data_5VC1 # _model_server_result.job_id oZxQyTXCi0B9QFrpoVXbWg _model_server_result.datetime_utc '2024-10-19 03:37:32' _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 5vc1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":207}' # _entry.id 5VC1 # _exptl.entry_id 5VC1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 106.12 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description DI(HYDROXYETHYL)ETHER _entity.pdbx_number_of_molecules 1 _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 5VC1 _cell.length_a 118.598 _cell.length_b 118.598 _cell.length_c 118.598 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VC1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BMA MAN C1 O1 . O3 HO3 . sing 4 ? 2 5 3 BMA MAN 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 2 n B NAG 1 B 1 NAG A 154 NAG 2 n B NAG 2 B 2 NAG A 155 NAG 2 n B MAN 3 B 3 MAN A 156 MAN 2 n B BMA 4 B 4 BMA A 157 BMA 2 n B BMA 5 B 5 BMA A 158 BMA # 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 19 A CYS 19 1_555 A SG CYS 117 A CYS 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 A SG CYS 90 A CYS 90 1_555 A SG CYS 109 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 A SG CYS 122 A CYS 122 1_555 A SG CYS 133 A CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 A SG CYS 144 A CYS 144 1_555 A SG CYS 153 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 66 A ASN 66 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale4 B O3 MAN . B MAN 3 1_555 B C1 BMA . B BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 B O6 MAN . B MAN 3 1_555 B C1 BMA . B BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? metalc ? metalc1 A OE1 GLU 80 A GLU 80 1_555 F CA CA . A CA 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc2 A OD1 ASN 82 A ASN 82 1_555 F CA CA . A CA 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc3 A OE1 GLU 88 A GLU 88 1_555 F CA CA . A CA 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc4 A OD1 ASN 105 A ASN 105 1_555 F CA CA . A CA 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc5 A O ASP 106 A ASP 106 1_555 F CA CA . A CA 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc6 A OD1 ASP 106 A ASP 106 1_555 F CA CA . A CA 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc7 F CA CA . A CA 209 24_555 B O3 BMA . B BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc8 F CA CA . A CA 209 24_555 B O4 BMA . B BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? # _chem_comp.formula 'C4 H10 O3' _chem_comp.formula_weight 106.12 _chem_comp.id PEG _chem_comp.mon_nstd_flag . _chem_comp.name DI(HYDROXYETHYL)ETHER _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PEG sing 328 n n C1 C2 PEG sing 329 n n C1 H11 PEG sing 330 n n C1 H12 PEG sing 331 n n O1 HO1 PEG sing 332 n n C2 O2 PEG sing 333 n n C2 H21 PEG sing 334 n n C2 H22 PEG sing 335 n n O2 C3 PEG sing 336 n n C3 C4 PEG sing 337 n n C3 H31 PEG sing 338 n n C3 H32 PEG sing 339 n n C4 O4 PEG sing 340 n n C4 H41 PEG sing 341 n n C4 H42 PEG sing 342 n n O4 HO4 PEG sing 343 n n # _atom_sites.entry_id 5VC1 _atom_sites.fract_transf_matrix[1][1] 0.008432 _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] 0.008432 _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] 0.008432 _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 PG4 A 1 206 1 PG4 PG4 . D 4 PEG A 1 207 2 PEG PEG . E 5 GOL A 1 208 1 GOL GOL . F 6 CA A 1 209 1 CA CA . G 7 HOH A 1 301 43 HOH HOH . G 7 HOH A 2 302 113 HOH HOH . G 7 HOH A 3 303 4 HOH HOH . G 7 HOH A 4 304 29 HOH HOH . G 7 HOH A 5 305 116 HOH HOH . G 7 HOH A 6 306 36 HOH HOH . G 7 HOH A 7 307 23 HOH HOH . G 7 HOH A 8 308 122 HOH HOH . G 7 HOH A 9 309 121 HOH HOH . G 7 HOH A 10 310 64 HOH HOH . G 7 HOH A 11 311 21 HOH HOH . G 7 HOH A 12 312 78 HOH HOH . G 7 HOH A 13 313 28 HOH HOH . G 7 HOH A 14 314 24 HOH HOH . G 7 HOH A 15 315 56 HOH HOH . G 7 HOH A 16 316 119 HOH HOH . G 7 HOH A 17 317 111 HOH HOH . G 7 HOH A 18 318 22 HOH HOH . G 7 HOH A 19 319 33 HOH HOH . G 7 HOH A 20 320 34 HOH HOH . G 7 HOH A 21 321 53 HOH HOH . G 7 HOH A 22 322 2 HOH HOH . G 7 HOH A 23 323 57 HOH HOH . G 7 HOH A 24 324 5 HOH HOH . G 7 HOH A 25 325 14 HOH HOH . G 7 HOH A 26 326 63 HOH HOH . G 7 HOH A 27 327 75 HOH HOH . G 7 HOH A 28 328 67 HOH HOH . G 7 HOH A 29 329 52 HOH HOH . G 7 HOH A 30 330 18 HOH HOH . G 7 HOH A 31 331 91 HOH HOH . G 7 HOH A 32 332 19 HOH HOH . G 7 HOH A 33 333 10 HOH HOH . G 7 HOH A 34 334 115 HOH HOH . G 7 HOH A 35 335 47 HOH HOH . G 7 HOH A 36 336 105 HOH HOH . G 7 HOH A 37 337 77 HOH HOH . G 7 HOH A 38 338 90 HOH HOH . G 7 HOH A 39 339 3 HOH HOH . G 7 HOH A 40 340 16 HOH HOH . G 7 HOH A 41 341 42 HOH HOH . G 7 HOH A 42 342 45 HOH HOH . G 7 HOH A 43 343 1 HOH HOH . G 7 HOH A 44 344 38 HOH HOH . G 7 HOH A 45 345 41 HOH HOH . G 7 HOH A 46 346 112 HOH HOH . G 7 HOH A 47 347 15 HOH HOH . G 7 HOH A 48 348 99 HOH HOH . G 7 HOH A 49 349 68 HOH HOH . G 7 HOH A 50 350 7 HOH HOH . G 7 HOH A 51 351 27 HOH HOH . G 7 HOH A 52 352 13 HOH HOH . G 7 HOH A 53 353 100 HOH HOH . G 7 HOH A 54 354 35 HOH HOH . G 7 HOH A 55 355 17 HOH HOH . G 7 HOH A 56 356 118 HOH HOH . G 7 HOH A 57 357 114 HOH HOH . G 7 HOH A 58 358 120 HOH HOH . G 7 HOH A 59 359 9 HOH HOH . G 7 HOH A 60 360 70 HOH HOH . G 7 HOH A 61 361 20 HOH HOH . G 7 HOH A 62 362 6 HOH HOH . G 7 HOH A 63 363 65 HOH HOH . G 7 HOH A 64 364 54 HOH HOH . G 7 HOH A 65 365 50 HOH HOH . G 7 HOH A 66 366 12 HOH HOH . G 7 HOH A 67 367 25 HOH HOH . G 7 HOH A 68 368 93 HOH HOH . G 7 HOH A 69 369 49 HOH HOH . G 7 HOH A 70 370 37 HOH HOH . G 7 HOH A 71 371 73 HOH HOH . G 7 HOH A 72 372 58 HOH HOH . G 7 HOH A 73 373 81 HOH HOH . G 7 HOH A 74 374 26 HOH HOH . G 7 HOH A 75 375 30 HOH HOH . G 7 HOH A 76 376 31 HOH HOH . G 7 HOH A 77 377 80 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 PEG . . . D 4 0.267 30.526 54.233 1 33.88 ? C1 PEG 207 A 1 HETATM 2 O O1 PEG . . . D 4 -0.415 29.664 53.367 1 33.97 ? O1 PEG 207 A 1 HETATM 3 C C2 PEG . . . D 4 0.586 29.842 55.562 1 50.29 ? C2 PEG 207 A 1 HETATM 4 O O2 PEG . . . D 4 1.717 30.434 56.143 1 48.73 ? O2 PEG 207 A 1 HETATM 5 C C3 PEG . . . D 4 2.891 30.299 55.392 1 38.78 ? C3 PEG 207 A 1 HETATM 6 C C4 PEG . . . D 4 3.261 28.819 55.273 1 43.77 ? C4 PEG 207 A 1 HETATM 7 O O4 PEG . . . D 4 3.753 28.368 56.507 1 50.33 ? O4 PEG 207 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 7 #