data_5LDA
#
_model_server_result.job_id            R-Csn0cyUhwdueBZrO8yAQ 
_model_server_result.datetime_utc      '2024-11-26 03:09:09' 
_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          5lda 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":601}' 
#
_entry.id    5LDA 
#
_exptl.entry_id    5LDA 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          97.3 
_cell.angle_gamma         90 
_cell.entry_id            5LDA 
_cell.length_a            47.11 
_cell.length_b            37.233 
_cell.length_c            59.528 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LDA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 A C MSE 1 A MSE 11 1_555 A N SER 2 A SER 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 A C GLU 53 A GLU 63 1_555 A N MSE 54 A MSE 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale3 A C MSE 54 A MSE 64 1_555 A N ASP 55 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale4 A C GLU 58 A GLU 68 1_555 A N MSE 59 A MSE 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale5 A C MSE 59 A MSE 69 1_555 A N LEU 60 A LEU 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale6 A C GLY 94 A GLY 104 1_555 A N MSE 95 A MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 A C MSE 95 A MSE 105 1_555 A N LYS 96 A LYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale8 B C MSE 23 B MSE 23 1_555 B N LYS 24 B LYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
metalc ? metalc1 A NE2 HIS 78 A HIS 88 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc2 A NE2 HIS 80 A HIS 90 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc3 A OD2 ASP 91 A ASP 101 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc4 C ZN ZN . A ZN 201 1_555 B OXT GLY 69 B GLY 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
#
_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                     5LDA 
_atom_sites.fract_transf_matrix[1][1]    0.021227 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002718 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.026858 
_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]    0.016936 
_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 3 ZN A 1 201 201 ZN ZN . 
D 4 GOL B 1 601 601 GOL GOL . 
E 5 HOH A 1 301 301 HOH HOH . 
E 5 HOH A 2 302 302 HOH HOH . 
E 5 HOH A 3 303 303 HOH HOH . 
E 5 HOH A 4 304 304 HOH HOH . 
E 5 HOH A 5 305 305 HOH HOH . 
E 5 HOH A 6 306 306 HOH HOH . 
E 5 HOH A 7 307 307 HOH HOH . 
E 5 HOH A 8 308 308 HOH HOH . 
E 5 HOH A 9 309 309 HOH HOH . 
E 5 HOH A 10 310 310 HOH HOH . 
E 5 HOH A 11 311 311 HOH HOH . 
E 5 HOH A 12 312 312 HOH HOH . 
E 5 HOH A 13 313 313 HOH HOH . 
E 5 HOH A 14 314 314 HOH HOH . 
E 5 HOH A 15 315 315 HOH HOH . 
E 5 HOH A 16 316 316 HOH HOH . 
E 5 HOH A 17 317 317 HOH HOH . 
E 5 HOH A 18 318 318 HOH HOH . 
E 5 HOH A 19 319 319 HOH HOH . 
E 5 HOH A 20 320 320 HOH HOH . 
E 5 HOH A 21 321 321 HOH HOH . 
E 5 HOH A 22 322 322 HOH HOH . 
E 5 HOH A 23 323 323 HOH HOH . 
E 5 HOH A 24 324 324 HOH HOH . 
E 5 HOH A 25 325 326 HOH HOH . 
E 5 HOH A 26 326 327 HOH HOH . 
E 5 HOH A 27 327 328 HOH HOH . 
E 5 HOH A 28 328 329 HOH HOH . 
E 5 HOH A 29 329 330 HOH HOH . 
E 5 HOH A 30 330 331 HOH HOH . 
E 5 HOH A 31 331 332 HOH HOH . 
E 5 HOH A 32 332 333 HOH HOH . 
E 5 HOH A 33 333 334 HOH HOH . 
E 5 HOH A 34 334 335 HOH HOH . 
E 5 HOH A 35 335 336 HOH HOH . 
E 5 HOH A 36 336 337 HOH HOH . 
E 5 HOH A 37 337 338 HOH HOH . 
E 5 HOH A 38 338 339 HOH HOH . 
E 5 HOH A 39 339 340 HOH HOH . 
E 5 HOH A 40 340 341 HOH HOH . 
E 5 HOH A 41 341 342 HOH HOH . 
E 5 HOH A 42 342 343 HOH HOH . 
E 5 HOH A 43 343 344 HOH HOH . 
E 5 HOH A 44 344 345 HOH HOH . 
E 5 HOH A 45 345 346 HOH HOH . 
E 5 HOH A 46 346 347 HOH HOH . 
E 5 HOH A 47 347 348 HOH HOH . 
E 5 HOH A 48 348 349 HOH HOH . 
E 5 HOH A 49 349 350 HOH HOH . 
E 5 HOH A 50 350 351 HOH HOH . 
E 5 HOH A 51 351 352 HOH HOH . 
E 5 HOH A 52 352 353 HOH HOH . 
E 5 HOH A 53 353 354 HOH HOH . 
E 5 HOH A 54 354 355 HOH HOH . 
E 5 HOH A 55 355 356 HOH HOH . 
E 5 HOH A 56 356 357 HOH HOH . 
E 5 HOH A 57 357 358 HOH HOH . 
E 5 HOH A 58 358 359 HOH HOH . 
E 5 HOH A 59 359 360 HOH HOH . 
E 5 HOH A 60 360 361 HOH HOH . 
E 5 HOH A 61 361 362 HOH HOH . 
E 5 HOH A 62 362 363 HOH HOH . 
E 5 HOH A 63 363 364 HOH HOH . 
E 5 HOH A 64 364 365 HOH HOH . 
E 5 HOH A 65 365 367 HOH HOH . 
E 5 HOH A 66 366 366 HOH HOH . 
E 5 HOH A 67 367 368 HOH HOH . 
E 5 HOH A 68 368 369 HOH HOH . 
E 5 HOH A 69 369 370 HOH HOH . 
E 5 HOH A 70 370 373 HOH HOH . 
E 5 HOH A 71 371 371 HOH HOH . 
E 5 HOH A 72 372 372 HOH HOH . 
E 5 HOH A 73 373 374 HOH HOH . 
E 5 HOH A 74 374 375 HOH HOH . 
E 5 HOH A 75 375 376 HOH HOH . 
E 5 HOH A 76 376 377 HOH HOH . 
E 5 HOH A 77 377 378 HOH HOH . 
E 5 HOH A 78 378 379 HOH HOH . 
E 5 HOH A 79 379 380 HOH HOH . 
E 5 HOH A 80 380 381 HOH HOH . 
E 5 HOH A 81 381 382 HOH HOH . 
E 5 HOH A 82 382 383 HOH HOH . 
F 5 HOH B 1 701 701 HOH HOH . 
F 5 HOH B 2 702 702 HOH HOH . 
F 5 HOH B 3 703 703 HOH HOH . 
F 5 HOH B 4 704 704 HOH HOH . 
F 5 HOH B 5 705 705 HOH HOH . 
F 5 HOH B 6 706 706 HOH HOH . 
F 5 HOH B 7 707 707 HOH HOH . 
F 5 HOH B 8 708 708 HOH HOH . 
F 5 HOH B 9 709 709 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 4 23.297 8.382 38.978 1 82.83 ? C1 GOL 601 B 1 
HETATM 2 O O1 GOL . . . D 4 23.468 9.261 37.902 1 80.45 ? O1 GOL 601 B 1 
HETATM 3 C C2 GOL . . . D 4 22.897 7.019 38.42 1 89.34 ? C2 GOL 601 B 1 
HETATM 4 O O2 GOL . . . D 4 21.627 7.145 37.846 1 92.74 ? O2 GOL 601 B 1 
HETATM 5 C C3 GOL . . . D 4 23.85 6.517 37.338 1 95.32 ? C3 GOL 601 B 1 
HETATM 6 O O3 GOL . . . D 4 23.412 5.248 36.939 1 94.61 ? O3 GOL 601 B 1 
HETATM 7 H H11 GOL . . . D 4 22.599 8.713 39.564 1 99.39 ? H11 GOL 601 B 1 
HETATM 8 H H12 GOL . . . D 4 24.129 8.302 39.472 1 99.39 ? H12 GOL 601 B 1 
HETATM 9 H HO1 GOL . . . D 4 23.138 10.019 38.1 1 96.54 ? HO1 GOL 601 B 1 
HETATM 10 H H2 GOL . . . D 4 22.862 6.373 39.143 1 107.2 ? H2 GOL 601 B 1 
HETATM 11 H HO2 GOL . . . D 4 21.044 6.824 38.375 1 111.29 ? HO2 GOL 601 B 1 
HETATM 12 H H31 GOL . . . D 4 23.837 7.122 36.581 1 114.38 ? H31 GOL 601 B 1 
HETATM 13 H H32 GOL . . . D 4 24.75 6.456 37.695 1 114.38 ? H32 GOL 601 B 1 
HETATM 14 H HO3 GOL . . . D 4 23.039 4.857 37.595 1 113.53 ? HO3 GOL 601 B 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           14 
#