data_3LXB # _model_server_result.job_id S_wxDNryCxTabXn0i6sf4w _model_server_result.datetime_utc '2024-11-26 18:07:15' _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 3lxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":801}' # _entry.id 3LXB # _exptl.entry_id 3LXB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 6 _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 3LXB _cell.length_a 59.79 _cell.length_b 106.996 _cell.length_c 181.598 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LXB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,G,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 H N N ? 5 K N N ? 5 L N N ? 5 M N N ? 5 N 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 . O3 HO3 . sing 4 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . 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 D 692 NAG 2 n C NAG 2 C 2 NAG D 693 NAG 2 n C BMA 3 C 3 BMA D 694 BMA 2 n C MAN 4 C 4 MAN D 695 MAN 3 n D NAG 1 D 1 NAG E 715 NAG 3 n D NAG 2 D 2 NAG E 716 NAG 2 n E NAG 1 E 1 NAG G 692 NAG 2 n E NAG 2 E 2 NAG G 693 NAG 2 n E BMA 3 E 3 BMA G 694 BMA 2 n E MAN 4 E 4 MAN G 695 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 21 A CYS 52 1_555 A SG CYS 63 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 25 A CYS 56 1_555 A SG CYS 32 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 A SG CYS 111 A CYS 142 1_555 A SG CYS 141 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 A SG CYS 171 A CYS 202 1_555 A SG CYS 192 A CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 347 A CYS 378 1_555 A SG CYS 351 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 B SG CYS 21 B CYS 52 1_555 B SG CYS 63 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 25 B CYS 56 1_555 B SG CYS 32 B CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf8 B SG CYS 111 B CYS 142 1_555 B SG CYS 141 B CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 B SG CYS 171 B CYS 202 1_555 B SG CYS 192 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 B SG CYS 347 B CYS 378 1_555 B SG CYS 351 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? covale ? covale1 A ND2 ASN 108 A ASN 139 1_555 F C1 NAG . A NAG 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 161 A ASN 192 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 184 A ASN 215 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B ND2 ASN 108 B ASN 139 1_555 I C1 NAG . B NAG 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 B ND2 ASN 161 B ASN 192 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 B ND2 ASN 184 B ASN 215 1_555 J C1 NAG . B NAG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? # _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 3LXB _atom_sites.fract_transf_matrix[1][1] 0.016725 _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] 0.009346 _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] 0.005507 _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 F 4 NAG A 1 639 639 NAG NAG . G 5 GOL A 1 802 802 GOL GOL . H 5 GOL A 1 803 803 GOL GOL . I 4 NAG B 1 639 639 NAG NAG . J 4 NAG B 1 715 715 NAG NAG . K 5 GOL B 1 801 801 GOL GOL . L 5 GOL B 1 804 804 GOL GOL . M 5 GOL B 1 811 811 GOL GOL . N 5 GOL B 1 812 812 GOL GOL . O 6 HOH A 1 3 3 HOH HOH . O 6 HOH A 2 6 6 HOH HOH . O 6 HOH A 3 7 7 HOH HOH . O 6 HOH A 4 12 12 HOH HOH . O 6 HOH A 5 17 17 HOH HOH . O 6 HOH A 6 18 18 HOH HOH . O 6 HOH A 7 20 20 HOH HOH . O 6 HOH A 8 26 26 HOH HOH . O 6 HOH A 9 27 27 HOH HOH . O 6 HOH A 10 28 28 HOH HOH . O 6 HOH A 11 436 33 HOH HOH . O 6 HOH A 12 437 44 HOH HOH . O 6 HOH A 13 438 46 HOH HOH . O 6 HOH A 14 439 50 HOH HOH . O 6 HOH A 15 440 51 HOH HOH . O 6 HOH A 16 441 52 HOH HOH . O 6 HOH A 17 442 106 HOH HOH . O 6 HOH A 18 443 110 HOH HOH . O 6 HOH A 19 444 111 HOH HOH . O 6 HOH A 20 445 122 HOH HOH . O 6 HOH A 21 446 123 HOH HOH . O 6 HOH A 22 447 125 HOH HOH . O 6 HOH A 23 448 126 HOH HOH . O 6 HOH A 24 449 137 HOH HOH . O 6 HOH A 25 450 148 HOH HOH . O 6 HOH A 26 451 180 HOH HOH . O 6 HOH A 27 452 452 HOH HOH . O 6 HOH A 28 453 200 HOH HOH . O 6 HOH A 29 454 454 HOH HOH . O 6 HOH A 30 455 201 HOH HOH . O 6 HOH A 31 456 205 HOH HOH . O 6 HOH A 32 457 208 HOH HOH . O 6 HOH A 33 458 212 HOH HOH . O 6 HOH A 34 459 220 HOH HOH . O 6 HOH A 35 460 221 HOH HOH . O 6 HOH A 36 461 225 HOH HOH . O 6 HOH A 37 462 227 HOH HOH . O 6 HOH A 38 463 228 HOH HOH . O 6 HOH A 39 464 261 HOH HOH . O 6 HOH A 40 465 268 HOH HOH . O 6 HOH A 41 466 277 HOH HOH . O 6 HOH A 42 467 278 HOH HOH . O 6 HOH A 43 468 302 HOH HOH . O 6 HOH A 44 469 311 HOH HOH . O 6 HOH A 45 470 316 HOH HOH . O 6 HOH A 46 471 333 HOH HOH . O 6 HOH A 47 472 340 HOH HOH . O 6 HOH A 48 473 341 HOH HOH . O 6 HOH A 49 474 358 HOH HOH . O 6 HOH A 50 475 363 HOH HOH . O 6 HOH A 51 476 387 HOH HOH . O 6 HOH A 52 477 433 HOH HOH . O 6 HOH A 53 525 525 HOH HOH . O 6 HOH A 54 538 538 HOH HOH . O 6 HOH A 55 575 575 HOH HOH . O 6 HOH A 56 641 641 HOH HOH . O 6 HOH A 57 711 711 HOH HOH . O 6 HOH A 58 723 723 HOH HOH . O 6 HOH A 59 886 886 HOH HOH . P 6 HOH B 1 9 9 HOH HOH . P 6 HOH B 2 10 10 HOH HOH . P 6 HOH B 3 11 11 HOH HOH . P 6 HOH B 4 13 13 HOH HOH . P 6 HOH B 5 19 19 HOH HOH . P 6 HOH B 6 23 23 HOH HOH . P 6 HOH B 7 24 24 HOH HOH . P 6 HOH B 8 25 25 HOH HOH . P 6 HOH B 9 29 29 HOH HOH . P 6 HOH B 10 30 30 HOH HOH . P 6 HOH B 11 436 32 HOH HOH . P 6 HOH B 12 437 34 HOH HOH . P 6 HOH B 13 438 36 HOH HOH . P 6 HOH B 14 439 439 HOH HOH . P 6 HOH B 15 440 440 HOH HOH . P 6 HOH B 16 441 37 HOH HOH . P 6 HOH B 17 442 39 HOH HOH . P 6 HOH B 18 443 40 HOH HOH . P 6 HOH B 19 444 41 HOH HOH . P 6 HOH B 20 445 42 HOH HOH . P 6 HOH B 21 446 43 HOH HOH . P 6 HOH B 22 447 45 HOH HOH . P 6 HOH B 23 448 47 HOH HOH . P 6 HOH B 24 449 48 HOH HOH . P 6 HOH B 25 450 49 HOH HOH . P 6 HOH B 26 451 451 HOH HOH . P 6 HOH B 27 452 61 HOH HOH . P 6 HOH B 28 453 97 HOH HOH . P 6 HOH B 29 454 99 HOH HOH . P 6 HOH B 30 455 134 HOH HOH . P 6 HOH B 31 456 158 HOH HOH . P 6 HOH B 32 457 166 HOH HOH . P 6 HOH B 33 458 167 HOH HOH . P 6 HOH B 34 459 185 HOH HOH . P 6 HOH B 35 460 189 HOH HOH . P 6 HOH B 36 461 197 HOH HOH . P 6 HOH B 37 462 233 HOH HOH . P 6 HOH B 38 463 246 HOH HOH . P 6 HOH B 39 464 248 HOH HOH . P 6 HOH B 40 465 249 HOH HOH . P 6 HOH B 41 466 255 HOH HOH . P 6 HOH B 42 467 260 HOH HOH . P 6 HOH B 43 468 279 HOH HOH . P 6 HOH B 44 469 282 HOH HOH . P 6 HOH B 45 470 297 HOH HOH . P 6 HOH B 46 471 324 HOH HOH . P 6 HOH B 47 472 342 HOH HOH . P 6 HOH B 48 473 351 HOH HOH . P 6 HOH B 49 474 357 HOH HOH . P 6 HOH B 50 475 364 HOH HOH . P 6 HOH B 51 476 368 HOH HOH . P 6 HOH B 52 477 369 HOH HOH . P 6 HOH B 53 478 391 HOH HOH . P 6 HOH B 54 479 408 HOH HOH . P 6 HOH B 55 480 420 HOH HOH . P 6 HOH B 56 481 423 HOH HOH . P 6 HOH B 57 482 431 HOH HOH . P 6 HOH B 58 483 483 HOH HOH . P 6 HOH B 59 487 487 HOH HOH . P 6 HOH B 60 497 497 HOH HOH . P 6 HOH B 61 504 504 HOH HOH . P 6 HOH B 62 512 512 HOH HOH . P 6 HOH B 63 558 558 HOH HOH . P 6 HOH B 64 567 567 HOH HOH . P 6 HOH B 65 578 578 HOH HOH . P 6 HOH B 66 581 581 HOH HOH . P 6 HOH B 67 598 598 HOH HOH . P 6 HOH B 68 613 613 HOH HOH . P 6 HOH B 69 630 630 HOH HOH . P 6 HOH B 70 666 666 HOH HOH . P 6 HOH B 71 799 799 HOH HOH . P 6 HOH B 72 868 868 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 . . . K 5 11.177 5.384 62.886 1 65.3 ? C1 GOL 801 B 1 HETATM 2 O O1 GOL . . . K 5 10.287 6.24 62.205 1 63.21 ? O1 GOL 801 B 1 HETATM 3 C C2 GOL . . . K 5 12.614 5.757 62.53 1 67.42 ? C2 GOL 801 B 1 HETATM 4 O O2 GOL . . . K 5 12.733 7.162 62.416 1 64.9 ? O2 GOL 801 B 1 HETATM 5 C C3 GOL . . . K 5 13.569 5.203 63.591 1 67.84 ? C3 GOL 801 B 1 HETATM 6 O O3 GOL . . . K 5 14.784 5.923 63.594 1 67.24 ? O3 GOL 801 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 508 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #