data_2DEG # _model_server_result.job_id FEgnOW6SUaSPzGveb1YdfA _model_server_result.datetime_utc '2025-04-27 00:37:24' _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 2deg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":2002}' # _entry.id 2DEG # _exptl.entry_id 2DEG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _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 2DEG _cell.length_a 65.324 _cell.length_b 65.324 _cell.length_c 202.366 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DEG _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,PQS _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,Q _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 101.183 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 J 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 A OE2 GLU 19 A GLU 19 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.742 ? metalc ? metalc2 A OE1 GLU 19 A GLU 19 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.634 ? metalc ? metalc3 A OE1 GLU 19 A GLU 19 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? C ? ? ? ? ? ? ? 2.74 ? metalc ? metalc4 L O HOH . A HOH 98 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? C ? ? ? ? ? ? ? 2.121 ? metalc ? metalc5 L O HOH . A HOH 98 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.885 ? metalc ? metalc6 B OE1 GLU 9 B GLU 9 1_555 G NA NA . B NA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc7 B OE1 GLU 19 B GLU 19 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.321 ? metalc ? metalc8 B OE1 GLU 19 B GLU 19 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? C ? ? ? ? ? ? ? 2.478 ? metalc ? metalc9 B OE2 GLU 19 B GLU 19 1_555 H MN MN . B MN 1003 1_555 ? ? ? ? C ? ? ? ? ? ? ? 2.442 ? metalc ? metalc10 G NA NA . B NA 1001 1_555 C OE2 GLU 61 C GLU 61 8_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc11 H MN MN . B MN 1003 1_555 M O HOH . B HOH 2024 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc12 H MN MN . B MN 1003 1_555 M O HOH . B HOH 2024 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc13 H MN MN . B MN 1003 1_555 M O HOH . B HOH 2024 1_555 ? C ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc14 H MN MN . B MN 1003 1_555 C OE1 GLU 19 C GLU 19 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc15 H MN MN . B MN 1003 1_555 C OE2 GLU 19 C GLU 19 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc16 H MN MN . B MN 1003 1_555 C OE1 GLU 19 C GLU 19 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc17 H MN MN . B MN 1003 1_555 D OE1 GLU 68 D GLU 68 1_655 ? A ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc18 H MN MN . B MN 1003 1_555 D OE1 GLU 68 D GLU 68 1_655 ? B ? ? ? ? ? ? ? ? ? ? 3.08 ? metalc ? metalc19 H MN MN . B MN 1003 1_555 D OE1 GLU 68 D GLU 68 1_655 ? C ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc20 D OE2 GLU 19 D GLU 19 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.085 ? metalc ? metalc21 D OE1 GLU 19 D GLU 19 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.546 ? metalc ? metalc22 E OE1 GLU 19 E GLU 19 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.226 ? metalc ? metalc23 P O HOH . E HOH 83 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.22 ? metalc ? metalc24 P O HOH . E HOH 83 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 F OE1 GLU 19 F GLU 19 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.227 ? metalc ? metalc26 F OE1 GLU 19 F GLU 19 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.398 ? metalc ? metalc27 F OE2 GLU 19 F GLU 19 1_555 K MN MN . F MN 1002 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.988 ? # _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 100 n n C1 C2 GOL sing 101 n n C1 H11 GOL sing 102 n n C1 H12 GOL sing 103 n n O1 HO1 GOL sing 104 n n C2 O2 GOL sing 105 n n C2 C3 GOL sing 106 n n C2 H2 GOL sing 107 n n O2 HO2 GOL sing 108 n n C3 O3 GOL sing 109 n n C3 H31 GOL sing 110 n n C3 H32 GOL sing 111 n n O3 HO3 GOL sing 112 n n # _atom_sites.entry_id 2DEG _atom_sites.fract_transf_matrix[1][1] 0.015308 _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] 0.015308 _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] 0.004942 _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 G 2 NA B 1 1001 1001 NA NA . H 3 MN B 1 1003 1003 MN MN . I 4 GOL B 1 2001 2001 GOL GOL . J 4 GOL D 1 2002 2002 GOL GOL . K 3 MN F 1 1002 1002 MN MN . L 5 HOH A 1 70 25 HOH HOH . L 5 HOH A 2 71 35 HOH HOH . L 5 HOH A 3 72 37 HOH HOH . L 5 HOH A 4 73 51 HOH HOH . L 5 HOH A 5 74 78 HOH HOH . L 5 HOH A 6 75 93 HOH HOH . L 5 HOH A 7 76 105 HOH HOH . L 5 HOH A 8 77 111 HOH HOH . L 5 HOH A 9 78 124 HOH HOH . L 5 HOH A 10 79 131 HOH HOH . L 5 HOH A 11 80 134 HOH HOH . L 5 HOH A 12 81 152 HOH HOH . L 5 HOH A 13 82 154 HOH HOH . L 5 HOH A 14 83 167 HOH HOH . L 5 HOH A 15 84 227 HOH HOH . L 5 HOH A 16 85 239 HOH HOH . L 5 HOH A 17 86 405 HOH HOH . L 5 HOH A 18 87 409 HOH HOH . L 5 HOH A 19 88 410 HOH HOH . L 5 HOH A 20 89 418 HOH HOH . L 5 HOH A 21 90 424 HOH HOH . L 5 HOH A 22 91 448 HOH HOH . L 5 HOH A 23 92 449 HOH HOH . L 5 HOH A 24 93 456 HOH HOH . L 5 HOH A 25 94 463 HOH HOH . L 5 HOH A 26 95 466 HOH HOH . L 5 HOH A 27 96 601 HOH HOH . L 5 HOH A 28 97 602 HOH HOH . L 5 HOH A 29 98 621 HOH HOH . L 5 HOH A 30 99 623 HOH HOH . L 5 HOH A 31 100 624 HOH HOH . M 5 HOH B 1 2002 2 HOH HOH . M 5 HOH B 2 2003 14 HOH HOH . M 5 HOH B 3 2004 70 HOH HOH . M 5 HOH B 4 2005 75 HOH HOH . M 5 HOH B 5 2006 80 HOH HOH . M 5 HOH B 6 2007 89 HOH HOH . M 5 HOH B 7 2008 97 HOH HOH . M 5 HOH B 8 2009 101 HOH HOH . M 5 HOH B 9 2010 110 HOH HOH . M 5 HOH B 10 2011 118 HOH HOH . M 5 HOH B 11 2012 138 HOH HOH . M 5 HOH B 12 2013 294 HOH HOH . M 5 HOH B 13 2014 344 HOH HOH . M 5 HOH B 14 2015 413 HOH HOH . M 5 HOH B 15 2016 422 HOH HOH . M 5 HOH B 16 2017 423 HOH HOH . M 5 HOH B 17 2018 451 HOH HOH . M 5 HOH B 18 2019 458 HOH HOH . M 5 HOH B 19 2020 464 HOH HOH . M 5 HOH B 20 2021 471 HOH HOH . M 5 HOH B 21 2022 475 HOH HOH . M 5 HOH B 22 2023 610 HOH HOH . M 5 HOH B 23 2024 622 HOH HOH . M 5 HOH B 24 2025 625 HOH HOH . N 5 HOH C 1 70 62 HOH HOH . N 5 HOH C 2 71 72 HOH HOH . N 5 HOH C 3 72 76 HOH HOH . N 5 HOH C 4 73 81 HOH HOH . N 5 HOH C 5 74 100 HOH HOH . N 5 HOH C 6 75 113 HOH HOH . N 5 HOH C 7 76 126 HOH HOH . N 5 HOH C 8 77 158 HOH HOH . N 5 HOH C 9 78 197 HOH HOH . N 5 HOH C 10 79 214 HOH HOH . N 5 HOH C 11 80 236 HOH HOH . N 5 HOH C 12 81 404 HOH HOH . N 5 HOH C 13 82 407 HOH HOH . N 5 HOH C 14 83 408 HOH HOH . N 5 HOH C 15 84 417 HOH HOH . N 5 HOH C 16 85 420 HOH HOH . N 5 HOH C 17 86 427 HOH HOH . N 5 HOH C 18 87 433 HOH HOH . N 5 HOH C 19 88 439 HOH HOH . N 5 HOH C 20 89 446 HOH HOH . N 5 HOH C 21 90 467 HOH HOH . N 5 HOH C 22 91 606 HOH HOH . O 5 HOH D 1 2003 1 HOH HOH . O 5 HOH D 2 2004 10 HOH HOH . O 5 HOH D 3 2005 12 HOH HOH . O 5 HOH D 4 2006 15 HOH HOH . O 5 HOH D 5 2007 18 HOH HOH . O 5 HOH D 6 2008 22 HOH HOH . O 5 HOH D 7 2009 23 HOH HOH . O 5 HOH D 8 2010 29 HOH HOH . O 5 HOH D 9 2011 34 HOH HOH . O 5 HOH D 10 2012 49 HOH HOH . O 5 HOH D 11 2013 59 HOH HOH . O 5 HOH D 12 2014 64 HOH HOH . O 5 HOH D 13 2015 66 HOH HOH . O 5 HOH D 14 2016 69 HOH HOH . O 5 HOH D 15 2017 94 HOH HOH . O 5 HOH D 16 2018 114 HOH HOH . O 5 HOH D 17 2019 121 HOH HOH . O 5 HOH D 18 2020 140 HOH HOH . O 5 HOH D 19 2021 149 HOH HOH . O 5 HOH D 20 2022 159 HOH HOH . O 5 HOH D 21 2023 172 HOH HOH . O 5 HOH D 22 2024 179 HOH HOH . O 5 HOH D 23 2025 192 HOH HOH . O 5 HOH D 24 2026 215 HOH HOH . O 5 HOH D 25 2027 291 HOH HOH . O 5 HOH D 26 2028 341 HOH HOH . O 5 HOH D 27 2029 414 HOH HOH . O 5 HOH D 28 2030 415 HOH HOH . O 5 HOH D 29 2031 421 HOH HOH . O 5 HOH D 30 2032 434 HOH HOH . O 5 HOH D 31 2033 438 HOH HOH . O 5 HOH D 32 2034 444 HOH HOH . O 5 HOH D 33 2035 445 HOH HOH . O 5 HOH D 34 2036 447 HOH HOH . O 5 HOH D 35 2037 452 HOH HOH . O 5 HOH D 36 2038 455 HOH HOH . O 5 HOH D 37 2039 459 HOH HOH . O 5 HOH D 38 2040 462 HOH HOH . O 5 HOH D 39 2041 470 HOH HOH . O 5 HOH D 40 2042 472 HOH HOH . O 5 HOH D 41 2043 480 HOH HOH . O 5 HOH D 42 2044 481 HOH HOH . P 5 HOH E 1 70 7 HOH HOH . P 5 HOH E 2 71 31 HOH HOH . P 5 HOH E 3 72 40 HOH HOH . P 5 HOH E 4 73 46 HOH HOH . P 5 HOH E 5 74 63 HOH HOH . P 5 HOH E 6 75 73 HOH HOH . P 5 HOH E 7 76 83 HOH HOH . P 5 HOH E 8 77 108 HOH HOH . P 5 HOH E 9 78 127 HOH HOH . P 5 HOH E 10 79 147 HOH HOH . P 5 HOH E 11 80 166 HOH HOH . P 5 HOH E 12 81 171 HOH HOH . P 5 HOH E 13 82 297 HOH HOH . P 5 HOH E 14 83 402 HOH HOH . P 5 HOH E 15 84 406 HOH HOH . P 5 HOH E 16 85 419 HOH HOH . P 5 HOH E 17 86 426 HOH HOH . P 5 HOH E 18 87 428 HOH HOH . P 5 HOH E 19 88 430 HOH HOH . P 5 HOH E 20 89 443 HOH HOH . P 5 HOH E 21 90 453 HOH HOH . P 5 HOH E 22 91 454 HOH HOH . P 5 HOH E 23 92 457 HOH HOH . P 5 HOH E 24 93 461 HOH HOH . P 5 HOH E 25 94 469 HOH HOH . P 5 HOH E 26 95 603 HOH HOH . P 5 HOH E 27 96 604 HOH HOH . P 5 HOH E 28 97 607 HOH HOH . Q 5 HOH F 1 1003 4 HOH HOH . Q 5 HOH F 2 1004 8 HOH HOH . Q 5 HOH F 3 1005 19 HOH HOH . Q 5 HOH F 4 1006 28 HOH HOH . Q 5 HOH F 5 1007 30 HOH HOH . Q 5 HOH F 6 1008 32 HOH HOH . Q 5 HOH F 7 1009 36 HOH HOH . Q 5 HOH F 8 1010 43 HOH HOH . Q 5 HOH F 9 1011 48 HOH HOH . Q 5 HOH F 10 1012 58 HOH HOH . Q 5 HOH F 11 1013 120 HOH HOH . Q 5 HOH F 12 1014 129 HOH HOH . Q 5 HOH F 13 1015 137 HOH HOH . Q 5 HOH F 14 1016 160 HOH HOH . Q 5 HOH F 15 1017 162 HOH HOH . Q 5 HOH F 16 1018 176 HOH HOH . Q 5 HOH F 17 1019 177 HOH HOH . Q 5 HOH F 18 1020 180 HOH HOH . Q 5 HOH F 19 1021 181 HOH HOH . Q 5 HOH F 20 1022 185 HOH HOH . Q 5 HOH F 21 1023 216 HOH HOH . Q 5 HOH F 22 1024 293 HOH HOH . Q 5 HOH F 23 1025 412 HOH HOH . Q 5 HOH F 24 1026 416 HOH HOH . Q 5 HOH F 25 1027 431 HOH HOH . Q 5 HOH F 26 1028 435 HOH HOH . Q 5 HOH F 27 1029 436 HOH HOH . Q 5 HOH F 28 1030 437 HOH HOH . Q 5 HOH F 29 1031 440 HOH HOH . Q 5 HOH F 30 1032 442 HOH HOH . Q 5 HOH F 31 1033 460 HOH HOH . Q 5 HOH F 32 1034 468 HOH HOH . Q 5 HOH F 33 1035 478 HOH HOH . Q 5 HOH F 34 1036 611 HOH HOH . Q 5 HOH F 35 1037 612 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 . . . J 4 -11.981 14.976 40.534 1 67.27 ? C1 GOL 2002 D 1 HETATM 2 O O1 GOL . . . J 4 -13.181 14.28 40.793 1 68.19 ? O1 GOL 2002 D 1 HETATM 3 C C2 GOL . . . J 4 -10.831 14.006 40.719 1 66.38 ? C2 GOL 2002 D 1 HETATM 4 O O2 GOL . . . J 4 -9.61 14.683 40.549 1 66.03 ? O2 GOL 2002 D 1 HETATM 5 C C3 GOL . . . J 4 -10.938 12.861 39.721 1 66.92 ? C3 GOL 2002 D 1 HETATM 6 O O3 GOL . . . J 4 -12.018 12.029 40.093 1 67.25 ? O3 GOL 2002 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #