data_4IBD # _model_server_result.job_id W4oNIzfM91kul9DTqlSW0w _model_server_result.datetime_utc '2024-12-12 19:57:40' _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 4ibd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 4IBD # _exptl.entry_id 4IBD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 4IBD _cell.length_a 51.562 _cell.length_b 65.485 _cell.length_c 72.596 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IBD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H 1 1 B,E,F,G,I 2 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 ? 3 D N N ? 3 F 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 metalc ? metalc1 B O LEU 21 B LEU 232 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc2 B O GLY 23 B GLY 234 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc3 G MG MG . B MG 403 1_555 I O HOH . B HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc4 G MG MG . B MG 403 1_555 I O HOH . B HOH 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? # _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 179 n n C1 C2 GOL sing 180 n n C1 H11 GOL sing 181 n n C1 H12 GOL sing 182 n n O1 HO1 GOL sing 183 n n C2 O2 GOL sing 184 n n C2 C3 GOL sing 185 n n C2 H2 GOL sing 186 n n O2 HO2 GOL sing 187 n n C3 O3 GOL sing 188 n n C3 H31 GOL sing 189 n n C3 H32 GOL sing 190 n n O3 HO3 GOL sing 191 n n # _atom_sites.entry_id 4IBD _atom_sites.fract_transf_matrix[1][1] 0.019394 _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] 0.015271 _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] 0.013775 _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 1DL A 1 401 1 1DL 1DL . D 3 GOL A 1 402 1 GOL GOL . E 2 1DL B 1 401 1 1DL 1DL . F 3 GOL B 1 402 1 GOL GOL . G 4 MG B 1 403 1 MG MG . H 5 HOH A 1 501 1 HOH HOH . H 5 HOH A 2 502 6 HOH HOH . H 5 HOH A 3 503 8 HOH HOH . H 5 HOH A 4 504 10 HOH HOH . H 5 HOH A 5 505 12 HOH HOH . H 5 HOH A 6 506 13 HOH HOH . H 5 HOH A 7 507 14 HOH HOH . H 5 HOH A 8 508 15 HOH HOH . H 5 HOH A 9 509 16 HOH HOH . H 5 HOH A 10 510 18 HOH HOH . H 5 HOH A 11 511 20 HOH HOH . H 5 HOH A 12 512 21 HOH HOH . H 5 HOH A 13 513 22 HOH HOH . H 5 HOH A 14 514 26 HOH HOH . H 5 HOH A 15 515 29 HOH HOH . H 5 HOH A 16 516 32 HOH HOH . H 5 HOH A 17 517 33 HOH HOH . H 5 HOH A 18 518 35 HOH HOH . H 5 HOH A 19 519 37 HOH HOH . H 5 HOH A 20 520 41 HOH HOH . H 5 HOH A 21 521 42 HOH HOH . H 5 HOH A 22 522 45 HOH HOH . H 5 HOH A 23 523 46 HOH HOH . H 5 HOH A 24 524 47 HOH HOH . H 5 HOH A 25 525 48 HOH HOH . H 5 HOH A 26 526 49 HOH HOH . H 5 HOH A 27 527 50 HOH HOH . H 5 HOH A 28 528 53 HOH HOH . H 5 HOH A 29 529 54 HOH HOH . H 5 HOH A 30 530 57 HOH HOH . H 5 HOH A 31 531 62 HOH HOH . H 5 HOH A 32 532 63 HOH HOH . H 5 HOH A 33 533 64 HOH HOH . H 5 HOH A 34 534 66 HOH HOH . H 5 HOH A 35 535 68 HOH HOH . H 5 HOH A 36 536 70 HOH HOH . H 5 HOH A 37 537 71 HOH HOH . H 5 HOH A 38 538 72 HOH HOH . H 5 HOH A 39 539 75 HOH HOH . H 5 HOH A 40 540 83 HOH HOH . H 5 HOH A 41 541 85 HOH HOH . H 5 HOH A 42 542 86 HOH HOH . H 5 HOH A 43 543 88 HOH HOH . H 5 HOH A 44 544 91 HOH HOH . H 5 HOH A 45 545 93 HOH HOH . H 5 HOH A 46 546 94 HOH HOH . H 5 HOH A 47 547 96 HOH HOH . H 5 HOH A 48 548 98 HOH HOH . H 5 HOH A 49 549 99 HOH HOH . H 5 HOH A 50 550 105 HOH HOH . H 5 HOH A 51 551 108 HOH HOH . H 5 HOH A 52 552 110 HOH HOH . H 5 HOH A 53 553 114 HOH HOH . H 5 HOH A 54 554 115 HOH HOH . H 5 HOH A 55 555 118 HOH HOH . H 5 HOH A 56 556 121 HOH HOH . H 5 HOH A 57 557 125 HOH HOH . H 5 HOH A 58 558 128 HOH HOH . H 5 HOH A 59 559 129 HOH HOH . H 5 HOH A 60 560 130 HOH HOH . H 5 HOH A 61 561 131 HOH HOH . H 5 HOH A 62 562 133 HOH HOH . H 5 HOH A 63 563 135 HOH HOH . H 5 HOH A 64 564 138 HOH HOH . H 5 HOH A 65 565 141 HOH HOH . H 5 HOH A 66 566 143 HOH HOH . H 5 HOH A 67 567 144 HOH HOH . H 5 HOH A 68 568 148 HOH HOH . H 5 HOH A 69 569 154 HOH HOH . H 5 HOH A 70 570 155 HOH HOH . H 5 HOH A 71 571 158 HOH HOH . H 5 HOH A 72 572 159 HOH HOH . H 5 HOH A 73 573 160 HOH HOH . H 5 HOH A 74 574 161 HOH HOH . H 5 HOH A 75 575 162 HOH HOH . H 5 HOH A 76 576 163 HOH HOH . H 5 HOH A 77 577 165 HOH HOH . H 5 HOH A 78 578 166 HOH HOH . H 5 HOH A 79 579 168 HOH HOH . H 5 HOH A 80 580 169 HOH HOH . H 5 HOH A 81 581 170 HOH HOH . H 5 HOH A 82 582 171 HOH HOH . H 5 HOH A 83 583 173 HOH HOH . H 5 HOH A 84 584 177 HOH HOH . H 5 HOH A 85 585 178 HOH HOH . H 5 HOH A 86 586 2 HOH HOH . H 5 HOH A 87 587 3 HOH HOH . H 5 HOH A 88 588 4 HOH HOH . H 5 HOH A 89 589 5 HOH HOH . H 5 HOH A 90 590 7 HOH HOH . H 5 HOH A 91 591 9 HOH HOH . H 5 HOH A 92 592 11 HOH HOH . H 5 HOH A 93 593 13 HOH HOH . H 5 HOH A 94 594 14 HOH HOH . H 5 HOH A 95 595 16 HOH HOH . H 5 HOH A 96 596 17 HOH HOH . H 5 HOH A 97 597 18 HOH HOH . H 5 HOH A 98 598 22 HOH HOH . H 5 HOH A 99 599 24 HOH HOH . H 5 HOH A 100 600 25 HOH HOH . H 5 HOH A 101 601 28 HOH HOH . H 5 HOH A 102 602 29 HOH HOH . H 5 HOH A 103 603 30 HOH HOH . H 5 HOH A 104 604 31 HOH HOH . H 5 HOH A 105 605 33 HOH HOH . I 5 HOH B 1 501 2 HOH HOH . I 5 HOH B 2 502 3 HOH HOH . I 5 HOH B 3 503 4 HOH HOH . I 5 HOH B 4 504 5 HOH HOH . I 5 HOH B 5 505 7 HOH HOH . I 5 HOH B 6 506 9 HOH HOH . I 5 HOH B 7 507 11 HOH HOH . I 5 HOH B 8 508 17 HOH HOH . I 5 HOH B 9 509 19 HOH HOH . I 5 HOH B 10 510 23 HOH HOH . I 5 HOH B 11 511 24 HOH HOH . I 5 HOH B 12 512 25 HOH HOH . I 5 HOH B 13 513 27 HOH HOH . I 5 HOH B 14 514 28 HOH HOH . I 5 HOH B 15 515 30 HOH HOH . I 5 HOH B 16 516 31 HOH HOH . I 5 HOH B 17 517 34 HOH HOH . I 5 HOH B 18 518 36 HOH HOH . I 5 HOH B 19 519 38 HOH HOH . I 5 HOH B 20 520 39 HOH HOH . I 5 HOH B 21 521 40 HOH HOH . I 5 HOH B 22 522 43 HOH HOH . I 5 HOH B 23 523 44 HOH HOH . I 5 HOH B 24 524 51 HOH HOH . I 5 HOH B 25 525 52 HOH HOH . I 5 HOH B 26 526 55 HOH HOH . I 5 HOH B 27 527 56 HOH HOH . I 5 HOH B 28 528 58 HOH HOH . I 5 HOH B 29 529 59 HOH HOH . I 5 HOH B 30 530 60 HOH HOH . I 5 HOH B 31 531 61 HOH HOH . I 5 HOH B 32 532 65 HOH HOH . I 5 HOH B 33 533 67 HOH HOH . I 5 HOH B 34 534 69 HOH HOH . I 5 HOH B 35 535 73 HOH HOH . I 5 HOH B 36 536 74 HOH HOH . I 5 HOH B 37 537 76 HOH HOH . I 5 HOH B 38 538 77 HOH HOH . I 5 HOH B 39 539 78 HOH HOH . I 5 HOH B 40 540 79 HOH HOH . I 5 HOH B 41 541 80 HOH HOH . I 5 HOH B 42 542 81 HOH HOH . I 5 HOH B 43 543 82 HOH HOH . I 5 HOH B 44 544 84 HOH HOH . I 5 HOH B 45 545 87 HOH HOH . I 5 HOH B 46 546 89 HOH HOH . I 5 HOH B 47 547 90 HOH HOH . I 5 HOH B 48 548 92 HOH HOH . I 5 HOH B 49 549 95 HOH HOH . I 5 HOH B 50 550 97 HOH HOH . I 5 HOH B 51 551 100 HOH HOH . I 5 HOH B 52 552 101 HOH HOH . I 5 HOH B 53 553 102 HOH HOH . I 5 HOH B 54 554 103 HOH HOH . I 5 HOH B 55 555 104 HOH HOH . I 5 HOH B 56 556 106 HOH HOH . I 5 HOH B 57 557 107 HOH HOH . I 5 HOH B 58 558 109 HOH HOH . I 5 HOH B 59 559 111 HOH HOH . I 5 HOH B 60 560 112 HOH HOH . I 5 HOH B 61 561 113 HOH HOH . I 5 HOH B 62 562 116 HOH HOH . I 5 HOH B 63 563 117 HOH HOH . I 5 HOH B 64 564 119 HOH HOH . I 5 HOH B 65 565 120 HOH HOH . I 5 HOH B 66 566 122 HOH HOH . I 5 HOH B 67 567 123 HOH HOH . I 5 HOH B 68 568 124 HOH HOH . I 5 HOH B 69 569 126 HOH HOH . I 5 HOH B 70 570 127 HOH HOH . I 5 HOH B 71 571 132 HOH HOH . I 5 HOH B 72 572 134 HOH HOH . I 5 HOH B 73 573 136 HOH HOH . I 5 HOH B 74 574 137 HOH HOH . I 5 HOH B 75 575 139 HOH HOH . I 5 HOH B 76 576 140 HOH HOH . I 5 HOH B 77 577 142 HOH HOH . I 5 HOH B 78 578 145 HOH HOH . I 5 HOH B 79 579 146 HOH HOH . I 5 HOH B 80 580 147 HOH HOH . I 5 HOH B 81 581 149 HOH HOH . I 5 HOH B 82 582 150 HOH HOH . I 5 HOH B 83 583 151 HOH HOH . I 5 HOH B 84 584 152 HOH HOH . I 5 HOH B 85 585 153 HOH HOH . I 5 HOH B 86 586 156 HOH HOH . I 5 HOH B 87 587 157 HOH HOH . I 5 HOH B 88 588 164 HOH HOH . I 5 HOH B 89 589 167 HOH HOH . I 5 HOH B 90 590 172 HOH HOH . I 5 HOH B 91 591 174 HOH HOH . I 5 HOH B 92 592 175 HOH HOH . I 5 HOH B 93 593 176 HOH HOH . I 5 HOH B 94 594 179 HOH HOH . I 5 HOH B 95 595 1 HOH HOH . I 5 HOH B 96 596 6 HOH HOH . I 5 HOH B 97 597 8 HOH HOH . I 5 HOH B 98 598 10 HOH HOH . I 5 HOH B 99 599 12 HOH HOH . I 5 HOH B 100 600 15 HOH HOH . I 5 HOH B 101 601 19 HOH HOH . I 5 HOH B 102 602 20 HOH HOH . I 5 HOH B 103 603 21 HOH HOH . I 5 HOH B 104 604 23 HOH HOH . I 5 HOH B 105 605 26 HOH HOH . I 5 HOH B 106 606 27 HOH HOH . I 5 HOH B 107 607 32 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 . . . F 3 -13.077 41.19 36.881 1 50.21 ? C1 GOL 402 B 1 HETATM 2 O O1 GOL . . . F 3 -12.525 41.764 38.043 1 56.34 ? O1 GOL 402 B 1 HETATM 3 C C2 GOL . . . F 3 -14.186 40.226 37.28 1 47.2 ? C2 GOL 402 B 1 HETATM 4 O O2 GOL . . . F 3 -15.178 40.233 36.274 1 52.33 ? O2 GOL 402 B 1 HETATM 5 C C3 GOL . . . F 3 -13.585 38.833 37.442 1 33.74 ? C3 GOL 402 B 1 HETATM 6 O O3 GOL . . . F 3 -14.578 37.833 37.508 1 25.08 ? O3 GOL 402 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 58 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 382 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 6 #