data_7BEM # _model_server_result.job_id eeC6QJ85NLaoms0uTosCQA _model_server_result.datetime_utc '2024-11-21 08:37:19' _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 7bem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 7BEM # _exptl.entry_id 7BEM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 120 _cell.entry_id 7BEM _cell.length_a 173.614 _cell.length_b 173.614 _cell.length_c 120.642 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall 'P 62 2 (x,y,z+1/3)' _symmetry.space_group_name_H-M 'P 62 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,L,M,N,O,P,Q _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 ? 5 E N N ? 5 I N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 A 1 NAG E 601 NAG 4 n D NAG 2 A 2 NAG E 701 NAG 4 n D FUC 3 A 3 FUC E 602 FUC # 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 disulf ? disulf1 A SG CYS 22 H CYS 22 1_555 A SG CYS 95 H CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 26 L CYS 23 1_555 B SG CYS 91 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 C SG CYS 13 E CYS 336 1_555 C SG CYS 38 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 C SG CYS 56 E CYS 379 1_555 C SG CYS 109 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 C SG CYS 157 E CYS 480 1_555 C SG CYS 165 E CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 C ND2 ASN 20 E ASN 343 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale3 D O6 NAG . A NAG 1 1_555 D C1 FUC . A FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 152 n n C1 C2 GOL sing 153 n n C1 H11 GOL sing 154 n n C1 H12 GOL sing 155 n n O1 HO1 GOL sing 156 n n C2 O2 GOL sing 157 n n C2 C3 GOL sing 158 n n C2 H2 GOL sing 159 n n O2 HO2 GOL sing 160 n n C3 O3 GOL sing 161 n n C3 H31 GOL sing 162 n n C3 H32 GOL sing 163 n n O3 HO3 GOL sing 164 n n # _atom_sites.entry_id 7BEM _atom_sites.fract_transf_matrix[1][1] 0.00576 _atom_sites.fract_transf_matrix[1][2] 0.003325 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006651 _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] 0.008289 _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 E 5 GOL H 1 501 501 GOL GOL . F 6 CL H 1 502 5 CL CL . G 7 PO4 L 1 201 1 PO4 PO4 . H 7 PO4 L 1 202 2 PO4 PO4 . I 5 GOL E 1 801 801 GOL GOL . J 8 PRO E 1 802 1301 PRO PRO . K 8 PRO E 1 803 1401 PRO PRO . L 8 PRO E 1 804 1501 PRO PRO . M 8 PRO E 1 805 1601 PRO PRO . N 6 CL E 1 806 2 CL CL . O 9 HOH H 1 601 5 HOH HOH . O 9 HOH H 2 602 16 HOH HOH . O 9 HOH H 3 603 10 HOH HOH . O 9 HOH H 4 604 2 HOH HOH . O 9 HOH H 5 605 3 HOH HOH . O 9 HOH H 6 606 4 HOH HOH . O 9 HOH H 7 607 11 HOH HOH . O 9 HOH H 8 608 19 HOH HOH . O 9 HOH H 9 609 32 HOH HOH . O 9 HOH H 10 610 8 HOH HOH . O 9 HOH H 11 611 13 HOH HOH . O 9 HOH H 12 612 22 HOH HOH . O 9 HOH H 13 613 23 HOH HOH . P 9 HOH L 1 301 12 HOH HOH . P 9 HOH L 2 302 14 HOH HOH . P 9 HOH L 3 303 6 HOH HOH . P 9 HOH L 4 304 7 HOH HOH . P 9 HOH L 5 305 29 HOH HOH . P 9 HOH L 6 306 21 HOH HOH . P 9 HOH L 7 307 20 HOH HOH . P 9 HOH L 8 308 30 HOH HOH . Q 9 HOH E 1 901 36 HOH HOH . Q 9 HOH E 2 902 18 HOH HOH . Q 9 HOH E 3 903 9 HOH HOH . Q 9 HOH E 4 904 17 HOH HOH . Q 9 HOH E 5 905 24 HOH HOH . Q 9 HOH E 6 906 31 HOH HOH . Q 9 HOH E 7 907 25 HOH HOH . Q 9 HOH E 8 908 34 HOH HOH . Q 9 HOH E 9 909 35 HOH HOH . Q 9 HOH E 10 910 28 HOH HOH . Q 9 HOH E 11 911 27 HOH HOH . Q 9 HOH E 12 912 26 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 C1 GOL . . . E 5 67.021 -65.406 -9.714 1 70.81 ? C1 GOL 501 H 1 HETATM 2 O O1 GOL . . . E 5 67.038 -66.762 -9.363 1 83.84 ? O1 GOL 501 H 1 HETATM 3 C C2 GOL . . . E 5 65.661 -64.83 -9.228 1 86.1 ? C2 GOL 501 H 1 HETATM 4 O O2 GOL . . . E 5 65.395 -63.577 -9.805 1 65.55 ? O2 GOL 501 H 1 HETATM 5 C C3 GOL . . . E 5 64.604 -65.997 -9.535 1 92.49 ? C3 GOL 501 H 1 HETATM 6 O O3 GOL . . . E 5 63.325 -65.694 -9.005 1 87.61 ? O3 GOL 501 H 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #