data_5LFR # _model_server_result.job_id Pcix7-qjHKdtJIuxkwSu5Q _model_server_result.datetime_utc '2025-01-03 03:39:44' _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 5lfr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":410}' # _entry.id 5LFR # _exptl.entry_id 5LFR _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 72.7 _cell.angle_beta 86.71 _cell.angle_gamma 83.01 _cell.entry_id 5LFR _cell.length_a 43.06 _cell.length_b 60.4 _cell.length_c 79.22 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LFR _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,E,F,G,H,I,J,K,L,M,V 1 1 B,D,N,O,P,Q,R,S,T,U,W 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 ? 6 I N N ? 6 J N N ? 6 K N N ? 6 Q N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . 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 2 n C NAG 1 C 1 NAG A 1099 NAG 2 n C NAG 2 C 2 NAG A 2099 NAG 2 n C BMA 3 C 3 BMA A 3099 BMA 2 n C MAN 4 C 4 MAN A 4099 MAN 2 n C MAN 5 C 5 MAN A 5099 MAN 3 n D NAG 1 D 1 NAG B 1099 NAG 3 n D NAG 2 D 2 NAG B 2099 NAG 3 n D BMA 3 D 3 BMA B 3099 BMA 3 n D MAN 4 D 4 MAN B 5099 MAN # 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 20 A CYS 37 1_555 A SG CYS 148 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 83 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 142 A CYS 159 1_555 A SG CYS 200 A CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 244 A CYS 261 1_555 A SG CYS 288 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 20 B CYS 37 1_555 B SG CYS 148 B CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 25 B CYS 42 1_555 B SG CYS 83 B CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 142 B CYS 159 1_555 B SG CYS 200 B CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 B SG CYS 244 B CYS 261 1_555 B SG CYS 288 B CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A CD1 TRP 5 A TRP 22 1_555 E C1 MAN . A MAN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale2 A ND2 ASN 82 A ASN 99 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 206 A ASN 223 1_555 F C1 NAG . A NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 A ND2 ASN 229 A ASN 246 1_555 G C1 NAG . A NAG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 A ND2 ASN 298 A ASN 315 1_555 H C1 NAG . A NAG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 B CD1 TRP 5 B TRP 22 1_555 N C1 MAN . B MAN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? covale ? covale7 B ND2 ASN 82 B ASN 99 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 B ND2 ASN 229 B ASN 246 1_555 O C1 NAG . B NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 B ND2 ASN 298 B ASN 315 1_555 P C1 NAG . B NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale12 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale13 C O3 MAN . C MAN 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale14 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale15 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale16 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? # _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 153 n n C1 C2 GOL sing 154 n n C1 H11 GOL sing 155 n n C1 H12 GOL sing 156 n n O1 HO1 GOL sing 157 n n C2 O2 GOL sing 158 n n C2 C3 GOL sing 159 n n C2 H2 GOL sing 160 n n O2 HO2 GOL sing 161 n n C3 O3 GOL sing 162 n n C3 H31 GOL sing 163 n n C3 H32 GOL sing 164 n n O3 HO3 GOL sing 165 n n # _atom_sites.entry_id 5LFR _atom_sites.fract_transf_matrix[1][1] 0.023223 _atom_sites.fract_transf_matrix[1][2] -0.002849 _atom_sites.fract_transf_matrix[1][3] -0.000524 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01668 _atom_sites.fract_transf_matrix[2][3] -0.005114 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013225 _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 4 MAN A 1 401 1022 MAN MAN . F 5 NAG A 1 407 1223 NAG NAG . G 5 NAG A 1 408 1246 NAG NAG . H 5 NAG A 1 409 1315 NAG NAG . I 6 GOL A 1 410 1 GOL GOL . J 6 GOL A 1 411 2 GOL GOL . K 6 GOL A 1 412 3 GOL GOL . L 7 SO4 A 1 413 2 SO4 SO4 . M 7 SO4 A 1 414 5 SO4 SO4 . N 4 MAN B 1 401 1022 MAN MAN . O 5 NAG B 1 406 1246 NAG NAG . P 5 NAG B 1 407 1315 NAG NAG . Q 6 GOL B 1 408 4 GOL GOL . R 7 SO4 B 1 409 1 SO4 SO4 . S 7 SO4 B 1 410 3 SO4 SO4 . T 7 SO4 B 1 411 4 SO4 SO4 . U 7 SO4 B 1 412 6 SO4 SO4 . V 8 HOH A 1 501 4 HOH HOH . V 8 HOH A 2 502 38 HOH HOH . V 8 HOH A 3 503 8 HOH HOH . V 8 HOH A 4 504 52 HOH HOH . V 8 HOH A 5 505 17 HOH HOH . V 8 HOH A 6 506 44 HOH HOH . V 8 HOH A 7 507 2 HOH HOH . V 8 HOH A 8 508 10 HOH HOH . V 8 HOH A 9 509 3 HOH HOH . V 8 HOH A 10 510 46 HOH HOH . V 8 HOH A 11 511 32 HOH HOH . V 8 HOH A 12 512 35 HOH HOH . V 8 HOH A 13 513 1 HOH HOH . V 8 HOH A 14 514 22 HOH HOH . V 8 HOH A 15 515 39 HOH HOH . V 8 HOH A 16 516 53 HOH HOH . V 8 HOH A 17 517 13 HOH HOH . V 8 HOH A 18 518 26 HOH HOH . V 8 HOH A 19 519 25 HOH HOH . V 8 HOH A 20 520 40 HOH HOH . V 8 HOH A 21 521 50 HOH HOH . V 8 HOH A 22 522 16 HOH HOH . V 8 HOH A 23 523 28 HOH HOH . V 8 HOH A 24 524 15 HOH HOH . V 8 HOH A 25 525 37 HOH HOH . V 8 HOH A 26 526 20 HOH HOH . V 8 HOH A 27 527 33 HOH HOH . V 8 HOH A 28 528 7 HOH HOH . V 8 HOH A 29 529 9 HOH HOH . V 8 HOH A 30 530 14 HOH HOH . V 8 HOH A 31 531 42 HOH HOH . V 8 HOH A 32 532 51 HOH HOH . V 8 HOH A 33 533 21 HOH HOH . V 8 HOH A 34 534 43 HOH HOH . V 8 HOH A 35 535 49 HOH HOH . V 8 HOH A 36 536 27 HOH HOH . V 8 HOH A 37 537 34 HOH HOH . V 8 HOH A 38 538 36 HOH HOH . W 8 HOH B 1 501 41 HOH HOH . W 8 HOH B 2 502 18 HOH HOH . W 8 HOH B 3 503 31 HOH HOH . W 8 HOH B 4 504 29 HOH HOH . W 8 HOH B 5 505 11 HOH HOH . W 8 HOH B 6 506 45 HOH HOH . W 8 HOH B 7 507 24 HOH HOH . W 8 HOH B 8 508 23 HOH HOH . W 8 HOH B 9 509 6 HOH HOH . W 8 HOH B 10 510 12 HOH HOH . W 8 HOH B 11 511 30 HOH HOH . W 8 HOH B 12 512 19 HOH HOH . W 8 HOH B 13 513 5 HOH HOH . W 8 HOH B 14 514 54 HOH HOH . W 8 HOH B 15 515 47 HOH HOH . W 8 HOH B 16 516 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 . . . I 6 -9.418 34.04 76.292 1 83.39 ? C1 GOL 410 A 1 HETATM 2 O O1 GOL . . . I 6 -10.166 35.045 75.646 1 84.52 ? O1 GOL 410 A 1 HETATM 3 C C2 GOL . . . I 6 -8.296 33.569 75.374 1 79.84 ? C2 GOL 410 A 1 HETATM 4 O O2 GOL . . . I 6 -8.127 34.493 74.323 1 86.85 ? O2 GOL 410 A 1 HETATM 5 C C3 GOL . . . I 6 -7.001 33.461 76.169 1 75.69 ? C3 GOL 410 A 1 HETATM 6 O O3 GOL . . . I 6 -5.936 33.16 75.297 1 73.61 ? O3 GOL 410 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 6 #