data_3VAG # _model_server_result.job_id iGSIJtz6TdkhlZ2Y-BP-rw _model_server_result.datetime_utc '2024-11-04 20:34:28' _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 3vag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":408}' # _entry.id 3VAG # _exptl.entry_id 3VAG _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 125.35 _cell.angle_gamma 90 _cell.entry_id 3VAG _cell.length_a 166.825 _cell.length_b 37.499 _cell.length_c 100.925 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VAG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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,Q,R,S,T,U,V,W,X _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 L N N ? 5 T N N # 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 covale ? covale1 C O3' DC 2 P DC 2 1_555 C P BRU 3 P BRU 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale2 C O3' BRU 3 P BRU 3 1_555 C P DU 4 P DU 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? covale ? covale3 D O3' DC 2 E DC 3 1_555 D P BRU 3 E BRU 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale4 D O3' BRU 3 E BRU 4 1_555 D P DU 4 E DU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? # _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 384 n n C1 C2 GOL sing 385 n n C1 H11 GOL sing 386 n n C1 H12 GOL sing 387 n n O1 HO1 GOL sing 388 n n C2 O2 GOL sing 389 n n C2 C3 GOL sing 390 n n C2 H2 GOL sing 391 n n O2 HO2 GOL sing 392 n n C3 O3 GOL sing 393 n n C3 H31 GOL sing 394 n n C3 H32 GOL sing 395 n n O3 HO3 GOL sing 396 n n # _atom_sites.entry_id 3VAG _atom_sites.fract_transf_matrix[1][1] 0.005994 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004252 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026667 _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] 0.012148 _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 3 DIO A 1 401 6 DIO DIO . F 3 DIO A 1 402 8 DIO DIO . G 3 DIO A 1 403 9 DIO DIO . H 4 SO4 A 1 404 5 SO4 SO4 . I 4 SO4 A 1 405 7 SO4 SO4 . J 4 SO4 A 1 406 8 SO4 SO4 . K 4 SO4 A 1 407 11 SO4 SO4 . L 5 GOL A 1 408 1 GOL GOL . M 3 DIO B 1 401 1 DIO DIO . N 3 DIO B 1 402 4 DIO DIO . O 3 DIO B 1 403 7 DIO DIO . P 6 CPQ B 1 404 101 CPQ CPQ . Q 4 SO4 B 1 405 1 SO4 SO4 . R 4 SO4 B 1 406 6 SO4 SO4 . S 4 SO4 B 1 407 9 SO4 SO4 . T 5 GOL B 1 408 2 GOL GOL . U 7 HOH A 1 501 1 HOH HOH . U 7 HOH A 2 502 2 HOH HOH . U 7 HOH A 3 503 7 HOH HOH . U 7 HOH A 4 504 9 HOH HOH . U 7 HOH A 5 505 10 HOH HOH . U 7 HOH A 6 506 11 HOH HOH . U 7 HOH A 7 507 14 HOH HOH . U 7 HOH A 8 508 15 HOH HOH . U 7 HOH A 9 509 16 HOH HOH . U 7 HOH A 10 510 20 HOH HOH . U 7 HOH A 11 511 22 HOH HOH . U 7 HOH A 12 512 26 HOH HOH . U 7 HOH A 13 513 27 HOH HOH . U 7 HOH A 14 514 34 HOH HOH . U 7 HOH A 15 515 39 HOH HOH . U 7 HOH A 16 516 40 HOH HOH . U 7 HOH A 17 517 41 HOH HOH . U 7 HOH A 18 518 43 HOH HOH . U 7 HOH A 19 519 45 HOH HOH . U 7 HOH A 20 520 53 HOH HOH . U 7 HOH A 21 521 54 HOH HOH . U 7 HOH A 22 522 55 HOH HOH . U 7 HOH A 23 523 57 HOH HOH . U 7 HOH A 24 524 58 HOH HOH . U 7 HOH A 25 525 60 HOH HOH . U 7 HOH A 26 526 61 HOH HOH . U 7 HOH A 27 527 65 HOH HOH . U 7 HOH A 28 528 67 HOH HOH . U 7 HOH A 29 529 68 HOH HOH . U 7 HOH A 30 530 69 HOH HOH . U 7 HOH A 31 531 70 HOH HOH . U 7 HOH A 32 532 72 HOH HOH . U 7 HOH A 33 533 76 HOH HOH . U 7 HOH A 34 534 77 HOH HOH . U 7 HOH A 35 535 78 HOH HOH . U 7 HOH A 36 536 79 HOH HOH . U 7 HOH A 37 537 80 HOH HOH . U 7 HOH A 38 538 83 HOH HOH . U 7 HOH A 39 539 88 HOH HOH . U 7 HOH A 40 540 91 HOH HOH . U 7 HOH A 41 541 92 HOH HOH . U 7 HOH A 42 542 93 HOH HOH . U 7 HOH A 43 543 94 HOH HOH . U 7 HOH A 44 544 95 HOH HOH . U 7 HOH A 45 545 96 HOH HOH . U 7 HOH A 46 546 98 HOH HOH . U 7 HOH A 47 547 99 HOH HOH . U 7 HOH A 48 548 101 HOH HOH . U 7 HOH A 49 549 104 HOH HOH . U 7 HOH A 50 550 105 HOH HOH . U 7 HOH A 51 551 106 HOH HOH . U 7 HOH A 52 552 108 HOH HOH . U 7 HOH A 53 553 111 HOH HOH . U 7 HOH A 54 554 115 HOH HOH . U 7 HOH A 55 555 116 HOH HOH . U 7 HOH A 56 556 122 HOH HOH . U 7 HOH A 57 557 124 HOH HOH . U 7 HOH A 58 558 126 HOH HOH . U 7 HOH A 59 559 128 HOH HOH . U 7 HOH A 60 560 130 HOH HOH . U 7 HOH A 61 561 133 HOH HOH . U 7 HOH A 62 562 137 HOH HOH . U 7 HOH A 63 563 138 HOH HOH . U 7 HOH A 64 564 139 HOH HOH . U 7 HOH A 65 565 141 HOH HOH . U 7 HOH A 66 566 145 HOH HOH . U 7 HOH A 67 567 146 HOH HOH . U 7 HOH A 68 568 147 HOH HOH . U 7 HOH A 69 569 148 HOH HOH . U 7 HOH A 70 570 149 HOH HOH . U 7 HOH A 71 571 150 HOH HOH . U 7 HOH A 72 572 49 HOH HOH . V 7 HOH B 1 501 5 HOH HOH . V 7 HOH B 2 502 6 HOH HOH . V 7 HOH B 3 503 8 HOH HOH . V 7 HOH B 4 504 12 HOH HOH . V 7 HOH B 5 505 17 HOH HOH . V 7 HOH B 6 506 18 HOH HOH . V 7 HOH B 7 507 19 HOH HOH . V 7 HOH B 8 508 21 HOH HOH . V 7 HOH B 9 509 23 HOH HOH . V 7 HOH B 10 510 24 HOH HOH . V 7 HOH B 11 511 25 HOH HOH . V 7 HOH B 12 512 28 HOH HOH . V 7 HOH B 13 513 29 HOH HOH . V 7 HOH B 14 514 30 HOH HOH . V 7 HOH B 15 515 31 HOH HOH . V 7 HOH B 16 516 32 HOH HOH . V 7 HOH B 17 517 33 HOH HOH . V 7 HOH B 18 518 35 HOH HOH . V 7 HOH B 19 519 36 HOH HOH . V 7 HOH B 20 520 42 HOH HOH . V 7 HOH B 21 521 48 HOH HOH . V 7 HOH B 22 522 51 HOH HOH . V 7 HOH B 23 523 52 HOH HOH . V 7 HOH B 24 524 56 HOH HOH . V 7 HOH B 25 525 62 HOH HOH . V 7 HOH B 26 526 63 HOH HOH . V 7 HOH B 27 527 66 HOH HOH . V 7 HOH B 28 528 71 HOH HOH . V 7 HOH B 29 529 73 HOH HOH . V 7 HOH B 30 530 75 HOH HOH . V 7 HOH B 31 531 81 HOH HOH . V 7 HOH B 32 532 82 HOH HOH . V 7 HOH B 33 533 84 HOH HOH . V 7 HOH B 34 534 85 HOH HOH . V 7 HOH B 35 535 86 HOH HOH . V 7 HOH B 36 536 89 HOH HOH . V 7 HOH B 37 537 97 HOH HOH . V 7 HOH B 38 538 102 HOH HOH . V 7 HOH B 39 539 107 HOH HOH . V 7 HOH B 40 540 110 HOH HOH . V 7 HOH B 41 541 112 HOH HOH . V 7 HOH B 42 542 113 HOH HOH . V 7 HOH B 43 543 117 HOH HOH . V 7 HOH B 44 544 118 HOH HOH . V 7 HOH B 45 545 119 HOH HOH . V 7 HOH B 46 546 121 HOH HOH . V 7 HOH B 47 547 127 HOH HOH . V 7 HOH B 48 548 129 HOH HOH . V 7 HOH B 49 549 131 HOH HOH . V 7 HOH B 50 550 132 HOH HOH . V 7 HOH B 51 551 134 HOH HOH . V 7 HOH B 52 552 136 HOH HOH . V 7 HOH B 53 553 140 HOH HOH . V 7 HOH B 54 554 142 HOH HOH . V 7 HOH B 55 555 143 HOH HOH . V 7 HOH B 56 556 144 HOH HOH . V 7 HOH B 57 557 151 HOH HOH . V 7 HOH B 58 558 152 HOH HOH . V 7 HOH B 59 559 153 HOH HOH . V 7 HOH B 60 560 154 HOH HOH . V 7 HOH B 61 561 155 HOH HOH . V 7 HOH B 62 562 156 HOH HOH . W 7 HOH P 1 101 3 HOH HOH . W 7 HOH P 2 102 4 HOH HOH . W 7 HOH P 3 103 13 HOH HOH . W 7 HOH P 4 104 38 HOH HOH . W 7 HOH P 5 105 47 HOH HOH . W 7 HOH P 6 106 50 HOH HOH . W 7 HOH P 7 107 100 HOH HOH . W 7 HOH P 8 108 109 HOH HOH . W 7 HOH P 9 109 114 HOH HOH . W 7 HOH P 10 110 120 HOH HOH . W 7 HOH P 11 111 123 HOH HOH . W 7 HOH P 12 112 125 HOH HOH . W 7 HOH P 13 113 135 HOH HOH . X 7 HOH E 1 101 37 HOH HOH . X 7 HOH E 2 102 44 HOH HOH . X 7 HOH E 3 103 46 HOH HOH . X 7 HOH E 4 104 59 HOH HOH . X 7 HOH E 5 105 64 HOH HOH . X 7 HOH E 6 106 74 HOH HOH . X 7 HOH E 7 107 87 HOH HOH . X 7 HOH E 8 108 90 HOH HOH . X 7 HOH E 9 109 103 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 . . . L 5 -1.922 -22.503 15.902 1 75.37 ? C1 GOL 408 A 1 HETATM 2 O O1 GOL . . . L 5 -3.213 -22.642 16.456 1 75.47 ? O1 GOL 408 A 1 HETATM 3 C C2 GOL . . . L 5 -0.892 -22.343 17.016 1 75.33 ? C2 GOL 408 A 1 HETATM 4 O O2 GOL . . . L 5 0.091 -21.42 16.616 1 75.17 ? O2 GOL 408 A 1 HETATM 5 C C3 GOL . . . L 5 -0.234 -23.673 17.373 1 75.54 ? C3 GOL 408 A 1 HETATM 6 O O3 GOL . . . L 5 -0.002 -23.724 18.763 1 75.55 ? O3 GOL 408 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #