data_3L6C # _model_server_result.job_id GI0JJI6Z433NDqDyA96N9g _model_server_result.datetime_utc '2024-11-04 22:38:16' _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 3l6c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":350}' # _entry.id 3L6C # _exptl.entry_id 3L6C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 3L6C _cell.length_a 110.593 _cell.length_b 110.593 _cell.length_c 47.917 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L6C _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # _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,G,H,I,J _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 # 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 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 covale ? covale1 A NZ LYS 56 A LYS 56 1_555 C C4A PLP . A PLP 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.28 ? covale ? covale2 B NZ LYS 56 B LYS 56 1_555 F C4A PLP . B PLP 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.256 ? metalc ? metalc1 A OE2 GLU 210 A GLU 210 1_555 D MN MN . A MN 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc2 A O ALA 214 A ALA 214 1_555 D MN MN . A MN 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc3 A OD1 ASP 216 A ASP 216 1_555 D MN MN . A MN 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc4 D MN MN . A MN 340 1_555 I O HOH . A HOH 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc5 D MN MN . A MN 340 1_555 I O HOH . A HOH 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc6 B OE2 GLU 210 B GLU 210 1_555 G MN MN . B MN 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc7 B O ALA 214 B ALA 214 1_555 G MN MN . B MN 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc8 B OD1 ASP 216 B ASP 216 1_555 G MN MN . B MN 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 268 n y N1 C6 PLP sing 269 n y C2 C2A PLP sing 270 n n C2 C3 PLP sing 271 n y C2A H2A1 PLP sing 272 n n C2A H2A2 PLP sing 273 n n C2A H2A3 PLP sing 274 n n C3 O3 PLP sing 275 n n C3 C4 PLP doub 276 n y O3 HO3 PLP sing 277 n n C4 C4A PLP sing 278 n n C4 C5 PLP sing 279 n y C4A O4A PLP doub 280 n n C4A H4A PLP sing 281 n n C5 C6 PLP doub 282 n y C5 C5A PLP sing 283 n n C6 H6 PLP sing 284 n n C5A O4P PLP sing 285 n n C5A H5A1 PLP sing 286 n n C5A H5A2 PLP sing 287 n n O4P P PLP sing 288 n n P O1P PLP doub 289 n n P O2P PLP sing 290 n n P O3P PLP sing 291 n n O2P HOP2 PLP sing 292 n n O3P HOP3 PLP sing 293 n n # _atom_sites.entry_id 3L6C _atom_sites.fract_transf_matrix[1][1] 0.009042 _atom_sites.fract_transf_matrix[1][2] 0.00522 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010441 _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] 0.020869 _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 PLP A 1 350 350 PLP PLP . D 3 MN A 1 340 340 MN MN . E 4 MLI A 1 341 341 MLI MLI . F 2 PLP B 1 350 350 PLP PLP . G 3 MN B 1 340 340 MN MN . H 4 MLI B 1 341 341 MLI MLI . I 5 HOH A 1 342 342 HOH HOH . I 5 HOH A 2 343 343 HOH HOH . I 5 HOH A 3 344 344 HOH HOH . I 5 HOH A 4 345 345 HOH HOH . I 5 HOH A 5 346 346 HOH HOH . I 5 HOH A 6 347 347 HOH HOH . I 5 HOH A 7 348 348 HOH HOH . I 5 HOH A 8 349 349 HOH HOH . I 5 HOH A 9 351 351 HOH HOH . I 5 HOH A 10 352 352 HOH HOH . I 5 HOH A 11 353 353 HOH HOH . I 5 HOH A 12 354 354 HOH HOH . I 5 HOH A 13 355 355 HOH HOH . I 5 HOH A 14 356 356 HOH HOH . I 5 HOH A 15 357 357 HOH HOH . I 5 HOH A 16 358 358 HOH HOH . I 5 HOH A 17 359 359 HOH HOH . I 5 HOH A 18 360 360 HOH HOH . I 5 HOH A 19 361 361 HOH HOH . I 5 HOH A 20 362 362 HOH HOH . I 5 HOH A 21 363 363 HOH HOH . I 5 HOH A 22 364 364 HOH HOH . I 5 HOH A 23 365 365 HOH HOH . I 5 HOH A 24 366 366 HOH HOH . I 5 HOH A 25 367 367 HOH HOH . I 5 HOH A 26 368 368 HOH HOH . I 5 HOH A 27 369 369 HOH HOH . I 5 HOH A 28 370 370 HOH HOH . I 5 HOH A 29 371 371 HOH HOH . I 5 HOH A 30 372 372 HOH HOH . I 5 HOH A 31 373 373 HOH HOH . I 5 HOH A 32 374 374 HOH HOH . I 5 HOH A 33 375 375 HOH HOH . I 5 HOH A 34 376 376 HOH HOH . I 5 HOH A 35 377 377 HOH HOH . I 5 HOH A 36 378 378 HOH HOH . I 5 HOH A 37 379 379 HOH HOH . I 5 HOH A 38 380 380 HOH HOH . I 5 HOH A 39 381 381 HOH HOH . I 5 HOH A 40 382 382 HOH HOH . I 5 HOH A 41 383 383 HOH HOH . I 5 HOH A 42 384 384 HOH HOH . I 5 HOH A 43 385 385 HOH HOH . I 5 HOH A 44 386 386 HOH HOH . I 5 HOH A 45 387 387 HOH HOH . I 5 HOH A 46 388 388 HOH HOH . I 5 HOH A 47 389 389 HOH HOH . I 5 HOH A 48 390 390 HOH HOH . I 5 HOH A 49 391 391 HOH HOH . I 5 HOH A 50 392 392 HOH HOH . I 5 HOH A 51 393 393 HOH HOH . I 5 HOH A 52 394 394 HOH HOH . I 5 HOH A 53 395 395 HOH HOH . I 5 HOH A 54 396 396 HOH HOH . I 5 HOH A 55 397 397 HOH HOH . I 5 HOH A 56 398 398 HOH HOH . I 5 HOH A 57 399 399 HOH HOH . I 5 HOH A 58 400 400 HOH HOH . I 5 HOH A 59 401 401 HOH HOH . I 5 HOH A 60 402 402 HOH HOH . I 5 HOH A 61 403 403 HOH HOH . I 5 HOH A 62 404 404 HOH HOH . J 5 HOH B 1 342 342 HOH HOH . J 5 HOH B 2 343 343 HOH HOH . J 5 HOH B 3 344 344 HOH HOH . J 5 HOH B 4 345 345 HOH HOH . J 5 HOH B 5 346 346 HOH HOH . J 5 HOH B 6 347 347 HOH HOH . J 5 HOH B 7 348 348 HOH HOH . J 5 HOH B 8 349 349 HOH HOH . J 5 HOH B 9 351 351 HOH HOH . J 5 HOH B 10 352 352 HOH HOH . J 5 HOH B 11 353 353 HOH HOH . J 5 HOH B 12 354 354 HOH HOH . J 5 HOH B 13 355 355 HOH HOH . J 5 HOH B 14 356 356 HOH HOH . J 5 HOH B 15 357 357 HOH HOH . J 5 HOH B 16 358 358 HOH HOH . J 5 HOH B 17 359 359 HOH HOH . J 5 HOH B 18 360 360 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 N1 PLP . . . C 2 16.957 -21.641 -8.362 1 30.17 ? N1 PLP 350 A 1 HETATM 2 C C2 PLP . . . C 2 17.481 -22.052 -7.164 1 28.62 ? C2 PLP 350 A 1 HETATM 3 C C2A PLP . . . C 2 18.875 -21.703 -6.692 1 27.36 ? C2A PLP 350 A 1 HETATM 4 C C3 PLP . . . C 2 16.696 -22.834 -6.345 1 28.73 ? C3 PLP 350 A 1 HETATM 5 O O3 PLP . . . C 2 17.199 -23.255 -5.158 1 30.35 ? O3 PLP 350 A 1 HETATM 6 C C4 PLP . . . C 2 15.413 -23.209 -6.725 1 27.25 ? C4 PLP 350 A 1 HETATM 7 C C4A PLP . . . C 2 14.66 -24.045 -5.733 1 29.02 ? C4A PLP 350 A 1 HETATM 8 C C5 PLP . . . C 2 14.893 -22.788 -7.958 1 25.81 ? C5 PLP 350 A 1 HETATM 9 C C6 PLP . . . C 2 15.696 -22.001 -8.767 1 27.29 ? C6 PLP 350 A 1 HETATM 10 C C5A PLP . . . C 2 13.514 -23.167 -8.459 1 27.21 ? C5A PLP 350 A 1 HETATM 11 O O4P PLP . . . C 2 12.431 -22.745 -7.637 1 23.24 ? O4P PLP 350 A 1 HETATM 12 P P PLP . . . C 2 11.015 -23.401 -7.792 1 23.38 ? P PLP 350 A 1 HETATM 13 O O1P PLP . . . C 2 11.112 -24.803 -7.374 1 20.49 ? O1P PLP 350 A 1 HETATM 14 O O2P PLP . . . C 2 10.713 -23.237 -9.277 1 25.75 ? O2P PLP 350 A 1 HETATM 15 O O3P PLP . . . C 2 10.081 -22.641 -6.901 1 23.76 ? O3P PLP 350 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #