data_3IJQ # _model_server_result.job_id '_R7f2n83klM3CBxRnt8lvQ' _model_server_result.datetime_utc '2024-11-23 03:11:24' _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 3ijq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":385}' # _entry.id 3IJQ # _exptl.entry_id 3IJQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.129 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'D-GLUTAMIC ACID' _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 90.32 _cell.angle_gamma 90 _cell.entry_id 3IJQ _cell.length_a 141.71 _cell.length_b 99.865 _cell.length_c 60.851 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IJQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 ? dimeric 2 author_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,E,J 1 1 B,F,G,H,I,K 1 2 A,B,C,D,E,F,G,H,I,J,K 2 1 # 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' 4_546 -x+1/2,y-1/2,-z+1 -1 0 0 0 1 0 0 0 -1 70.515146 -49.9325 60.850051 # 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 G 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 C ALA . A ALA 384 1_555 D N DGL . A DGL 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 F C ALA . B ALA 384 1_555 G N DGL . B DGL 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? metalc ? metalc1 A OD2 ASP 179 A ASP 224 1_555 E MG MG . A MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc2 A OE1 GLU 206 A GLU 251 1_555 E MG MG . A MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc3 A OD2 ASP 231 A ASP 276 1_555 E MG MG . A MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc4 E MG MG . A MG 386 1_555 J O HOH . A HOH 387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc5 B OD2 ASP 179 B ASP 224 1_555 H MG MG . B MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc6 B OE1 GLU 206 B GLU 251 1_555 H MG MG . B MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc7 B OD2 ASP 231 B ASP 276 1_555 H MG MG . B MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc8 G OXT DGL . B DGL 385 1_555 H MG MG . B MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc9 G O DGL . B DGL 385 1_555 H MG MG . B MG 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc10 H MG MG . B MG 386 1_555 K O HOH . B HOH 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.731 ? # _chem_comp.formula 'C5 H9 N O4' _chem_comp.formula_weight 147.129 _chem_comp.id DGL _chem_comp.mon_nstd_flag . _chem_comp.name 'D-GLUTAMIC ACID' _chem_comp.type 'd-peptide linking' _chem_comp.pdbx_synonyms ? # 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 N CA DGL sing 83 n n N H DGL sing 84 n n N H2 DGL sing 85 n n CA C DGL sing 86 n n CA CB DGL sing 87 n n CA HA DGL sing 88 n n C O DGL doub 89 n n C OXT DGL sing 90 n n CB CG DGL sing 91 n n CB HB2 DGL sing 92 n n CB HB3 DGL sing 93 n n CG CD DGL sing 94 n n CG HG2 DGL sing 95 n n CG HG3 DGL sing 96 n n CD OE1 DGL doub 97 n n CD OE2 DGL sing 98 n n OE2 HE2 DGL sing 99 n n OXT HXT DGL sing 100 n n # _atom_sites.entry_id 3IJQ _atom_sites.fract_transf_matrix[1][1] 0.007057 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000039 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010014 _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] 0.016434 _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 ALA A 1 384 1 ALA ALA . D 3 DGL A 1 385 2 DGL DGL . E 4 MG A 1 386 1 MG MG . F 2 ALA B 1 384 1 ALA ALA . G 3 DGL B 1 385 2 DGL DGL . H 4 MG B 1 386 2 MG MG . I 5 SO4 B 1 387 3 SO4 SO4 . J 6 HOH A 1 387 1 HOH HOH . J 6 HOH A 2 388 4 HOH HOH . J 6 HOH A 3 389 14 HOH HOH . J 6 HOH A 4 390 16 HOH HOH . J 6 HOH A 5 391 20 HOH HOH . J 6 HOH A 6 392 25 HOH HOH . J 6 HOH A 7 393 26 HOH HOH . J 6 HOH A 8 394 28 HOH HOH . J 6 HOH A 9 395 29 HOH HOH . J 6 HOH A 10 396 31 HOH HOH . J 6 HOH A 11 397 33 HOH HOH . J 6 HOH A 12 398 34 HOH HOH . J 6 HOH A 13 399 35 HOH HOH . J 6 HOH A 14 400 36 HOH HOH . J 6 HOH A 15 401 37 HOH HOH . J 6 HOH A 16 402 39 HOH HOH . J 6 HOH A 17 403 44 HOH HOH . J 6 HOH A 18 404 46 HOH HOH . J 6 HOH A 19 405 48 HOH HOH . J 6 HOH A 20 406 49 HOH HOH . J 6 HOH A 21 407 52 HOH HOH . J 6 HOH A 22 408 54 HOH HOH . J 6 HOH A 23 409 57 HOH HOH . J 6 HOH A 24 410 61 HOH HOH . J 6 HOH A 25 411 64 HOH HOH . J 6 HOH A 26 412 65 HOH HOH . J 6 HOH A 27 413 67 HOH HOH . J 6 HOH A 28 414 70 HOH HOH . J 6 HOH A 29 415 71 HOH HOH . J 6 HOH A 30 416 72 HOH HOH . J 6 HOH A 31 417 77 HOH HOH . J 6 HOH A 32 418 79 HOH HOH . J 6 HOH A 33 419 80 HOH HOH . J 6 HOH A 34 420 83 HOH HOH . J 6 HOH A 35 421 84 HOH HOH . J 6 HOH A 36 422 92 HOH HOH . J 6 HOH A 37 423 95 HOH HOH . J 6 HOH A 38 424 97 HOH HOH . J 6 HOH A 39 425 100 HOH HOH . J 6 HOH A 40 426 102 HOH HOH . J 6 HOH A 41 427 104 HOH HOH . J 6 HOH A 42 428 105 HOH HOH . J 6 HOH A 43 429 106 HOH HOH . J 6 HOH A 44 430 108 HOH HOH . J 6 HOH A 45 431 113 HOH HOH . J 6 HOH A 46 432 115 HOH HOH . J 6 HOH A 47 433 125 HOH HOH . J 6 HOH A 48 434 127 HOH HOH . J 6 HOH A 49 435 128 HOH HOH . J 6 HOH A 50 436 130 HOH HOH . J 6 HOH A 51 437 132 HOH HOH . J 6 HOH A 52 438 134 HOH HOH . J 6 HOH A 53 439 136 HOH HOH . J 6 HOH A 54 440 139 HOH HOH . J 6 HOH A 55 441 140 HOH HOH . J 6 HOH A 56 442 141 HOH HOH . J 6 HOH A 57 443 146 HOH HOH . J 6 HOH A 58 444 147 HOH HOH . J 6 HOH A 59 445 148 HOH HOH . J 6 HOH A 60 446 153 HOH HOH . J 6 HOH A 61 447 154 HOH HOH . J 6 HOH A 62 448 155 HOH HOH . J 6 HOH A 63 449 164 HOH HOH . J 6 HOH A 64 450 167 HOH HOH . J 6 HOH A 65 451 173 HOH HOH . J 6 HOH A 66 452 174 HOH HOH . J 6 HOH A 67 453 176 HOH HOH . J 6 HOH A 68 454 178 HOH HOH . J 6 HOH A 69 455 180 HOH HOH . J 6 HOH A 70 456 181 HOH HOH . J 6 HOH A 71 457 182 HOH HOH . J 6 HOH A 72 458 187 HOH HOH . J 6 HOH A 73 459 188 HOH HOH . J 6 HOH A 74 460 193 HOH HOH . J 6 HOH A 75 461 196 HOH HOH . J 6 HOH A 76 462 200 HOH HOH . J 6 HOH A 77 463 204 HOH HOH . J 6 HOH A 78 464 205 HOH HOH . J 6 HOH A 79 465 206 HOH HOH . J 6 HOH A 80 466 207 HOH HOH . J 6 HOH A 81 467 208 HOH HOH . J 6 HOH A 82 468 210 HOH HOH . J 6 HOH A 83 469 211 HOH HOH . J 6 HOH A 84 470 212 HOH HOH . J 6 HOH A 85 488 214 HOH HOH . K 6 HOH B 1 388 2 HOH HOH . K 6 HOH B 2 389 3 HOH HOH . K 6 HOH B 3 390 6 HOH HOH . K 6 HOH B 4 391 7 HOH HOH . K 6 HOH B 5 392 8 HOH HOH . K 6 HOH B 6 393 9 HOH HOH . K 6 HOH B 7 394 11 HOH HOH . K 6 HOH B 8 395 13 HOH HOH . K 6 HOH B 9 396 15 HOH HOH . K 6 HOH B 10 397 18 HOH HOH . K 6 HOH B 11 398 19 HOH HOH . K 6 HOH B 12 399 21 HOH HOH . K 6 HOH B 13 400 22 HOH HOH . K 6 HOH B 14 401 23 HOH HOH . K 6 HOH B 15 402 24 HOH HOH . K 6 HOH B 16 403 27 HOH HOH . K 6 HOH B 17 404 30 HOH HOH . K 6 HOH B 18 405 32 HOH HOH . K 6 HOH B 19 406 38 HOH HOH . K 6 HOH B 20 407 40 HOH HOH . K 6 HOH B 21 408 41 HOH HOH . K 6 HOH B 22 409 43 HOH HOH . K 6 HOH B 23 410 45 HOH HOH . K 6 HOH B 24 411 50 HOH HOH . K 6 HOH B 25 412 51 HOH HOH . K 6 HOH B 26 413 53 HOH HOH . K 6 HOH B 27 414 55 HOH HOH . K 6 HOH B 28 415 58 HOH HOH . K 6 HOH B 29 416 60 HOH HOH . K 6 HOH B 30 417 62 HOH HOH . K 6 HOH B 31 418 66 HOH HOH . K 6 HOH B 32 419 68 HOH HOH . K 6 HOH B 33 420 69 HOH HOH . K 6 HOH B 34 421 81 HOH HOH . K 6 HOH B 35 422 82 HOH HOH . K 6 HOH B 36 423 85 HOH HOH . K 6 HOH B 37 424 86 HOH HOH . K 6 HOH B 38 425 87 HOH HOH . K 6 HOH B 39 426 88 HOH HOH . K 6 HOH B 40 427 89 HOH HOH . K 6 HOH B 41 428 90 HOH HOH . K 6 HOH B 42 429 91 HOH HOH . K 6 HOH B 43 430 93 HOH HOH . K 6 HOH B 44 431 94 HOH HOH . K 6 HOH B 45 432 96 HOH HOH . K 6 HOH B 46 433 98 HOH HOH . K 6 HOH B 47 434 101 HOH HOH . K 6 HOH B 48 435 103 HOH HOH . K 6 HOH B 49 436 110 HOH HOH . K 6 HOH B 50 437 111 HOH HOH . K 6 HOH B 51 438 112 HOH HOH . K 6 HOH B 52 439 114 HOH HOH . K 6 HOH B 53 440 116 HOH HOH . K 6 HOH B 54 441 119 HOH HOH . K 6 HOH B 55 442 120 HOH HOH . K 6 HOH B 56 443 121 HOH HOH . K 6 HOH B 57 444 122 HOH HOH . K 6 HOH B 58 445 123 HOH HOH . K 6 HOH B 59 446 124 HOH HOH . K 6 HOH B 60 447 126 HOH HOH . K 6 HOH B 61 448 129 HOH HOH . K 6 HOH B 62 449 133 HOH HOH . K 6 HOH B 63 450 135 HOH HOH . K 6 HOH B 64 451 137 HOH HOH . K 6 HOH B 65 452 138 HOH HOH . K 6 HOH B 66 453 142 HOH HOH . K 6 HOH B 67 454 144 HOH HOH . K 6 HOH B 68 455 145 HOH HOH . K 6 HOH B 69 456 149 HOH HOH . K 6 HOH B 70 457 150 HOH HOH . K 6 HOH B 71 458 152 HOH HOH . K 6 HOH B 72 459 156 HOH HOH . K 6 HOH B 73 460 157 HOH HOH . K 6 HOH B 74 461 159 HOH HOH . K 6 HOH B 75 462 160 HOH HOH . K 6 HOH B 76 463 161 HOH HOH . K 6 HOH B 77 464 162 HOH HOH . K 6 HOH B 78 465 163 HOH HOH . K 6 HOH B 79 466 165 HOH HOH . K 6 HOH B 80 467 166 HOH HOH . K 6 HOH B 81 468 168 HOH HOH . K 6 HOH B 82 469 171 HOH HOH . K 6 HOH B 83 470 172 HOH HOH . K 6 HOH B 84 471 177 HOH HOH . K 6 HOH B 85 472 179 HOH HOH . K 6 HOH B 86 473 184 HOH HOH . K 6 HOH B 87 474 185 HOH HOH . K 6 HOH B 88 475 186 HOH HOH . K 6 HOH B 89 476 189 HOH HOH . K 6 HOH B 90 477 190 HOH HOH . K 6 HOH B 91 478 191 HOH HOH . K 6 HOH B 92 479 192 HOH HOH . K 6 HOH B 93 480 194 HOH HOH . K 6 HOH B 94 481 197 HOH HOH . K 6 HOH B 95 482 198 HOH HOH . K 6 HOH B 96 483 199 HOH HOH . K 6 HOH B 97 484 201 HOH HOH . K 6 HOH B 98 485 203 HOH HOH . K 6 HOH B 99 486 209 HOH HOH . K 6 HOH B 100 487 213 HOH HOH . K 6 HOH B 101 489 215 HOH HOH . K 6 HOH B 102 490 216 HOH HOH . K 6 HOH B 103 491 217 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 N N DGL . . . G 3 12.224 30.186 36.06 1 35.52 ? N DGL 385 B 1 HETATM 2 C CA DGL . . . G 3 10.852 30.367 36.619 1 35.89 ? CA DGL 385 B 1 HETATM 3 C C DGL . . . G 3 10.879 30.998 38.042 1 38.76 ? C DGL 385 B 1 HETATM 4 O O DGL . . . G 3 9.774 31.305 38.569 1 35.48 ? O DGL 385 B 1 HETATM 5 C CB DGL . . . G 3 10.03 31.235 35.639 1 36.02 ? CB DGL 385 B 1 HETATM 6 C CG DGL . . . G 3 10.355 30.962 34.166 1 37.94 ? CG DGL 385 B 1 HETATM 7 C CD DGL . . . G 3 9.341 31.395 33.128 1 37.4 ? CD DGL 385 B 1 HETATM 8 O OE1 DGL . . . G 3 8.108 31.408 33.397 1 38.6 ? OE1 DGL 385 B 1 HETATM 9 O OE2 DGL . . . G 3 9.789 31.703 32.011 1 38.53 ? OE2 DGL 385 B 1 HETATM 10 O OXT DGL . . . G 3 11.978 31.176 38.626 1 40.03 ? OXT DGL 385 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #