data_6YBB # _model_server_result.job_id zo5Klt017q3EFC1NlRAo6w _model_server_result.datetime_utc '2024-11-16 01:29:20' _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 6ybb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":603}' # _entry.id 6YBB # _exptl.entry_id 6YBB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 7 _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 6YBB _cell.length_a 61.43 _cell.length_b 169.59 _cell.length_c 177.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YBB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,R,S,T,U _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 ? 7 M N N ? 7 P 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 metalc ? metalc1 A OG1 THR 16 A THR 16 1_555 G MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc2 G MG MG . A MG 301 1_555 H O3G ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc3 G MG MG . A MG 301 1_555 H O2B ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc4 G MG MG . A MG 301 1_555 H O1A ATP . A ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc5 G MG MG . A MG 301 1_555 Q O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc6 G MG MG . A MG 301 1_555 Q O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc7 B OG1 THR 16 B THR 16 1_555 I MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc8 I MG MG . B MG 301 1_555 J O2B ATP . B ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc9 I MG MG . B MG 301 1_555 J O3G ATP . B ATP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc10 I MG MG . B MG 301 1_555 R O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc11 I MG MG . B MG 301 1_555 R O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? # _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 254 n n C1 C2 GOL sing 255 n n C1 H11 GOL sing 256 n n C1 H12 GOL sing 257 n n O1 HO1 GOL sing 258 n n C2 O2 GOL sing 259 n n C2 C3 GOL sing 260 n n C2 H2 GOL sing 261 n n O2 HO2 GOL sing 262 n n C3 O3 GOL sing 263 n n C3 H31 GOL sing 264 n n C3 H32 GOL sing 265 n n O3 HO3 GOL sing 266 n n # _atom_sites.entry_id 6YBB _atom_sites.fract_transf_matrix[1][1] 0.016279 _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] 0.005897 _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] 0.005631 _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 G 4 MG A 1 301 1 MG MG . H 5 ATP A 1 302 1 ATP ATP . I 4 MG B 1 301 2 MG MG . J 5 ATP B 1 302 2 ATP ATP . K 6 C2E E 1 601 3 C2E C2E . L 6 C2E E 1 602 4 C2E C2E . M 7 GOL E 1 603 1 GOL GOL . N 6 C2E F 1 601 1 C2E C2E . O 6 C2E F 1 602 2 C2E C2E . P 7 GOL F 1 603 2 GOL GOL . Q 8 HOH A 1 401 52 HOH HOH . Q 8 HOH A 2 402 31 HOH HOH . Q 8 HOH A 3 403 41 HOH HOH . Q 8 HOH A 4 404 7 HOH HOH . Q 8 HOH A 5 405 40 HOH HOH . Q 8 HOH A 6 406 2 HOH HOH . R 8 HOH B 1 401 11 HOH HOH . R 8 HOH B 2 402 9 HOH HOH . R 8 HOH B 3 403 23 HOH HOH . S 8 HOH D 1 101 19 HOH HOH . S 8 HOH D 2 102 26 HOH HOH . T 8 HOH E 1 701 66 HOH HOH . T 8 HOH E 2 702 56 HOH HOH . T 8 HOH E 3 703 6 HOH HOH . T 8 HOH E 4 704 4 HOH HOH . T 8 HOH E 5 705 16 HOH HOH . T 8 HOH E 6 706 5 HOH HOH . T 8 HOH E 7 707 47 HOH HOH . U 8 HOH F 1 701 51 HOH HOH . U 8 HOH F 2 702 65 HOH HOH . U 8 HOH F 3 703 60 HOH HOH . U 8 HOH F 4 704 27 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 . . . M 7 47.61 197.507 -15.8 1 95.14 ? C1 GOL 603 E 1 HETATM 2 O O1 GOL . . . M 7 48.494 196.47 -15.505 1 95.43 ? O1 GOL 603 E 1 HETATM 3 C C2 GOL . . . M 7 47.85 198.625 -14.767 1 91.77 ? C2 GOL 603 E 1 HETATM 4 O O2 GOL . . . M 7 46.866 199.597 -14.833 1 93.31 ? O2 GOL 603 E 1 HETATM 5 C C3 GOL . . . M 7 47.87 197.903 -13.404 1 86.56 ? C3 GOL 603 E 1 HETATM 6 O O3 GOL . . . M 7 48.24 198.849 -12.448 1 82.9 ? O3 GOL 603 E 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #