data_6VTU # _model_server_result.job_id 2YLH9jRsU_upPHAPQGofQQ _model_server_result.datetime_utc '2024-11-04 22:05:17' _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 6vtu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 6VTU # _exptl.entry_id 6VTU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 6VTU _cell.length_a 115.238 _cell.length_b 115.238 _cell.length_c 98.476 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VTU _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _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 ? 3 2 1 MAN MAN C1 O1 . O2 HO2 . sing 2 ? 3 3 2 MAN MAN C1 O1 . O2 HO2 . 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 3 n C MAN 1 A 1 MAN P 79 MAN 3 n C MAN 2 A 2 MAN P 80 MAN 3 n C MAN 3 A 3 MAN P 81 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 22 H CYS 22 1_555 A SG CYS 97 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 151 H CYS 135 1_555 A SG CYS 207 H CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 22 L CYS 23 1_555 B SG CYS 90 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 138 L CYS 134 1_555 B SG CYS 197 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 C O2 MAN . A MAN 1 1_555 C C1 MAN . A MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 C O2 MAN . A MAN 2 1_555 C C1 MAN . A MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 6VTU _atom_sites.fract_transf_matrix[1][1] 0.008678 _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] 0.008678 _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] 0.010155 _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 D 4 GOL H 1 301 1 GOL GOL . E 5 HOH H 1 401 39 HOH HOH . E 5 HOH H 2 402 26 HOH HOH . E 5 HOH H 3 403 27 HOH HOH . E 5 HOH H 4 404 53 HOH HOH . E 5 HOH H 5 405 141 HOH HOH . E 5 HOH H 6 406 99 HOH HOH . E 5 HOH H 7 407 84 HOH HOH . E 5 HOH H 8 408 58 HOH HOH . E 5 HOH H 9 409 23 HOH HOH . E 5 HOH H 10 410 25 HOH HOH . E 5 HOH H 11 411 61 HOH HOH . E 5 HOH H 12 412 36 HOH HOH . E 5 HOH H 13 413 20 HOH HOH . E 5 HOH H 14 414 55 HOH HOH . E 5 HOH H 15 415 9 HOH HOH . E 5 HOH H 16 416 57 HOH HOH . E 5 HOH H 17 417 14 HOH HOH . E 5 HOH H 18 418 18 HOH HOH . E 5 HOH H 19 419 10 HOH HOH . E 5 HOH H 20 420 69 HOH HOH . E 5 HOH H 21 421 24 HOH HOH . E 5 HOH H 22 422 116 HOH HOH . E 5 HOH H 23 423 129 HOH HOH . E 5 HOH H 24 424 73 HOH HOH . E 5 HOH H 25 425 110 HOH HOH . E 5 HOH H 26 426 70 HOH HOH . E 5 HOH H 27 427 92 HOH HOH . E 5 HOH H 28 428 71 HOH HOH . E 5 HOH H 29 429 77 HOH HOH . E 5 HOH H 30 430 107 HOH HOH . E 5 HOH H 31 431 104 HOH HOH . E 5 HOH H 32 432 35 HOH HOH . E 5 HOH H 33 433 117 HOH HOH . E 5 HOH H 34 434 12 HOH HOH . E 5 HOH H 35 435 85 HOH HOH . E 5 HOH H 36 436 13 HOH HOH . E 5 HOH H 37 437 37 HOH HOH . E 5 HOH H 38 438 42 HOH HOH . E 5 HOH H 39 439 106 HOH HOH . E 5 HOH H 40 440 11 HOH HOH . E 5 HOH H 41 441 60 HOH HOH . E 5 HOH H 42 442 8 HOH HOH . E 5 HOH H 43 443 76 HOH HOH . E 5 HOH H 44 444 82 HOH HOH . E 5 HOH H 45 445 93 HOH HOH . E 5 HOH H 46 446 154 HOH HOH . E 5 HOH H 47 447 86 HOH HOH . E 5 HOH H 48 448 148 HOH HOH . E 5 HOH H 49 449 137 HOH HOH . E 5 HOH H 50 450 139 HOH HOH . E 5 HOH H 51 451 17 HOH HOH . E 5 HOH H 52 452 134 HOH HOH . E 5 HOH H 53 453 67 HOH HOH . E 5 HOH H 54 454 68 HOH HOH . E 5 HOH H 55 455 146 HOH HOH . E 5 HOH H 56 456 66 HOH HOH . E 5 HOH H 57 457 56 HOH HOH . E 5 HOH H 58 458 50 HOH HOH . E 5 HOH H 59 459 156 HOH HOH . E 5 HOH H 60 460 109 HOH HOH . E 5 HOH H 61 461 65 HOH HOH . E 5 HOH H 62 462 15 HOH HOH . E 5 HOH H 63 463 118 HOH HOH . E 5 HOH H 64 464 28 HOH HOH . E 5 HOH H 65 465 112 HOH HOH . E 5 HOH H 66 466 115 HOH HOH . E 5 HOH H 67 467 150 HOH HOH . E 5 HOH H 68 468 119 HOH HOH . E 5 HOH H 69 469 88 HOH HOH . E 5 HOH H 70 470 133 HOH HOH . E 5 HOH H 71 471 135 HOH HOH . E 5 HOH H 72 472 90 HOH HOH . E 5 HOH H 73 473 140 HOH HOH . E 5 HOH H 74 474 159 HOH HOH . E 5 HOH H 75 475 81 HOH HOH . E 5 HOH H 76 476 2 HOH HOH . E 5 HOH H 77 477 123 HOH HOH . E 5 HOH H 78 478 158 HOH HOH . E 5 HOH H 79 479 136 HOH HOH . E 5 HOH H 80 480 152 HOH HOH . E 5 HOH H 81 481 157 HOH HOH . E 5 HOH H 82 482 105 HOH HOH . E 5 HOH H 83 483 101 HOH HOH . E 5 HOH H 84 484 122 HOH HOH . E 5 HOH H 85 485 87 HOH HOH . E 5 HOH H 86 486 111 HOH HOH . E 5 HOH H 87 487 83 HOH HOH . E 5 HOH H 88 488 149 HOH HOH . E 5 HOH H 89 489 160 HOH HOH . E 5 HOH H 90 490 124 HOH HOH . E 5 HOH H 91 491 114 HOH HOH . E 5 HOH H 92 492 127 HOH HOH . E 5 HOH H 93 493 144 HOH HOH . F 5 HOH L 1 301 52 HOH HOH . F 5 HOH L 2 302 89 HOH HOH . F 5 HOH L 3 303 41 HOH HOH . F 5 HOH L 4 304 7 HOH HOH . F 5 HOH L 5 305 16 HOH HOH . F 5 HOH L 6 306 130 HOH HOH . F 5 HOH L 7 307 29 HOH HOH . F 5 HOH L 8 308 80 HOH HOH . F 5 HOH L 9 309 74 HOH HOH . F 5 HOH L 10 310 34 HOH HOH . F 5 HOH L 11 311 64 HOH HOH . F 5 HOH L 12 312 19 HOH HOH . F 5 HOH L 13 313 30 HOH HOH . F 5 HOH L 14 314 103 HOH HOH . F 5 HOH L 15 315 33 HOH HOH . F 5 HOH L 16 316 62 HOH HOH . F 5 HOH L 17 317 63 HOH HOH . F 5 HOH L 18 318 4 HOH HOH . F 5 HOH L 19 319 59 HOH HOH . F 5 HOH L 20 320 100 HOH HOH . F 5 HOH L 21 321 48 HOH HOH . F 5 HOH L 22 322 97 HOH HOH . F 5 HOH L 23 323 94 HOH HOH . F 5 HOH L 24 324 138 HOH HOH . F 5 HOH L 25 325 151 HOH HOH . F 5 HOH L 26 326 3 HOH HOH . F 5 HOH L 27 327 79 HOH HOH . F 5 HOH L 28 328 43 HOH HOH . F 5 HOH L 29 329 46 HOH HOH . F 5 HOH L 30 330 91 HOH HOH . F 5 HOH L 31 331 45 HOH HOH . F 5 HOH L 32 332 40 HOH HOH . F 5 HOH L 33 333 47 HOH HOH . F 5 HOH L 34 334 31 HOH HOH . F 5 HOH L 35 335 32 HOH HOH . F 5 HOH L 36 336 38 HOH HOH . F 5 HOH L 37 337 121 HOH HOH . F 5 HOH L 38 338 51 HOH HOH . F 5 HOH L 39 339 98 HOH HOH . F 5 HOH L 40 340 108 HOH HOH . F 5 HOH L 41 341 54 HOH HOH . F 5 HOH L 42 342 155 HOH HOH . F 5 HOH L 43 343 75 HOH HOH . F 5 HOH L 44 344 44 HOH HOH . F 5 HOH L 45 345 132 HOH HOH . F 5 HOH L 46 346 102 HOH HOH . F 5 HOH L 47 347 145 HOH HOH . F 5 HOH L 48 348 78 HOH HOH . F 5 HOH L 49 349 142 HOH HOH . F 5 HOH L 50 350 49 HOH HOH . F 5 HOH L 51 351 96 HOH HOH . F 5 HOH L 52 352 131 HOH HOH . F 5 HOH L 53 353 6 HOH HOH . F 5 HOH L 54 354 5 HOH HOH . F 5 HOH L 55 355 21 HOH HOH . F 5 HOH L 56 356 72 HOH HOH . F 5 HOH L 57 357 126 HOH HOH . F 5 HOH L 58 358 128 HOH HOH . F 5 HOH L 59 359 22 HOH HOH . F 5 HOH L 60 360 153 HOH HOH . F 5 HOH L 61 361 120 HOH HOH . F 5 HOH L 62 362 125 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 . . . D 4 -12.651 34.466 -18.65 1 45.34 ? C1 GOL 301 H 1 HETATM 2 O O1 GOL . . . D 4 -12.957 33.218 -18.064 1 46.67 ? O1 GOL 301 H 1 HETATM 3 C C2 GOL . . . D 4 -11.672 35.229 -17.762 1 46.15 ? C2 GOL 301 H 1 HETATM 4 O O2 GOL . . . D 4 -10.378 34.677 -17.906 1 38.15 ? O2 GOL 301 H 1 HETATM 5 C C3 GOL . . . D 4 -11.658 36.693 -18.194 1 49.11 ? C3 GOL 301 H 1 HETATM 6 O O3 GOL . . . D 4 -11.327 37.537 -17.109 1 45.03 ? O3 GOL 301 H 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #