data_5YVD # _model_server_result.job_id zWjLpxcdGeXUYA2L8REveg _model_server_result.datetime_utc '2024-10-19 16:23:33' _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 5yvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5YVD # _exptl.entry_id 5YVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method nat _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 90 _cell.angle_gamma 120 _cell.entry_id 5YVD _cell.length_a 145.643 _cell.length_b 145.643 _cell.length_c 96.653 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1,2,3 B,D,F 1 4,5,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_765 -y+2,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 218.4645 126.130538 0 3 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 252.261076 0 4 'crystal symmetry operation' 7_444 x-2/3,y-1/3,z-1/3 1 0 0 0 1 0 0 0 1 -72.8215 -42.043513 -32.217667 5 'crystal symmetry operation' 8_754 -y+7/3,x-y+2/3,z-1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 291.286 84.087025 -32.217667 6 'crystal symmetry operation' 9_674 -x+y+4/3,-x+8/3,z-1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 336.348101 -32.217667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _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 5YVD _atom_sites.fract_transf_matrix[1][1] 0.006866 _atom_sites.fract_transf_matrix[1][2] 0.003964 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007928 _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] 0.010346 _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 2 GOL A 1 401 1411 GOL GOL . D 2 GOL B 1 401 1411 GOL GOL . E 3 HOH A 1 501 37 HOH HOH . E 3 HOH A 2 502 104 HOH HOH . E 3 HOH A 3 503 62 HOH HOH . E 3 HOH A 4 504 26 HOH HOH . E 3 HOH A 5 505 47 HOH HOH . E 3 HOH A 6 506 22 HOH HOH . E 3 HOH A 7 507 75 HOH HOH . E 3 HOH A 8 508 34 HOH HOH . E 3 HOH A 9 509 7 HOH HOH . E 3 HOH A 10 510 11 HOH HOH . E 3 HOH A 11 511 92 HOH HOH . E 3 HOH A 12 512 114 HOH HOH . E 3 HOH A 13 513 110 HOH HOH . E 3 HOH A 14 514 23 HOH HOH . E 3 HOH A 15 515 38 HOH HOH . E 3 HOH A 16 516 60 HOH HOH . E 3 HOH A 17 517 46 HOH HOH . E 3 HOH A 18 518 71 HOH HOH . E 3 HOH A 19 519 20 HOH HOH . E 3 HOH A 20 520 5 HOH HOH . E 3 HOH A 21 521 28 HOH HOH . E 3 HOH A 22 522 17 HOH HOH . E 3 HOH A 23 523 64 HOH HOH . E 3 HOH A 24 524 9 HOH HOH . E 3 HOH A 25 525 50 HOH HOH . E 3 HOH A 26 526 24 HOH HOH . E 3 HOH A 27 527 49 HOH HOH . E 3 HOH A 28 528 122 HOH HOH . E 3 HOH A 29 529 52 HOH HOH . E 3 HOH A 30 530 84 HOH HOH . E 3 HOH A 31 531 100 HOH HOH . E 3 HOH A 32 532 93 HOH HOH . E 3 HOH A 33 533 81 HOH HOH . E 3 HOH A 34 534 127 HOH HOH . E 3 HOH A 35 535 54 HOH HOH . E 3 HOH A 36 536 68 HOH HOH . E 3 HOH A 37 537 128 HOH HOH . E 3 HOH A 38 538 70 HOH HOH . E 3 HOH A 39 539 25 HOH HOH . E 3 HOH A 40 540 74 HOH HOH . E 3 HOH A 41 541 35 HOH HOH . E 3 HOH A 42 542 86 HOH HOH . E 3 HOH A 43 543 131 HOH HOH . E 3 HOH A 44 544 119 HOH HOH . E 3 HOH A 45 545 123 HOH HOH . E 3 HOH A 46 546 33 HOH HOH . E 3 HOH A 47 547 132 HOH HOH . E 3 HOH A 48 548 53 HOH HOH . E 3 HOH A 49 549 58 HOH HOH . E 3 HOH A 50 550 121 HOH HOH . E 3 HOH A 51 551 67 HOH HOH . E 3 HOH A 52 552 125 HOH HOH . E 3 HOH A 53 553 106 HOH HOH . E 3 HOH A 54 554 107 HOH HOH . E 3 HOH A 55 555 87 HOH HOH . E 3 HOH A 56 556 27 HOH HOH . E 3 HOH A 57 557 113 HOH HOH . E 3 HOH A 58 558 80 HOH HOH . E 3 HOH A 59 559 102 HOH HOH . E 3 HOH A 60 560 42 HOH HOH . E 3 HOH A 61 561 129 HOH HOH . E 3 HOH A 62 562 79 HOH HOH . F 3 HOH B 1 501 72 HOH HOH . F 3 HOH B 2 502 29 HOH HOH . F 3 HOH B 3 503 96 HOH HOH . F 3 HOH B 4 504 19 HOH HOH . F 3 HOH B 5 505 97 HOH HOH . F 3 HOH B 6 506 111 HOH HOH . F 3 HOH B 7 507 31 HOH HOH . F 3 HOH B 8 508 69 HOH HOH . F 3 HOH B 9 509 32 HOH HOH . F 3 HOH B 10 510 108 HOH HOH . F 3 HOH B 11 511 12 HOH HOH . F 3 HOH B 12 512 16 HOH HOH . F 3 HOH B 13 513 51 HOH HOH . F 3 HOH B 14 514 14 HOH HOH . F 3 HOH B 15 515 4 HOH HOH . F 3 HOH B 16 516 43 HOH HOH . F 3 HOH B 17 517 134 HOH HOH . F 3 HOH B 18 518 57 HOH HOH . F 3 HOH B 19 519 95 HOH HOH . F 3 HOH B 20 520 78 HOH HOH . F 3 HOH B 21 521 112 HOH HOH . F 3 HOH B 22 522 21 HOH HOH . F 3 HOH B 23 523 103 HOH HOH . F 3 HOH B 24 524 56 HOH HOH . F 3 HOH B 25 525 59 HOH HOH . F 3 HOH B 26 526 83 HOH HOH . F 3 HOH B 27 527 41 HOH HOH . F 3 HOH B 28 528 40 HOH HOH . F 3 HOH B 29 529 66 HOH HOH . F 3 HOH B 30 530 124 HOH HOH . F 3 HOH B 31 531 63 HOH HOH . F 3 HOH B 32 532 15 HOH HOH . F 3 HOH B 33 533 30 HOH HOH . F 3 HOH B 34 534 73 HOH HOH . F 3 HOH B 35 535 44 HOH HOH . F 3 HOH B 36 536 98 HOH HOH . F 3 HOH B 37 537 82 HOH HOH . F 3 HOH B 38 538 91 HOH HOH . F 3 HOH B 39 539 61 HOH HOH . F 3 HOH B 40 540 109 HOH HOH . F 3 HOH B 41 541 77 HOH HOH . F 3 HOH B 42 542 99 HOH HOH . F 3 HOH B 43 543 3 HOH HOH . F 3 HOH B 44 544 126 HOH HOH . F 3 HOH B 45 545 133 HOH HOH . F 3 HOH B 46 546 120 HOH HOH . F 3 HOH B 47 547 130 HOH HOH . F 3 HOH B 48 548 65 HOH HOH . F 3 HOH B 49 549 18 HOH HOH . F 3 HOH B 50 550 115 HOH HOH . F 3 HOH B 51 551 48 HOH HOH . F 3 HOH B 52 552 13 HOH HOH . F 3 HOH B 53 553 117 HOH HOH . F 3 HOH B 54 554 76 HOH HOH . F 3 HOH B 55 555 55 HOH HOH . F 3 HOH B 56 556 105 HOH HOH . F 3 HOH B 57 557 101 HOH HOH . F 3 HOH B 58 558 36 HOH HOH . F 3 HOH B 59 559 85 HOH HOH . F 3 HOH B 60 560 45 HOH HOH . F 3 HOH B 61 561 8 HOH HOH . F 3 HOH B 62 562 90 HOH HOH . F 3 HOH B 63 563 88 HOH HOH . F 3 HOH B 64 564 116 HOH HOH . F 3 HOH B 65 565 118 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 2 114.767 163.53 14.432 1 47.47 ? C1 GOL 401 B 1 HETATM 2 O O1 GOL . . . D 2 114.973 164.534 13.435 1 46.42 ? O1 GOL 401 B 1 HETATM 3 C C2 GOL . . . D 2 115.405 162.203 13.995 1 47.26 ? C2 GOL 401 B 1 HETATM 4 O O2 GOL . . . D 2 114.586 161.508 13.039 1 40.01 ? O2 GOL 401 B 1 HETATM 5 C C3 GOL . . . D 2 115.696 161.34 15.236 1 50.12 ? C3 GOL 401 B 1 HETATM 6 O O3 GOL . . . D 2 114.866 161.602 16.405 1 48.53 ? O3 GOL 401 B 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #