data_3E2Z # _model_server_result.job_id bvNPKeHn8I_XMoaCo6Y1Sg _model_server_result.datetime_utc '2024-12-03 22:51:55' _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 3e2z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":456}' # _entry.id 3E2Z # _exptl.entry_id 3E2Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 248.173 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _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 90 _cell.angle_gamma 90 _cell.entry_id 3E2Z _cell.length_a 91.49 _cell.length_b 91.49 _cell.length_c 233.501 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E2Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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,K _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 5 _struct_asym.id F _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 GLY 239 A GLY 280 1_555 A N LLP 240 A LLP 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C LLP 240 A LLP 281 1_555 A N THR 241 A THR 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? # _chem_comp.formula 'C8 H13 N2 O5 P' _chem_comp.formula_weight 248.173 _chem_comp.id PMP _chem_comp.mon_nstd_flag . _chem_comp.name "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "PYRIDOXAMINE-5'-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 PMP doub 347 n y N1 C6 PMP sing 348 n y C2 C2A PMP sing 349 n n C2 C3 PMP sing 350 n y C2A H2A1 PMP sing 351 n n C2A H2A2 PMP sing 352 n n C2A H2A3 PMP sing 353 n n C3 O3 PMP sing 354 n n C3 C4 PMP doub 355 n y O3 HO3 PMP sing 356 n n C4 C4A PMP sing 357 n n C4 C5 PMP sing 358 n y C4A N4A PMP sing 359 n n C4A H4A1 PMP sing 360 n n C4A H4A2 PMP sing 361 n n N4A HNA1 PMP sing 362 n n N4A HNA2 PMP sing 363 n n C5 C6 PMP doub 364 n y C5 C5A PMP sing 365 n n C6 H6 PMP sing 366 n n C5A O4P PMP sing 367 n n C5A H5A1 PMP sing 368 n n C5A H5A2 PMP sing 369 n n O4P P PMP sing 370 n n P O1P PMP doub 371 n n P O2P PMP sing 372 n n P O3P PMP sing 373 n n O2P HOP2 PMP sing 374 n n O3P HOP3 PMP sing 375 n n # _atom_sites.entry_id 3E2Z _atom_sites.fract_transf_matrix[1][1] 0.01093 _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] 0.01093 _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] 0.004283 _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 KYN A 1 456 1 KYN KYN . D 4 GOL A 1 457 1 GOL GOL . E 4 GOL A 1 458 1 GOL GOL . F 5 PMP B 1 456 1 PMP PMP . G 3 KYN B 1 457 1 KYN KYN . H 4 GOL B 1 458 1 GOL GOL . I 4 GOL B 1 459 1 GOL GOL . J 6 HOH A 1 459 1 HOH HOH . J 6 HOH A 2 460 3 HOH HOH . J 6 HOH A 3 461 4 HOH HOH . J 6 HOH A 4 462 5 HOH HOH . J 6 HOH A 5 463 6 HOH HOH . J 6 HOH A 6 464 7 HOH HOH . J 6 HOH A 7 465 8 HOH HOH . J 6 HOH A 8 466 9 HOH HOH . J 6 HOH A 9 467 15 HOH HOH . J 6 HOH A 10 468 17 HOH HOH . J 6 HOH A 11 469 18 HOH HOH . J 6 HOH A 12 470 19 HOH HOH . J 6 HOH A 13 471 20 HOH HOH . J 6 HOH A 14 472 23 HOH HOH . J 6 HOH A 15 473 24 HOH HOH . J 6 HOH A 16 474 25 HOH HOH . J 6 HOH A 17 475 28 HOH HOH . J 6 HOH A 18 476 29 HOH HOH . J 6 HOH A 19 477 33 HOH HOH . J 6 HOH A 20 478 34 HOH HOH . J 6 HOH A 21 479 35 HOH HOH . J 6 HOH A 22 480 39 HOH HOH . J 6 HOH A 23 481 41 HOH HOH . J 6 HOH A 24 482 45 HOH HOH . J 6 HOH A 25 483 46 HOH HOH . J 6 HOH A 26 484 49 HOH HOH . J 6 HOH A 27 485 51 HOH HOH . J 6 HOH A 28 486 52 HOH HOH . J 6 HOH A 29 487 53 HOH HOH . J 6 HOH A 30 488 56 HOH HOH . J 6 HOH A 31 489 58 HOH HOH . J 6 HOH A 32 490 59 HOH HOH . J 6 HOH A 33 491 61 HOH HOH . J 6 HOH A 34 492 62 HOH HOH . J 6 HOH A 35 493 65 HOH HOH . J 6 HOH A 36 494 66 HOH HOH . J 6 HOH A 37 495 69 HOH HOH . J 6 HOH A 38 496 70 HOH HOH . J 6 HOH A 39 497 71 HOH HOH . J 6 HOH A 40 498 74 HOH HOH . J 6 HOH A 41 499 76 HOH HOH . J 6 HOH A 42 500 77 HOH HOH . J 6 HOH A 43 501 80 HOH HOH . J 6 HOH A 44 502 81 HOH HOH . J 6 HOH A 45 503 82 HOH HOH . J 6 HOH A 46 504 83 HOH HOH . K 6 HOH B 1 460 2 HOH HOH . K 6 HOH B 2 461 10 HOH HOH . K 6 HOH B 3 462 11 HOH HOH . K 6 HOH B 4 463 12 HOH HOH . K 6 HOH B 5 464 13 HOH HOH . K 6 HOH B 6 465 14 HOH HOH . K 6 HOH B 7 466 16 HOH HOH . K 6 HOH B 8 467 21 HOH HOH . K 6 HOH B 9 468 22 HOH HOH . K 6 HOH B 10 469 26 HOH HOH . K 6 HOH B 11 470 27 HOH HOH . K 6 HOH B 12 471 30 HOH HOH . K 6 HOH B 13 472 31 HOH HOH . K 6 HOH B 14 473 32 HOH HOH . K 6 HOH B 15 474 36 HOH HOH . K 6 HOH B 16 475 37 HOH HOH . K 6 HOH B 17 476 38 HOH HOH . K 6 HOH B 18 477 40 HOH HOH . K 6 HOH B 19 478 42 HOH HOH . K 6 HOH B 20 479 43 HOH HOH . K 6 HOH B 21 480 44 HOH HOH . K 6 HOH B 22 481 47 HOH HOH . K 6 HOH B 23 482 48 HOH HOH . K 6 HOH B 24 483 50 HOH HOH . K 6 HOH B 25 484 54 HOH HOH . K 6 HOH B 26 485 55 HOH HOH . K 6 HOH B 27 486 57 HOH HOH . K 6 HOH B 28 487 60 HOH HOH . K 6 HOH B 29 488 63 HOH HOH . K 6 HOH B 30 489 64 HOH HOH . K 6 HOH B 31 490 67 HOH HOH . K 6 HOH B 32 491 68 HOH HOH . K 6 HOH B 33 492 72 HOH HOH . K 6 HOH B 34 493 73 HOH HOH . K 6 HOH B 35 494 75 HOH HOH . K 6 HOH B 36 495 78 HOH HOH . K 6 HOH B 37 496 79 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 PMP . . . F 5 18.768 -23.398 3.378 1 28.5 ? N1 PMP 456 B 1 HETATM 2 C C2 PMP . . . F 5 18.402 -23.798 4.658 1 29.19 ? C2 PMP 456 B 1 HETATM 3 C C2A PMP . . . F 5 17.854 -22.705 5.548 1 25.42 ? C2A PMP 456 B 1 HETATM 4 C C3 PMP . . . F 5 18.532 -25.178 5.034 1 28.05 ? C3 PMP 456 B 1 HETATM 5 O O3 PMP . . . F 5 18.133 -25.631 6.281 1 20.31 ? O3 PMP 456 B 1 HETATM 6 C C4 PMP . . . F 5 19.087 -26.083 4.106 1 28.16 ? C4 PMP 456 B 1 HETATM 7 C C4A PMP . . . F 5 19.522 -27.455 4.629 1 27.63 ? C4A PMP 456 B 1 HETATM 8 N N4A PMP . . . F 5 18.436 -28.07 5.35 1 28.22 ? N4A PMP 456 B 1 HETATM 9 C C5 PMP . . . F 5 19.394 -25.64 2.771 1 29.36 ? C5 PMP 456 B 1 HETATM 10 C C6 PMP . . . F 5 19.24 -24.29 2.465 1 28.27 ? C6 PMP 456 B 1 HETATM 11 C C5A PMP . . . F 5 19.955 -26.467 1.579 1 28.52 ? C5A PMP 456 B 1 HETATM 12 O O4P PMP . . . F 5 19.543 -27.817 1.466 1 25.91 ? O4P PMP 456 B 1 HETATM 13 P P PMP . . . F 5 19.345 -28.498 0.04 1 21.99 ? P PMP 456 B 1 HETATM 14 O O1P PMP . . . F 5 19.702 -29.939 0.266 1 19.9 ? O1P PMP 456 B 1 HETATM 15 O O2P PMP . . . F 5 17.939 -28.187 -0.476 1 14.66 ? O2P PMP 456 B 1 HETATM 16 O O3P PMP . . . F 5 20.447 -27.919 -0.845 1 22.06 ? O3P PMP 456 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 16 #