data_2HHF # _model_server_result.job_id WJmHdVvGtafs12G560L04g _model_server_result.datetime_utc '2024-10-11 13:21:55' _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 2hhf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 2HHF # _exptl.entry_id 2HHF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _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 100.72 _cell.angle_gamma 90 _cell.entry_id 2HHF _cell.length_a 58.123 _cell.length_b 104.183 _cell.length_c 58.264 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HHF _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,G _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 ? 3 C N N ? 3 D 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 disulf ? disulf1 A SG CYS 315 A CYS 315 1_555 A SG CYS 318 A CYS 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 B SG CYS 315 B CYS 815 1_555 B SG CYS 318 B CYS 818 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A C LEU 107 A LEU 107 1_555 A N OCS 108 A OCS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale2 A C OCS 108 A OCS 108 1_555 A N LEU 109 A LEU 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale3 A C LEU 140 A LEU 140 1_555 A N TYO 141 A TYO 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? covale ? covale4 A C TYO 141 A TYO 141 1_555 A N VAL 142 A VAL 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale5 A NZ LYS 202 A LYS 202 1_555 C C4A PLP . A PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.383 ? covale ? covale6 D C4A PLP . B PLP 401 1_555 B NZ LYS 202 B LYS 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.382 ? covale ? covale7 B C LEU 107 B LEU 607 1_555 B N OCS 108 B OCS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale8 B C OCS 108 B OCS 608 1_555 B N LEU 109 B LEU 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 309 n y N1 C6 PLP sing 310 n y C2 C2A PLP sing 311 n n C2 C3 PLP sing 312 n y C2A H2A1 PLP sing 313 n n C2A H2A2 PLP sing 314 n n C2A H2A3 PLP sing 315 n n C3 O3 PLP sing 316 n n C3 C4 PLP doub 317 n y O3 HO3 PLP sing 318 n n C4 C4A PLP sing 319 n n C4 C5 PLP sing 320 n y C4A O4A PLP doub 321 n n C4A H4A PLP sing 322 n n C5 C6 PLP doub 323 n y C5 C5A PLP sing 324 n n C6 H6 PLP sing 325 n n C5A O4P PLP sing 326 n n C5A H5A1 PLP sing 327 n n C5A H5A2 PLP sing 328 n n O4P P PLP sing 329 n n P O1P PLP doub 330 n n P O2P PLP sing 331 n n P O3P PLP sing 332 n n O2P HOP2 PLP sing 333 n n O3P HOP3 PLP sing 334 n n # _atom_sites.entry_id 2HHF _atom_sites.fract_transf_matrix[1][1] 0.017205 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003257 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009598 _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] 0.017468 _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 PLP A 1 400 400 PLP PLP . D 3 PLP B 1 401 401 PLP PLP . E 4 EPE B 1 430 430 EPE EPE . F 5 HOH A 1 401 3 HOH HOH . F 5 HOH A 2 402 5 HOH HOH . F 5 HOH A 3 403 6 HOH HOH . F 5 HOH A 4 404 7 HOH HOH . F 5 HOH A 5 405 8 HOH HOH . F 5 HOH A 6 406 12 HOH HOH . F 5 HOH A 7 407 13 HOH HOH . F 5 HOH A 8 408 16 HOH HOH . F 5 HOH A 9 409 19 HOH HOH . F 5 HOH A 10 410 20 HOH HOH . F 5 HOH A 11 411 21 HOH HOH . F 5 HOH A 12 412 23 HOH HOH . F 5 HOH A 13 413 26 HOH HOH . F 5 HOH A 14 414 29 HOH HOH . F 5 HOH A 15 415 32 HOH HOH . F 5 HOH A 16 416 33 HOH HOH . F 5 HOH A 17 417 39 HOH HOH . F 5 HOH A 18 418 40 HOH HOH . F 5 HOH A 19 419 42 HOH HOH . F 5 HOH A 20 420 44 HOH HOH . F 5 HOH A 21 421 45 HOH HOH . F 5 HOH A 22 422 50 HOH HOH . F 5 HOH A 23 423 52 HOH HOH . F 5 HOH A 24 424 54 HOH HOH . F 5 HOH A 25 425 58 HOH HOH . F 5 HOH A 26 426 59 HOH HOH . F 5 HOH A 27 427 60 HOH HOH . F 5 HOH A 28 428 62 HOH HOH . F 5 HOH A 29 429 63 HOH HOH . F 5 HOH A 30 430 65 HOH HOH . F 5 HOH A 31 431 68 HOH HOH . F 5 HOH A 32 432 70 HOH HOH . F 5 HOH A 33 433 72 HOH HOH . F 5 HOH A 34 434 73 HOH HOH . F 5 HOH A 35 435 74 HOH HOH . F 5 HOH A 36 436 75 HOH HOH . F 5 HOH A 37 437 78 HOH HOH . F 5 HOH A 38 438 79 HOH HOH . F 5 HOH A 39 439 80 HOH HOH . F 5 HOH A 40 440 91 HOH HOH . F 5 HOH A 41 441 92 HOH HOH . F 5 HOH A 42 442 93 HOH HOH . F 5 HOH A 43 443 94 HOH HOH . F 5 HOH A 44 444 98 HOH HOH . F 5 HOH A 45 445 100 HOH HOH . F 5 HOH A 46 446 103 HOH HOH . F 5 HOH A 47 447 105 HOH HOH . F 5 HOH A 48 448 107 HOH HOH . F 5 HOH A 49 449 110 HOH HOH . F 5 HOH A 50 450 113 HOH HOH . F 5 HOH A 51 451 115 HOH HOH . F 5 HOH A 52 452 116 HOH HOH . F 5 HOH A 53 453 119 HOH HOH . F 5 HOH A 54 454 122 HOH HOH . F 5 HOH A 55 455 123 HOH HOH . F 5 HOH A 56 456 124 HOH HOH . F 5 HOH A 57 457 125 HOH HOH . F 5 HOH A 58 458 126 HOH HOH . F 5 HOH A 59 459 129 HOH HOH . F 5 HOH A 60 460 130 HOH HOH . F 5 HOH A 61 461 132 HOH HOH . F 5 HOH A 62 462 137 HOH HOH . F 5 HOH A 63 463 138 HOH HOH . F 5 HOH A 64 464 139 HOH HOH . F 5 HOH A 65 465 142 HOH HOH . F 5 HOH A 66 466 143 HOH HOH . F 5 HOH A 67 467 144 HOH HOH . F 5 HOH A 68 468 145 HOH HOH . F 5 HOH A 69 469 148 HOH HOH . F 5 HOH A 70 470 149 HOH HOH . F 5 HOH A 71 471 153 HOH HOH . F 5 HOH A 72 472 154 HOH HOH . F 5 HOH A 73 473 156 HOH HOH . F 5 HOH A 74 474 157 HOH HOH . F 5 HOH A 75 475 158 HOH HOH . F 5 HOH A 76 476 160 HOH HOH . F 5 HOH A 77 477 162 HOH HOH . F 5 HOH A 78 478 164 HOH HOH . F 5 HOH A 79 479 166 HOH HOH . F 5 HOH A 80 480 172 HOH HOH . F 5 HOH A 81 481 176 HOH HOH . F 5 HOH A 82 482 177 HOH HOH . F 5 HOH A 83 483 179 HOH HOH . F 5 HOH A 84 484 180 HOH HOH . F 5 HOH A 85 485 183 HOH HOH . F 5 HOH A 86 486 184 HOH HOH . F 5 HOH A 87 487 185 HOH HOH . F 5 HOH A 88 488 186 HOH HOH . F 5 HOH A 89 489 187 HOH HOH . F 5 HOH A 90 490 189 HOH HOH . F 5 HOH A 91 491 191 HOH HOH . F 5 HOH A 92 492 195 HOH HOH . F 5 HOH A 93 493 198 HOH HOH . F 5 HOH A 94 494 199 HOH HOH . F 5 HOH A 95 495 202 HOH HOH . F 5 HOH A 96 496 204 HOH HOH . F 5 HOH A 97 497 205 HOH HOH . G 5 HOH B 1 1 1 HOH HOH . G 5 HOH B 2 2 2 HOH HOH . G 5 HOH B 3 4 4 HOH HOH . G 5 HOH B 4 9 9 HOH HOH . G 5 HOH B 5 10 10 HOH HOH . G 5 HOH B 6 11 11 HOH HOH . G 5 HOH B 7 14 14 HOH HOH . G 5 HOH B 8 15 15 HOH HOH . G 5 HOH B 9 17 17 HOH HOH . G 5 HOH B 10 18 18 HOH HOH . G 5 HOH B 11 22 22 HOH HOH . G 5 HOH B 12 24 24 HOH HOH . G 5 HOH B 13 25 25 HOH HOH . G 5 HOH B 14 27 27 HOH HOH . G 5 HOH B 15 28 28 HOH HOH . G 5 HOH B 16 30 30 HOH HOH . G 5 HOH B 17 31 31 HOH HOH . G 5 HOH B 18 34 34 HOH HOH . G 5 HOH B 19 35 35 HOH HOH . G 5 HOH B 20 36 36 HOH HOH . G 5 HOH B 21 37 37 HOH HOH . G 5 HOH B 22 38 38 HOH HOH . G 5 HOH B 23 41 41 HOH HOH . G 5 HOH B 24 43 43 HOH HOH . G 5 HOH B 25 46 46 HOH HOH . G 5 HOH B 26 47 47 HOH HOH . G 5 HOH B 27 48 48 HOH HOH . G 5 HOH B 28 49 49 HOH HOH . G 5 HOH B 29 51 51 HOH HOH . G 5 HOH B 30 53 53 HOH HOH . G 5 HOH B 31 55 55 HOH HOH . G 5 HOH B 32 56 56 HOH HOH . G 5 HOH B 33 57 57 HOH HOH . G 5 HOH B 34 61 61 HOH HOH . G 5 HOH B 35 64 64 HOH HOH . G 5 HOH B 36 66 66 HOH HOH . G 5 HOH B 37 67 67 HOH HOH . G 5 HOH B 38 69 69 HOH HOH . G 5 HOH B 39 71 71 HOH HOH . G 5 HOH B 40 76 76 HOH HOH . G 5 HOH B 41 77 77 HOH HOH . G 5 HOH B 42 81 81 HOH HOH . G 5 HOH B 43 82 82 HOH HOH . G 5 HOH B 44 83 83 HOH HOH . G 5 HOH B 45 84 84 HOH HOH . G 5 HOH B 46 85 85 HOH HOH . G 5 HOH B 47 86 86 HOH HOH . G 5 HOH B 48 87 87 HOH HOH . G 5 HOH B 49 88 88 HOH HOH . G 5 HOH B 50 89 89 HOH HOH . G 5 HOH B 51 90 90 HOH HOH . G 5 HOH B 52 95 95 HOH HOH . G 5 HOH B 53 96 96 HOH HOH . G 5 HOH B 54 97 97 HOH HOH . G 5 HOH B 55 99 99 HOH HOH . G 5 HOH B 56 101 101 HOH HOH . G 5 HOH B 57 102 102 HOH HOH . G 5 HOH B 58 104 104 HOH HOH . G 5 HOH B 59 106 106 HOH HOH . G 5 HOH B 60 108 108 HOH HOH . G 5 HOH B 61 109 109 HOH HOH . G 5 HOH B 62 111 111 HOH HOH . G 5 HOH B 63 112 112 HOH HOH . G 5 HOH B 64 114 114 HOH HOH . G 5 HOH B 65 117 117 HOH HOH . G 5 HOH B 66 118 118 HOH HOH . G 5 HOH B 67 120 120 HOH HOH . G 5 HOH B 68 121 121 HOH HOH . G 5 HOH B 69 127 127 HOH HOH . G 5 HOH B 70 128 128 HOH HOH . G 5 HOH B 71 131 131 HOH HOH . G 5 HOH B 72 133 133 HOH HOH . G 5 HOH B 73 134 134 HOH HOH . G 5 HOH B 74 135 135 HOH HOH . G 5 HOH B 75 136 136 HOH HOH . G 5 HOH B 76 140 140 HOH HOH . G 5 HOH B 77 141 141 HOH HOH . G 5 HOH B 78 146 146 HOH HOH . G 5 HOH B 79 147 147 HOH HOH . G 5 HOH B 80 150 150 HOH HOH . G 5 HOH B 81 151 151 HOH HOH . G 5 HOH B 82 152 152 HOH HOH . G 5 HOH B 83 155 155 HOH HOH . G 5 HOH B 84 159 159 HOH HOH . G 5 HOH B 85 161 161 HOH HOH . G 5 HOH B 86 163 163 HOH HOH . G 5 HOH B 87 165 165 HOH HOH . G 5 HOH B 88 167 167 HOH HOH . G 5 HOH B 89 168 168 HOH HOH . G 5 HOH B 90 169 169 HOH HOH . G 5 HOH B 91 170 170 HOH HOH . G 5 HOH B 92 171 171 HOH HOH . G 5 HOH B 93 173 173 HOH HOH . G 5 HOH B 94 174 174 HOH HOH . G 5 HOH B 95 175 175 HOH HOH . G 5 HOH B 96 178 178 HOH HOH . G 5 HOH B 97 181 181 HOH HOH . G 5 HOH B 98 182 182 HOH HOH . G 5 HOH B 99 188 188 HOH HOH . G 5 HOH B 100 190 190 HOH HOH . G 5 HOH B 101 192 192 HOH HOH . G 5 HOH B 102 193 193 HOH HOH . G 5 HOH B 103 194 194 HOH HOH . G 5 HOH B 104 196 196 HOH HOH . G 5 HOH B 105 197 197 HOH HOH . G 5 HOH B 106 200 200 HOH HOH . G 5 HOH B 107 201 201 HOH HOH . G 5 HOH B 108 203 203 HOH HOH . G 5 HOH B 109 206 206 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 . . . D 3 2.393 5.007 -3.529 1 19.43 ? N1 PLP 401 B 1 HETATM 2 C C2 PLP . . . D 3 3.603 4.746 -2.986 1 20.33 ? C2 PLP 401 B 1 HETATM 3 C C2A PLP . . . D 3 3.784 3.421 -2.172 1 21.76 ? C2A PLP 401 B 1 HETATM 4 C C3 PLP . . . D 3 4.637 5.669 -3.17 1 21.05 ? C3 PLP 401 B 1 HETATM 5 O O3 PLP . . . D 3 5.822 5.408 -2.635 1 22.92 ? O3 PLP 401 B 1 HETATM 6 C C4 PLP . . . D 3 4.434 6.855 -3.903 1 19.85 ? C4 PLP 401 B 1 HETATM 7 C C4A PLP . . . D 3 5.62 7.865 -4.063 1 24.65 ? C4A PLP 401 B 1 HETATM 8 C C5 PLP . . . D 3 3.141 7.066 -4.463 1 19.17 ? C5 PLP 401 B 1 HETATM 9 C C6 PLP . . . D 3 2.157 6.143 -4.264 1 19.3 ? C6 PLP 401 B 1 HETATM 10 C C5A PLP . . . D 3 2.765 8.211 -5.333 1 21.8 ? C5A PLP 401 B 1 HETATM 11 O O4P PLP . . . D 3 3.011 9.457 -4.821 1 20.07 ? O4P PLP 401 B 1 HETATM 12 P P PLP . . . D 3 3.191 10.673 -5.776 1 18.22 ? P PLP 401 B 1 HETATM 13 O O1P PLP . . . D 3 4.444 10.668 -6.484 1 16.62 ? O1P PLP 401 B 1 HETATM 14 O O2P PLP . . . D 3 3.338 11.774 -4.711 1 18.62 ? O2P PLP 401 B 1 HETATM 15 O O3P PLP . . . D 3 1.918 10.901 -6.489 1 15.48 ? O3P PLP 401 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #