data_2EFY # _model_server_result.job_id krv8Y7pg-VMBOeN37AFcdw _model_server_result.datetime_utc '2024-12-03 14:36:59' _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 2efy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":413}' # _entry.id 2EFY # _exptl.entry_id 2EFY _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 90 _cell.entry_id 2EFY _cell.length_a 100.76 _cell.length_b 100.76 _cell.length_c 65.22 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2EFY _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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 E 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 40 A LYS 40 1_555 C C4A PLP . A PLP 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 B NZ LYS 40 B LYS 40 1_555 E C4A PLP . B PLP 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? # _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 278 n y N1 C6 PLP sing 279 n y C2 C2A PLP sing 280 n n C2 C3 PLP sing 281 n y C2A H2A1 PLP sing 282 n n C2A H2A2 PLP sing 283 n n C2A H2A3 PLP sing 284 n n C3 O3 PLP sing 285 n n C3 C4 PLP doub 286 n y O3 HO3 PLP sing 287 n n C4 C4A PLP sing 288 n n C4 C5 PLP sing 289 n y C4A O4A PLP doub 290 n n C4A H4A PLP sing 291 n n C5 C6 PLP doub 292 n y C5 C5A PLP sing 293 n n C6 H6 PLP sing 294 n n C5A O4P PLP sing 295 n n C5A H5A1 PLP sing 296 n n C5A H5A2 PLP sing 297 n n O4P P PLP sing 298 n n P O1P PLP doub 299 n n P O2P PLP sing 300 n n P O3P PLP sing 301 n n O2P HOP2 PLP sing 302 n n O3P HOP3 PLP sing 303 n n # _atom_sites.entry_id 2EFY _atom_sites.fract_transf_matrix[1][1] 0.009925 _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] 0.009925 _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] 0.015333 _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 1 413 413 PLP PLP . D 3 4AT A 1 414 414 4AT 4AB . E 2 PLP B 1 913 913 PLP PLP . F 3 4AT B 1 914 914 4AT 4AB . G 4 HOH A 1 415 1 HOH HOH . G 4 HOH A 2 416 3 HOH HOH . G 4 HOH A 3 417 4 HOH HOH . G 4 HOH A 4 418 5 HOH HOH . G 4 HOH A 5 419 6 HOH HOH . G 4 HOH A 6 420 7 HOH HOH . G 4 HOH A 7 421 8 HOH HOH . G 4 HOH A 8 422 9 HOH HOH . G 4 HOH A 9 423 10 HOH HOH . G 4 HOH A 10 424 12 HOH HOH . G 4 HOH A 11 425 14 HOH HOH . G 4 HOH A 12 426 16 HOH HOH . G 4 HOH A 13 427 18 HOH HOH . G 4 HOH A 14 428 19 HOH HOH . G 4 HOH A 15 429 21 HOH HOH . G 4 HOH A 16 430 24 HOH HOH . G 4 HOH A 17 431 27 HOH HOH . G 4 HOH A 18 432 29 HOH HOH . G 4 HOH A 19 433 33 HOH HOH . G 4 HOH A 20 434 36 HOH HOH . G 4 HOH A 21 435 37 HOH HOH . G 4 HOH A 22 436 41 HOH HOH . G 4 HOH A 23 437 42 HOH HOH . G 4 HOH A 24 438 45 HOH HOH . G 4 HOH A 25 439 46 HOH HOH . G 4 HOH A 26 440 47 HOH HOH . G 4 HOH A 27 441 52 HOH HOH . G 4 HOH A 28 442 58 HOH HOH . G 4 HOH A 29 443 59 HOH HOH . G 4 HOH A 30 444 61 HOH HOH . G 4 HOH A 31 445 62 HOH HOH . G 4 HOH A 32 446 63 HOH HOH . G 4 HOH A 33 447 64 HOH HOH . G 4 HOH A 34 448 65 HOH HOH . G 4 HOH A 35 449 67 HOH HOH . G 4 HOH A 36 450 74 HOH HOH . G 4 HOH A 37 451 75 HOH HOH . G 4 HOH A 38 452 76 HOH HOH . G 4 HOH A 39 453 77 HOH HOH . G 4 HOH A 40 454 78 HOH HOH . G 4 HOH A 41 455 79 HOH HOH . G 4 HOH A 42 456 80 HOH HOH . G 4 HOH A 43 457 81 HOH HOH . G 4 HOH A 44 458 82 HOH HOH . G 4 HOH A 45 459 83 HOH HOH . G 4 HOH A 46 460 84 HOH HOH . G 4 HOH A 47 461 87 HOH HOH . G 4 HOH A 48 462 88 HOH HOH . G 4 HOH A 49 463 90 HOH HOH . G 4 HOH A 50 464 91 HOH HOH . G 4 HOH A 51 465 92 HOH HOH . G 4 HOH A 52 466 94 HOH HOH . G 4 HOH A 53 467 98 HOH HOH . G 4 HOH A 54 468 100 HOH HOH . G 4 HOH A 55 469 101 HOH HOH . G 4 HOH A 56 470 102 HOH HOH . G 4 HOH A 57 471 103 HOH HOH . G 4 HOH A 58 472 104 HOH HOH . G 4 HOH A 59 473 105 HOH HOH . G 4 HOH A 60 474 107 HOH HOH . G 4 HOH A 61 475 108 HOH HOH . G 4 HOH A 62 476 114 HOH HOH . G 4 HOH A 63 477 115 HOH HOH . G 4 HOH A 64 478 118 HOH HOH . G 4 HOH A 65 479 120 HOH HOH . G 4 HOH A 66 480 121 HOH HOH . G 4 HOH A 67 481 124 HOH HOH . G 4 HOH A 68 482 129 HOH HOH . G 4 HOH A 69 483 130 HOH HOH . G 4 HOH A 70 484 133 HOH HOH . G 4 HOH A 71 485 137 HOH HOH . G 4 HOH A 72 486 140 HOH HOH . G 4 HOH A 73 487 141 HOH HOH . G 4 HOH A 74 488 143 HOH HOH . G 4 HOH A 75 489 146 HOH HOH . G 4 HOH A 76 490 149 HOH HOH . G 4 HOH A 77 491 150 HOH HOH . G 4 HOH A 78 492 153 HOH HOH . G 4 HOH A 79 493 156 HOH HOH . G 4 HOH A 80 494 159 HOH HOH . H 4 HOH B 1 915 2 HOH HOH . H 4 HOH B 2 916 11 HOH HOH . H 4 HOH B 3 917 13 HOH HOH . H 4 HOH B 4 918 15 HOH HOH . H 4 HOH B 5 919 17 HOH HOH . H 4 HOH B 6 920 20 HOH HOH . H 4 HOH B 7 921 22 HOH HOH . H 4 HOH B 8 922 23 HOH HOH . H 4 HOH B 9 923 25 HOH HOH . H 4 HOH B 10 924 26 HOH HOH . H 4 HOH B 11 925 28 HOH HOH . H 4 HOH B 12 926 30 HOH HOH . H 4 HOH B 13 927 31 HOH HOH . H 4 HOH B 14 928 32 HOH HOH . H 4 HOH B 15 929 34 HOH HOH . H 4 HOH B 16 930 35 HOH HOH . H 4 HOH B 17 931 38 HOH HOH . H 4 HOH B 18 932 39 HOH HOH . H 4 HOH B 19 933 40 HOH HOH . H 4 HOH B 20 934 43 HOH HOH . H 4 HOH B 21 935 44 HOH HOH . H 4 HOH B 22 936 48 HOH HOH . H 4 HOH B 23 937 49 HOH HOH . H 4 HOH B 24 938 50 HOH HOH . H 4 HOH B 25 939 51 HOH HOH . H 4 HOH B 26 940 53 HOH HOH . H 4 HOH B 27 941 54 HOH HOH . H 4 HOH B 28 942 55 HOH HOH . H 4 HOH B 29 943 56 HOH HOH . H 4 HOH B 30 944 57 HOH HOH . H 4 HOH B 31 945 60 HOH HOH . H 4 HOH B 32 946 66 HOH HOH . H 4 HOH B 33 947 68 HOH HOH . H 4 HOH B 34 948 69 HOH HOH . H 4 HOH B 35 949 70 HOH HOH . H 4 HOH B 36 950 71 HOH HOH . H 4 HOH B 37 951 72 HOH HOH . H 4 HOH B 38 952 73 HOH HOH . H 4 HOH B 39 953 85 HOH HOH . H 4 HOH B 40 954 86 HOH HOH . H 4 HOH B 41 955 89 HOH HOH . H 4 HOH B 42 956 93 HOH HOH . H 4 HOH B 43 957 95 HOH HOH . H 4 HOH B 44 958 96 HOH HOH . H 4 HOH B 45 959 97 HOH HOH . H 4 HOH B 46 960 99 HOH HOH . H 4 HOH B 47 961 106 HOH HOH . H 4 HOH B 48 962 109 HOH HOH . H 4 HOH B 49 963 110 HOH HOH . H 4 HOH B 50 964 111 HOH HOH . H 4 HOH B 51 965 112 HOH HOH . H 4 HOH B 52 966 113 HOH HOH . H 4 HOH B 53 967 116 HOH HOH . H 4 HOH B 54 968 117 HOH HOH . H 4 HOH B 55 969 119 HOH HOH . H 4 HOH B 56 970 122 HOH HOH . H 4 HOH B 57 971 123 HOH HOH . H 4 HOH B 58 972 125 HOH HOH . H 4 HOH B 59 973 126 HOH HOH . H 4 HOH B 60 974 127 HOH HOH . H 4 HOH B 61 975 128 HOH HOH . H 4 HOH B 62 976 131 HOH HOH . H 4 HOH B 63 977 132 HOH HOH . H 4 HOH B 64 978 134 HOH HOH . H 4 HOH B 65 979 135 HOH HOH . H 4 HOH B 66 980 136 HOH HOH . H 4 HOH B 67 981 138 HOH HOH . H 4 HOH B 68 982 139 HOH HOH . H 4 HOH B 69 983 142 HOH HOH . H 4 HOH B 70 984 144 HOH HOH . H 4 HOH B 71 985 145 HOH HOH . H 4 HOH B 72 986 147 HOH HOH . H 4 HOH B 73 987 148 HOH HOH . H 4 HOH B 74 988 151 HOH HOH . H 4 HOH B 75 989 152 HOH HOH . H 4 HOH B 76 990 154 HOH HOH . H 4 HOH B 77 991 155 HOH HOH . H 4 HOH B 78 992 157 HOH HOH . H 4 HOH B 79 993 158 HOH HOH . H 4 HOH B 80 994 160 HOH HOH . H 4 HOH B 81 995 161 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 19.607 52.735 -5.057 1 25.72 ? N1 PLP 413 A 1 HETATM 2 C C2 PLP . . . C 2 20.192 51.595 -5.518 1 25.77 ? C2 PLP 413 A 1 HETATM 3 C C2A PLP . . . C 2 21.178 50.845 -4.552 1 25.15 ? C2A PLP 413 A 1 HETATM 4 C C3 PLP . . . C 2 19.909 51.142 -6.808 1 23.51 ? C3 PLP 413 A 1 HETATM 5 O O3 PLP . . . C 2 20.499 50.017 -7.273 1 19.58 ? O3 PLP 413 A 1 HETATM 6 C C4 PLP . . . C 2 19.03 51.862 -7.615 1 24.97 ? C4 PLP 413 A 1 HETATM 7 C C4A PLP . . . C 2 18.704 51.373 -9.014 1 24.62 ? C4A PLP 413 A 1 HETATM 8 C C5 PLP . . . C 2 18.437 53.041 -7.106 1 25.34 ? C5 PLP 413 A 1 HETATM 9 C C6 PLP . . . C 2 18.745 53.443 -5.839 1 26.61 ? C6 PLP 413 A 1 HETATM 10 C C5A PLP . . . C 2 17.462 53.96 -7.878 1 26.28 ? C5A PLP 413 A 1 HETATM 11 O O4P PLP . . . C 2 16.229 53.463 -8.489 1 30.36 ? O4P PLP 413 A 1 HETATM 12 P P PLP . . . C 2 15.929 53.935 -10.014 1 27.4 ? P PLP 413 A 1 HETATM 13 O O1P PLP . . . C 2 17.017 53.511 -10.912 1 26.56 ? O1P PLP 413 A 1 HETATM 14 O O2P PLP . . . C 2 14.653 53.07 -10.355 1 28.01 ? O2P PLP 413 A 1 HETATM 15 O O3P PLP . . . C 2 15.583 55.363 -9.982 1 27.49 ? O3P PLP 413 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #