data_5UFU # _model_server_result.job_id bSVLPr2lvylagQJCxGiknA _model_server_result.datetime_utc '2025-01-10 05:15:59' _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 5ufu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 5UFU # _exptl.entry_id 5UFU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 442.892 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol _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 5UFU _cell.length_a 124.264 _cell.length_b 124.264 _cell.length_c 401.569 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UFU _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # 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 author_and_software_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M 2 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' 10_554 -y,-x,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -66.928167 # _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 ARG 173 A ARG 171 1_555 A N TPO 174 A TPO 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale2 A C TPO 174 A TPO 172 1_555 A N SER 175 A SER 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C23 H23 Cl N2 O5' _chem_comp.formula_weight 442.892 _chem_comp.id 85V _chem_comp.mon_nstd_flag . _chem_comp.name 1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol _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 C28 C27 85V sing 1 n n C28 C26 85V sing 2 n n C5 C4 85V doub 3 n y C5 C6 85V sing 4 n y C4 C3 85V sing 5 n y C18 C17 85V sing 6 n n C18 O19 85V sing 7 n n C14 O16 85V sing 8 n n C14 N13 85V sing 9 n y C14 N15 85V doub 10 n y O16 C17 85V sing 11 n n N13 C10 85V sing 12 n y C17 C21 85V sing 13 n n N15 C9 85V sing 14 n y C9 C10 85V doub 15 n y C9 C8 85V sing 16 n y C10 C11 85V sing 17 n y C8 C7 85V doub 18 n y C11 C12 85V doub 19 n y C7 C12 85V sing 20 n y C7 C6 85V sing 21 n n C12 CL 85V sing 22 n n C27 C26 85V sing 23 n n C6 C1 85V doub 24 n y C3 C26 85V sing 25 n n C3 C2 85V doub 26 n y C26 C29 85V sing 27 n n O19 C20 85V sing 28 n n C1 C2 85V sing 29 n y C29 O30 85V sing 30 n n C21 C20 85V sing 31 n n C21 O22 85V sing 32 n n C20 C24 85V sing 33 n n O22 C23 85V sing 34 n n C23 C24 85V sing 35 n n C24 O25 85V sing 36 n n C4 H1 85V sing 37 n n C20 H2 85V sing 38 n n C21 H3 85V sing 39 n n C8 H4 85V sing 40 n n C18 H5 85V sing 41 n n C18 H6 85V sing 42 n n C1 H7 85V sing 43 n n C2 H8 85V sing 44 n n C5 H9 85V sing 45 n n C11 H10 85V sing 46 n n N13 H11 85V sing 47 n n C17 H13 85V sing 48 n n C23 H14 85V sing 49 n n C23 H15 85V sing 50 n n C24 H16 85V sing 51 n n O25 H17 85V sing 52 n n C27 H18 85V sing 53 n n C27 H19 85V sing 54 n n C28 H20 85V sing 55 n n C28 H21 85V sing 56 n n C29 H22 85V sing 57 n n C29 H23 85V sing 58 n n O30 H24 85V sing 59 n n # _atom_sites.entry_id 5UFU _atom_sites.fract_transf_matrix[1][1] 0.008047 _atom_sites.fract_transf_matrix[1][2] 0.004646 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009292 _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] 0.00249 _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 D 4 STU A 1 601 4000 STU STU . E 5 85V A 1 602 4000 85V PFE . F 6 CL A 1 603 6 CL CL . G 6 CL A 1 604 7 CL CL . H 6 CL A 1 605 8 CL CL . I 7 SO4 A 1 606 2 SO4 SO4 . J 8 AMP C 1 401 1 AMP AMP . K 8 AMP C 1 402 2 AMP AMP . L 9 ADP C 1 403 3 ADP ADP . M 7 SO4 C 1 404 3 SO4 SO4 . # 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 C4 85V . . . E 5 -13.241 24.3 -40.268 1 49.76 ? C4 85V 602 A 1 HETATM 2 C C7 85V . . . E 5 -15.382 27.343 -39.559 1 53.97 ? C7 85V 602 A 1 HETATM 3 C C6 85V . . . E 5 -14.268 26.35 -39.498 1 52.52 ? C6 85V 602 A 1 HETATM 4 C C9 85V . . . E 5 -17.745 27.765 -39.732 1 54.14 ? C9 85V 602 A 1 HETATM 5 C C20 85V . . . E 5 -23.343 28.136 -37.837 1 54 ? C20 85V 602 A 1 HETATM 6 C C21 85V . . . E 5 -22.1 27.407 -38.353 1 52.49 ? C21 85V 602 A 1 HETATM 7 C C8 85V . . . E 5 -16.692 26.862 -39.659 1 54.57 ? C8 85V 602 A 1 HETATM 8 C C18 85V . . . E 5 -23.249 28.623 -40.042 1 52.08 ? C18 85V 602 A 1 HETATM 9 C C26 85V . . . E 5 -11.059 23.415 -39.332 1 47.46 ? C26 85V 602 A 1 HETATM 10 C C1 85V . . . E 5 -13.232 26.471 -38.571 1 51.46 ? C1 85V 602 A 1 HETATM 11 C C2 85V . . . E 5 -12.22 25.528 -38.501 1 50.13 ? C2 85V 602 A 1 HETATM 12 C C3 85V . . . E 5 -12.204 24.428 -39.353 1 48.44 ? C3 85V 602 A 1 HETATM 13 C C5 85V . . . E 5 -14.251 25.242 -40.343 1 51.96 ? C5 85V 602 A 1 HETATM 14 C C10 85V . . . E 5 -17.527 29.143 -39.73 1 54.04 ? C10 85V 602 A 1 HETATM 15 C C11 85V . . . E 5 -16.23 29.64 -39.636 1 54.01 ? C11 85V 602 A 1 HETATM 16 C C12 85V . . . E 5 -15.18 28.746 -39.544 1 54.62 ? C12 85V 602 A 1 HETATM 17 CL CL 85V . . . E 5 -13.588 29.406 -39.397 1 57.79 ? CL 85V 602 A 1 HETATM 18 N N13 85V . . . E 5 -18.74 29.816 -39.78 1 53.99 ? N13 85V 602 A 1 HETATM 19 C C14 85V . . . E 5 -19.624 28.855 -39.789 1 53.64 ? C14 85V 602 A 1 HETATM 20 N N15 85V . . . E 5 -19.121 27.6 -39.768 1 53.78 ? N15 85V 602 A 1 HETATM 21 O O16 85V . . . E 5 -20.938 29.048 -39.788 1 52.65 ? O16 85V 602 A 1 HETATM 22 C C17 85V . . . E 5 -21.91 27.964 -39.769 1 51.94 ? C17 85V 602 A 1 HETATM 23 O O19 85V . . . E 5 -23.59 29.185 -38.776 1 52.21 ? O19 85V 602 A 1 HETATM 24 O O22 85V . . . E 5 -21.031 27.744 -37.463 1 54.4 ? O22 85V 602 A 1 HETATM 25 C C23 85V . . . E 5 -21.459 28.834 -36.62 1 56.35 ? C23 85V 602 A 1 HETATM 26 C C24 85V . . . E 5 -22.951 28.654 -36.452 1 56.81 ? C24 85V 602 A 1 HETATM 27 O O25 85V . . . E 5 -23.624 29.858 -36.072 1 58.36 ? O25 85V 602 A 1 HETATM 28 C C27 85V . . . E 5 -9.647 23.901 -39.538 1 46.77 ? C27 85V 602 A 1 HETATM 29 C C28 85V . . . E 5 -10.33 23.151 -40.627 1 46.39 ? C28 85V 602 A 1 HETATM 30 C C29 85V . . . E 5 -11.244 22.221 -38.392 1 50.04 ? C29 85V 602 A 1 HETATM 31 O O30 85V . . . E 5 -10.852 22.555 -37.069 1 51.18 ? O30 85V 602 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #