data_7BEP # _model_server_result.job_id V1BJL7J5yyiRRo90Xd54SA _model_server_result.datetime_utc '2024-11-01 16:25:51' _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 7bep # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":701}' # _entry.id 7BEP # _exptl.entry_id 7BEP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 12 _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 90 _cell.entry_id 7BEP _cell.length_a 108.76 _cell.length_b 113.221 _cell.length_c 302.773 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BEP _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' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? pentameric 5 author_defined_assembly 1 ? pentameric 5 author_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,K,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,RA,SA,TA,UA 1 1 F,G,H,I,J,L,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,VA,WA,XA,YA 2 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 ? 12 U N N ? 12 IA N N ? 12 KA N N ? 12 LA N N # _pdbx_entity_branch.entity_id 6 _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 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 6 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 6 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 6 6 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 6 n K NAG 1 J 1 NAG E 621 NAG 6 n K NAG 2 J 2 NAG E 622 NAG 6 n K BMA 3 J 3 BMA E 623 BMA 6 n K MAN 4 J 4 MAN E 625 MAN 6 n K MAN 5 J 5 MAN E 624 MAN 6 n K FUC 6 J 6 FUC E 620 FUC 6 n L NAG 1 K 1 NAG C 621 NAG 6 n L NAG 2 K 2 NAG C 622 NAG 6 n L BMA 3 K 3 BMA C 623 BMA 6 n L MAN 4 K 4 MAN C 625 MAN 6 n L MAN 5 K 5 MAN C 624 MAN 6 n L FUC 6 K 6 FUC C 620 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 13 E CYS 336 1_555 A SG CYS 38 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 56 E CYS 379 1_555 A SG CYS 109 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 68 E CYS 391 1_555 A SG CYS 202 E CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 157 E CYS 480 1_555 A SG CYS 165 E CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 35 A CYS 22 1_555 B SG CYS 109 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 B SG CYS 165 A CYS 152 1_555 B SG CYS 221 A CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 C SG CYS 36 B CYS 23 1_555 C SG CYS 101 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf8 C SG CYS 147 B CYS 134 1_555 C SG CYS 207 B CYS 194 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 147 B CYS 134 1_555 C SG CYS 207 B CYS 194 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 D SG CYS 22 H CYS 22 1_555 D SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 D SG CYS 154 H CYS 154 1_555 D SG CYS 210 H CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 D SG CYS 230 H CYS 230 1_555 E SG CYS 214 L CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 E SG CYS 23 L CYS 23 1_555 E SG CYS 89 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf14 E SG CYS 134 L CYS 134 1_555 E SG CYS 194 L CYS 194 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 E SG CYS 134 L CYS 134 1_555 E SG CYS 194 L CYS 194 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 F SG CYS 13 C CYS 336 1_555 F SG CYS 38 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 F SG CYS 56 C CYS 379 1_555 F SG CYS 109 C CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf18 F SG CYS 68 C CYS 391 1_555 F SG CYS 202 C CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf19 F SG CYS 157 C CYS 480 1_555 F SG CYS 165 C CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf20 G SG CYS 35 D CYS 22 1_555 G SG CYS 109 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf21 G SG CYS 165 D CYS 152 1_555 G SG CYS 221 D CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf22 H SG CYS 36 F CYS 23 1_555 H SG CYS 101 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf23 H SG CYS 147 F CYS 134 1_555 H SG CYS 207 F CYS 194 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.035 ? disulf ? disulf24 H SG CYS 147 F CYS 134 1_555 H SG CYS 207 F CYS 194 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.034 ? disulf ? disulf25 I SG CYS 22 G CYS 22 1_555 I SG CYS 96 G CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf26 I SG CYS 154 G CYS 154 1_555 I SG CYS 210 G CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf27 I SG CYS 230 G CYS 230 1_555 J SG CYS 214 I CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf28 J SG CYS 23 I CYS 23 1_555 J SG CYS 89 I CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf29 J SG CYS 134 I CYS 134 1_555 J SG CYS 194 I CYS 194 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.036 ? disulf ? disulf30 J SG CYS 134 I CYS 134 1_555 J SG CYS 194 I CYS 194 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 20 E ASN 343 1_555 K C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 F ND2 ASN 20 C ASN 343 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 K O4 NAG . J NAG 1 1_555 K C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 K O6 NAG . J NAG 1 1_555 K C1 FUC . J FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 K O4 NAG . J NAG 2 1_555 K C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 K O3 BMA . J BMA 3 1_555 K C1 MAN . J MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 K O6 BMA . J BMA 3 1_555 K C1 MAN . J MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale8 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 L O6 NAG . K NAG 1 1_555 L C1 FUC . K FUC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 L O4 NAG . K NAG 2 1_555 L C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale11 L O3 BMA . K BMA 3 1_555 L C1 MAN . K MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 L O6 BMA . K BMA 3 1_555 L C1 MAN . K MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 7BEP _atom_sites.fract_transf_matrix[1][1] 0.009195 _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] 0.008832 _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] 0.003303 _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 M 7 IMD E 1 801 801 IMD IMD . N 8 CL A 1 301 1 CL CL . O 8 CL A 1 302 2 CL CL . P 9 GLU A 1 303 301 GLU GLU . Q 10 GLY A 1 304 301 GLY GLY . R 11 PGE B 1 301 301 PGE PGE . S 8 CL B 1 302 3 CL CL . T 8 CL B 1 303 6 CL CL . U 12 GOL H 1 701 701 GOL GOL . V 7 IMD H 1 702 301 IMD IMD . W 10 GLY H 1 703 401 GLY GLY . X 7 IMD H 1 704 501 IMD IMD . Y 8 CL H 1 705 9 CL CL . Z 13 PG4 L 1 301 301 PG4 PG4 . AA 10 GLY L 1 302 401 GLY GLY . BA 7 IMD C 1 701 701 IMD IMD . CA 8 CL C 1 702 8 CL CL . DA 8 CL D 1 301 301 CL CL . EA 8 CL D 1 302 401 CL CL . FA 14 PEG D 1 303 501 PEG PEG . GA 9 GLU D 1 304 601 GLU GLU . HA 8 CL F 1 301 301 CL CL . IA 12 GOL F 1 302 401 GOL GOL . JA 10 GLY F 1 303 501 GLY GLY . KA 12 GOL G 1 301 301 GOL GOL . LA 12 GOL G 1 302 401 GOL GOL . MA 10 GLY G 1 303 501 GLY GLY . NA 7 IMD G 1 304 601 IMD IMD . OA 10 GLY G 1 305 701 GLY GLY . PA 13 PG4 I 1 301 301 PG4 PG4 . QA 8 CL I 1 302 7 CL CL . RA 15 HOH E 1 901 18 HOH HOH . RA 15 HOH E 2 902 15 HOH HOH . SA 15 HOH A 1 401 10 HOH HOH . SA 15 HOH A 2 402 1 HOH HOH . TA 15 HOH H 1 801 3 HOH HOH . TA 15 HOH H 2 802 7 HOH HOH . TA 15 HOH H 3 803 13 HOH HOH . TA 15 HOH H 4 804 4 HOH HOH . TA 15 HOH H 5 805 302 HOH HOH . UA 15 HOH L 1 401 20 HOH HOH . VA 15 HOH C 1 801 11 HOH HOH . VA 15 HOH C 2 802 5 HOH HOH . VA 15 HOH C 3 803 17 HOH HOH . WA 15 HOH D 1 401 6 HOH HOH . XA 15 HOH F 1 401 2 HOH HOH . XA 15 HOH F 2 402 12 HOH HOH . YA 15 HOH G 1 401 9 HOH HOH . YA 15 HOH G 2 402 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 . . . U 12 0.294 -11.825 20.9 1 105.89 ? C1 GOL 701 H 1 HETATM 2 O O1 GOL . . . U 12 0.477 -11.39 22.219 1 94.67 ? O1 GOL 701 H 1 HETATM 3 C C2 GOL . . . U 12 0.449 -13.374 20.891 1 104.3 ? C2 GOL 701 H 1 HETATM 4 O O2 GOL . . . U 12 -0.357 -13.985 21.84 1 101.65 ? O2 GOL 701 H 1 HETATM 5 C C3 GOL . . . U 12 0.075 -13.815 19.451 1 106.17 ? C3 GOL 701 H 1 HETATM 6 O O3 GOL . . . U 12 -1.309 -14.03 19.431 1 103.42 ? O3 GOL 701 H 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 373 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 6 #