 C C2 RFZ . . . E 5 52.663 -13.595 -13.472 1 96.25 ? C2 RFZ 336 A 1 
HETATM 8 C C7 RFZ . . . E 5 52.227 -14.903 -13.367 1 109.22 ? C7 RFZ 336 A 1 
HETATM 9 N N2 RFZ . . . E 5 50.997 -15.439 -13.304 1 117.51 ? N2 RFZ 336 A 1 
HETATM 10 C C1 RFZ . . . E 5 51.142 -16.778 -13.201 1 123.47 ? C1 RFZ 336 A 1 
HETATM 11 N N1 RFZ . . . E 5 52.445 -17.084 -13.201 1 123.12 ? N1 RFZ 336 A 1 
HETATM 12 C C1' RFZ . . . E 5 52.999 -18.453 -13.105 1 131.4 ? C1' RFZ 336 A 1 
HETATM 13 O O4' RFZ . . . E 5 52.02 -19.361 -13.615 1 135.29 ? O4' RFZ 336 A 1 
HETATM 14 C C4' RFZ . . . E 5 51.464 -20.177 -12.579 1 139.56 ? C4' RFZ 336 A 1 
HETATM 15 C C5' RFZ . . . E 5 49.96 -19.948 -12.513 1 140.7 ? C5' RFZ 336 A 1 
HETATM 16 O O5' RFZ . . . E 5 49.407 -19.995 -13.836 1 141.19 ? O5' RFZ 336 A 1 
HETATM 17 C C3' RFZ . . . E 5 52.158 -19.799 -11.275 1 141.42 ? C3' RFZ 336 A 1 
HETATM 18 O O3' RFZ . . . E 5 52.691 -20.965 -10.639 1 142.5 ? O3' RFZ 336 A 1 
HETATM 19 C C2' RFZ . . . E 5 53.238 -18.786 -11.643 1 138.85 ? C2' RFZ 336 A 1 
HETATM 20 O O2' RFZ . . . E 5 54.572 -19.298 -11.48 1 141.44 ? O2' RFZ 336 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#