data_7A3T # _model_server_result.job_id tbIBHGCZ8PxcrhUDmGL9rA _model_server_result.datetime_utc '2024-11-09 01:57:20' _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 7a3t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":504}' # _entry.id 7A3T # _exptl.entry_id 7A3T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 4 _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 7A3T _cell.length_a 110.309 _cell.length_b 110.309 _cell.length_c 217.337 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7A3T _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,H,I,M 1 1,3 B,C,J,K,L,N,O 1 2,4 # 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' 3_444 -x+y-1,-x-1,z-1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -55.1545 -95.530396 -72.445667 3 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 6_445 -x-1,-x+y-1,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 -55.1545 -95.530396 72.445667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 H N N ? 6 I N N ? 6 L 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 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 4 5 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 B 1 NAG A 397 NAG 4 n D NAG 2 B 2 NAG A 398 NAG 4 n D BMA 3 B 3 BMA A 401 BMA 4 n D MAN 4 B 4 MAN A 403 MAN 4 n D FUC 5 B 5 FUC A 402 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 3 A CYS 3 1_555 A SG CYS 30 A CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 A SG CYS 60 A CYS 60 1_555 A SG CYS 121 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf3 A SG CYS 74 A CYS 74 1_555 A SG CYS 105 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf4 A SG CYS 92 A CYS 92 1_555 A SG CYS 116 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? disulf ? disulf5 A SG CYS 107 A CYS 107 1_555 A SG CYS 311 A CYS 311 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf6 A SG CYS 183 A CYS 183 1_555 A SG CYS 283 A CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 A SG CYS 300 A CYS 300 1_555 A SG CYS 331 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? disulf ? disulf8 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf9 B SG CYS 149 H CYS 140 1_555 B SG CYS 205 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf10 C SG CYS 25 L CYS 23 1_555 C SG CYS 90 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 C SG CYS 137 L CYS 134 1_555 C SG CYS 197 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 67 A ASN 67 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale2 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 D O6 NAG . B NAG 1 1_555 D C1 FUC . B FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 D O4 NAG . B NAG 2 1_555 D C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 D O6 BMA . B BMA 3 1_555 D C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? # _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 176 n n C1 C2 GOL sing 177 n n C1 H11 GOL sing 178 n n C1 H12 GOL sing 179 n n O1 HO1 GOL sing 180 n n C2 O2 GOL sing 181 n n C2 C3 GOL sing 182 n n C2 H2 GOL sing 183 n n O2 HO2 GOL sing 184 n n C3 O3 GOL sing 185 n n C3 H31 GOL sing 186 n n C3 H32 GOL sing 187 n n O3 HO3 GOL sing 188 n n # _atom_sites.entry_id 7A3T _atom_sites.fract_transf_matrix[1][1] 0.009065 _atom_sites.fract_transf_matrix[1][2] 0.005234 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010468 _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] 0.004601 _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 SO4 A 1 501 4 SO4 SO4 . F 5 SO4 A 1 502 7 SO4 SO4 . G 6 GOL A 1 503 7 GOL GOL . H 6 GOL A 1 504 8 GOL GOL . I 6 GOL A 1 505 9 GOL GOL . J 5 SO4 H 1 301 9 SO4 SO4 . K 5 SO4 H 1 302 10 SO4 SO4 . L 6 GOL L 1 301 3 GOL GOL . M 7 HOH A 1 601 3 HOH HOH . M 7 HOH A 2 602 22 HOH HOH . N 7 HOH H 1 401 21 HOH HOH . O 7 HOH L 1 401 1 HOH HOH . O 7 HOH L 2 402 9 HOH HOH . O 7 HOH L 3 403 19 HOH HOH . O 7 HOH L 4 404 13 HOH HOH . O 7 HOH L 5 405 8 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 . . . H 6 -6.933 -36.277 -21.224 1 68.38 ? C1 GOL 504 A 1 HETATM 2 O O1 GOL . . . H 6 -6.133 -37.345 -21.638 1 72.8 ? O1 GOL 504 A 1 HETATM 3 C C2 GOL . . . H 6 -6.09 -34.986 -21.436 1 75.54 ? C2 GOL 504 A 1 HETATM 4 O O2 GOL . . . H 6 -4.893 -35.016 -20.717 1 97.5 ? O2 GOL 504 A 1 HETATM 5 C C3 GOL . . . H 6 -5.849 -34.891 -22.968 1 53.72 ? C3 GOL 504 A 1 HETATM 6 O O3 GOL . . . H 6 -5.068 -33.749 -23.162 1 62.74 ? O3 GOL 504 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #