data_4YXB # _model_server_result.job_id 4pYiPdQNx0Il8N7iDXp6Qw _model_server_result.datetime_utc '2025-04-02 20:57:11' _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 4yxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 4YXB # _exptl.entry_id 4YXB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 69.085 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description IMIDAZOLE _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 90 _cell.entry_id 4YXB _cell.length_a 75.15 _cell.length_b 81.5 _cell.length_c 89.96 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YXB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 trimeric 3 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,F,G,H 1 1 D 2 1 E,I 3 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 F _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 ALA 140 A ALA 140 1_555 A N MSE 141 A MSE 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 A C MSE 141 A MSE 141 1_555 A N GLN 142 A GLN 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C ILE 147 A ILE 147 1_555 A N MSE 148 A MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 A C MSE 148 A MSE 148 1_555 A N ASP 149 A ASP 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C ARG 162 A ARG 162 1_555 A N MSE 163 A MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 A C MSE 163 A MSE 163 1_555 A N THR 164 A THR 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C ARG 221 A ARG 221 1_555 A N MSE 222 A MSE 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 A C MSE 222 A MSE 222 1_555 A N ARG 223 A ARG 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale9 B C ILE 147 B ILE 147 1_555 B N MSE 148 B MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 B C MSE 148 B MSE 148 1_555 B N ASP 149 B ASP 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale11 B C ARG 162 B ARG 162 1_555 B N MSE 163 B MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale12 B C MSE 163 B MSE 163 1_555 B N THR 164 B THR 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 B C ARG 221 B ARG 221 1_555 B N MSE 222 B MSE 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale14 B C MSE 222 B MSE 222 1_555 B N ARG 223 B ARG 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale15 E C UNK 1 E UNK 301 1_555 E N UNK 2 E UNK 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale16 E C UNK 2 E UNK 302 1_555 E N UNK 3 E UNK 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale17 E C UNK 3 E UNK 303 1_555 E N UNK 4 E UNK 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale18 E C UNK 4 E UNK 304 1_555 E N UNK 5 E UNK 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale19 E C UNK 5 E UNK 305 1_555 E N UNK 6 E UNK 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _chem_comp.formula 'C3 H5 N2 1' _chem_comp.formula_weight 69.085 _chem_comp.id IMD _chem_comp.mon_nstd_flag . _chem_comp.name IMIDAZOLE _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 N1 C2 IMD sing 160 n y N1 C5 IMD sing 161 n y N1 HN1 IMD sing 162 n n C2 N3 IMD doub 163 n y C2 H2 IMD sing 164 n n N3 C4 IMD sing 165 n y N3 HN3 IMD sing 166 n n C4 C5 IMD doub 167 n y C4 H4 IMD sing 168 n n C5 H5 IMD sing 169 n n # _atom_sites.entry_id 4YXB _atom_sites.fract_transf_matrix[1][1] 0.013307 _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] 0.01227 _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] 0.011116 _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 F 5 IMD A 1 301 1 IMD IMD . G 6 HOH A 1 401 19 HOH HOH . G 6 HOH A 2 402 5 HOH HOH . G 6 HOH A 3 403 2 HOH HOH . G 6 HOH A 4 404 7 HOH HOH . G 6 HOH A 5 405 13 HOH HOH . G 6 HOH A 6 406 9 HOH HOH . G 6 HOH A 7 407 12 HOH HOH . G 6 HOH A 8 408 21 HOH HOH . G 6 HOH A 9 409 20 HOH HOH . H 6 HOH B 1 301 4 HOH HOH . H 6 HOH B 2 302 3 HOH HOH . H 6 HOH B 3 303 6 HOH HOH . H 6 HOH B 4 304 11 HOH HOH . H 6 HOH B 5 305 8 HOH HOH . H 6 HOH B 6 306 1 HOH HOH . H 6 HOH B 7 307 16 HOH HOH . H 6 HOH B 8 308 17 HOH HOH . H 6 HOH B 9 309 18 HOH HOH . H 6 HOH B 10 310 14 HOH HOH . H 6 HOH B 11 311 10 HOH HOH . H 6 HOH B 12 312 22 HOH HOH . H 6 HOH B 13 313 15 HOH HOH . I 6 HOH E 1 401 23 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 N N1 IMD . . . F 5 41.784 30.561 46.214 1 80.92 ? N1 IMD 301 A 1 HETATM 2 C C2 IMD . . . F 5 41.843 30.168 47.511 1 69.71 ? C2 IMD 301 A 1 HETATM 3 N N3 IMD . . . F 5 41.391 31.168 48.3 1 68.11 ? N3 IMD 301 A 1 HETATM 4 C C4 IMD . . . F 5 41.047 32.199 47.49 1 75.6 ? C4 IMD 301 A 1 HETATM 5 C C5 IMD . . . F 5 41.292 31.822 46.17 1 72.84 ? C5 IMD 301 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 5 #