data_8VBO # _model_server_result.job_id 3ISvEA3rAsj0JJ14gahv7w _model_server_result.datetime_utc '2024-11-24 16:22:58' _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 8vbo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 8VBO # _exptl.entry_id 8VBO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _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 90 _cell.entry_id 8VBO _cell.length_a 70.107 _cell.length_b 150.891 _cell.length_c 51.318 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VBO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 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,I _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 C N N ? 3 D N 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 disulf ? disulf1 A SG CYS 22 L CYS 23 1_555 A SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 138 L CYS 134 1_555 A SG CYS 197 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 215 L CYS 211 1_555 B SG CYS 265 H CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 22 H CYS 22 1_555 B SG CYS 95 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 106 H CYS 103 1_555 B SG CYS 126 H CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 116 H CYS 113 1_555 B SG CYS 130 H CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 189 H CYS 186 1_555 B SG CYS 245 H CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 8VBO _atom_sites.fract_transf_matrix[1][1] 0.014264 _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] 0.006627 _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] 0.019486 _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 GOL H 1 301 302 GOL GOL . D 3 GOL H 1 302 303 GOL GOL . E 4 SO4 H 1 303 1 SO4 SO4 . F 4 SO4 H 1 304 2 SO4 SO4 . G 4 SO4 H 1 305 3 SO4 SO4 . H 5 HOH L 1 301 32 HOH HOH . H 5 HOH L 2 302 25 HOH HOH . H 5 HOH L 3 303 4 HOH HOH . H 5 HOH L 4 304 2 HOH HOH . H 5 HOH L 5 305 5 HOH HOH . H 5 HOH L 6 306 21 HOH HOH . H 5 HOH L 7 307 8 HOH HOH . H 5 HOH L 8 308 39 HOH HOH . H 5 HOH L 9 309 28 HOH HOH . H 5 HOH L 10 310 30 HOH HOH . H 5 HOH L 11 311 12 HOH HOH . H 5 HOH L 12 312 15 HOH HOH . H 5 HOH L 13 313 6 HOH HOH . H 5 HOH L 14 314 17 HOH HOH . H 5 HOH L 15 315 13 HOH HOH . H 5 HOH L 16 316 1 HOH HOH . H 5 HOH L 17 317 7 HOH HOH . H 5 HOH L 18 318 3 HOH HOH . H 5 HOH L 19 319 19 HOH HOH . H 5 HOH L 20 320 24 HOH HOH . H 5 HOH L 21 321 18 HOH HOH . H 5 HOH L 22 322 22 HOH HOH . H 5 HOH L 23 323 47 HOH HOH . I 5 HOH H 1 401 31 HOH HOH . I 5 HOH H 2 402 35 HOH HOH . I 5 HOH H 3 403 38 HOH HOH . I 5 HOH H 4 404 41 HOH HOH . I 5 HOH H 5 405 51 HOH HOH . I 5 HOH H 6 406 36 HOH HOH . I 5 HOH H 7 407 9 HOH HOH . I 5 HOH H 8 408 29 HOH HOH . I 5 HOH H 9 409 14 HOH HOH . I 5 HOH H 10 410 23 HOH HOH . I 5 HOH H 11 411 10 HOH HOH . I 5 HOH H 12 412 11 HOH HOH . I 5 HOH H 13 413 16 HOH HOH . I 5 HOH H 14 414 27 HOH HOH . I 5 HOH H 15 415 20 HOH HOH . I 5 HOH H 16 416 26 HOH HOH . I 5 HOH H 17 417 49 HOH HOH . I 5 HOH H 18 418 43 HOH HOH . I 5 HOH H 19 419 40 HOH HOH . I 5 HOH H 20 420 48 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 . . . C 3 -17.001 28.723 -2.52 1 49.06 ? C1 GOL 301 H 1 HETATM 2 O O1 GOL . . . C 3 -16.28 29.585 -1.677 1 45.87 ? O1 GOL 301 H 1 HETATM 3 C C2 GOL . . . C 3 -17.201 27.412 -1.745 1 49.78 ? C2 GOL 301 H 1 HETATM 4 O O2 GOL . . . C 3 -17.569 27.663 -0.431 1 47.81 ? O2 GOL 301 H 1 HETATM 5 C C3 GOL . . . C 3 -18.283 26.634 -2.533 1 51.58 ? C3 GOL 301 H 1 HETATM 6 O O3 GOL . . . C 3 -17.823 25.306 -2.659 1 54.56 ? O3 GOL 301 H 1 HETATM 7 H H11 GOL . . . C 3 -16.537 28.538 -3.352 1 59.01 ? H11 GOL 301 H 1 HETATM 8 H H12 GOL . . . C 3 -17.866 29.083 -2.773 1 59.01 ? H12 GOL 301 H 1 HETATM 9 H HO1 GOL . . . C 3 -16.276 29.225 -0.901 1 55.18 ? HO1 GOL 301 H 1 HETATM 10 H H2 GOL . . . C 3 -16.38 26.896 -1.707 1 59.86 ? H2 GOL 301 H 1 HETATM 11 H H31 GOL . . . C 3 -18.428 27.074 -3.385 1 62.03 ? H31 GOL 301 H 1 HETATM 12 H H32 GOL . . . C 3 -19.128 26.706 -2.06 1 62.03 ? H32 GOL 301 H 1 HETATM 13 H HO3 GOL . . . C 3 -18.328 24.911 -3.226 1 65.61 ? HO3 GOL 301 H 1 # _model_server_stats.io_time_ms 117 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 13 #