data_8B08 # _model_server_result.job_id Ssn4qH5P1Lt3FYULFH8Qrw _model_server_result.datetime_utc '2024-11-27 21:56:56' _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 8b08 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 8B08 # _exptl.entry_id 8B08 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 336.235 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE' _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 94.75 _cell.angle_gamma 90 _cell.entry_id 8B08 _cell.length_a 182.482 _cell.length_b 60.093 _cell.length_c 67.341 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B08 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 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,H,I _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 E _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 metalc ? metalc1 B O GLY 232 B GLY 232 1_555 D CS CS . B CS 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc2 B O GLY 268 B GLY 268 1_555 D CS CS . B CS 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.157 ? metalc ? metalc3 B O PHE 306 B PHE 306 1_555 D CS CS . B CS 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc4 B O SER 308 B SER 308 1_555 D CS CS . B CS 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.481 ? metalc ? metalc5 D CS CS . B CS 401 1_555 I O HOH . B HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? # _chem_comp.formula 'C11 H17 N2 O8 P' _chem_comp.formula_weight 336.235 _chem_comp.id PLS _chem_comp.mon_nstd_flag . _chem_comp.name '[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PYRIDOXYL-SERINE-5-MONOPHOSPHATE # 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 N CA PLS sing 278 n n N C4A PLS sing 279 n n N HN PLS sing 280 n n CA CB PLS sing 281 n n CA C PLS sing 282 n n CA HA PLS sing 283 n n CB OG PLS sing 284 n n CB HB1 PLS sing 285 n n CB HB2 PLS sing 286 n n OG HOG PLS sing 287 n n C O PLS doub 288 n n C OXT PLS sing 289 n n OXT HXT PLS sing 290 n n N1 C2 PLS doub 291 n y N1 C6 PLS sing 292 n y C2 C2A PLS sing 293 n n C2 C3 PLS sing 294 n y C2A H2A1 PLS sing 295 n n C2A H2A2 PLS sing 296 n n C2A H2A3 PLS sing 297 n n C3 O3 PLS sing 298 n n C3 C4 PLS doub 299 n y O3 HO3 PLS sing 300 n n C4 C4A PLS sing 301 n n C4 C5 PLS sing 302 n y C4A H4A1 PLS sing 303 n n C4A H4A2 PLS sing 304 n n C5 C6 PLS doub 305 n y C5 C5A PLS sing 306 n n C6 H6 PLS sing 307 n n C5A O4P PLS sing 308 n n C5A H5A1 PLS sing 309 n n C5A H5A2 PLS sing 310 n n O4P P PLS sing 311 n n P O1P PLS doub 312 n n P O2P PLS sing 313 n n P O3P PLS sing 314 n n O2P HOP2 PLS sing 315 n n O3P HOP3 PLS sing 316 n n # _atom_sites.entry_id 8B08 _atom_sites.fract_transf_matrix[1][1] 0.00548 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000455 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016641 _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] 0.014901 _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 G3P A 1 301 301 G3P G3P . D 4 CS B 1 401 401 CS CS . E 5 PLS B 1 402 501 PLS PLS . F 6 CL B 1 403 1 CL CL . G 6 CL B 1 404 2 CL CL . H 7 HOH A 1 401 41 HOH HOH . H 7 HOH A 2 402 39 HOH HOH . H 7 HOH A 3 403 85 HOH HOH . H 7 HOH A 4 404 68 HOH HOH . H 7 HOH A 5 405 63 HOH HOH . H 7 HOH A 6 406 37 HOH HOH . H 7 HOH A 7 407 21 HOH HOH . H 7 HOH A 8 408 26 HOH HOH . H 7 HOH A 9 409 54 HOH HOH . H 7 HOH A 10 410 79 HOH HOH . H 7 HOH A 11 411 48 HOH HOH . H 7 HOH A 12 412 123 HOH HOH . H 7 HOH A 13 413 27 HOH HOH . H 7 HOH A 14 414 92 HOH HOH . H 7 HOH A 15 415 64 HOH HOH . H 7 HOH A 16 416 24 HOH HOH . H 7 HOH A 17 417 69 HOH HOH . H 7 HOH A 18 418 14 HOH HOH . H 7 HOH A 19 419 50 HOH HOH . H 7 HOH A 20 420 35 HOH HOH . H 7 HOH A 21 421 34 HOH HOH . H 7 HOH A 22 422 75 HOH HOH . H 7 HOH A 23 423 62 HOH HOH . H 7 HOH A 24 424 40 HOH HOH . H 7 HOH A 25 425 25 HOH HOH . H 7 HOH A 26 426 56 HOH HOH . H 7 HOH A 27 427 71 HOH HOH . H 7 HOH A 28 428 116 HOH HOH . H 7 HOH A 29 429 90 HOH HOH . H 7 HOH A 30 430 95 HOH HOH . H 7 HOH A 31 431 104 HOH HOH . H 7 HOH A 32 432 135 HOH HOH . H 7 HOH A 33 433 136 HOH HOH . H 7 HOH A 34 434 88 HOH HOH . H 7 HOH A 35 435 134 HOH HOH . H 7 HOH A 36 436 137 HOH HOH . H 7 HOH A 37 437 91 HOH HOH . I 7 HOH B 1 501 82 HOH HOH . I 7 HOH B 2 502 72 HOH HOH . I 7 HOH B 3 503 9 HOH HOH . I 7 HOH B 4 504 38 HOH HOH . I 7 HOH B 5 505 106 HOH HOH . I 7 HOH B 6 506 17 HOH HOH . I 7 HOH B 7 507 57 HOH HOH . I 7 HOH B 8 508 61 HOH HOH . I 7 HOH B 9 509 10 HOH HOH . I 7 HOH B 10 510 49 HOH HOH . I 7 HOH B 11 511 42 HOH HOH . I 7 HOH B 12 512 105 HOH HOH . I 7 HOH B 13 513 52 HOH HOH . I 7 HOH B 14 514 55 HOH HOH . I 7 HOH B 15 515 13 HOH HOH . I 7 HOH B 16 516 60 HOH HOH . I 7 HOH B 17 517 107 HOH HOH . I 7 HOH B 18 518 16 HOH HOH . I 7 HOH B 19 519 65 HOH HOH . I 7 HOH B 20 520 12 HOH HOH . I 7 HOH B 21 521 125 HOH HOH . I 7 HOH B 22 522 122 HOH HOH . I 7 HOH B 23 523 74 HOH HOH . I 7 HOH B 24 524 59 HOH HOH . I 7 HOH B 25 525 73 HOH HOH . I 7 HOH B 26 526 3 HOH HOH . I 7 HOH B 27 527 118 HOH HOH . I 7 HOH B 28 528 81 HOH HOH . I 7 HOH B 29 529 18 HOH HOH . I 7 HOH B 30 530 11 HOH HOH . I 7 HOH B 31 531 45 HOH HOH . I 7 HOH B 32 532 66 HOH HOH . I 7 HOH B 33 533 124 HOH HOH . I 7 HOH B 34 534 78 HOH HOH . I 7 HOH B 35 535 5 HOH HOH . I 7 HOH B 36 536 51 HOH HOH . I 7 HOH B 37 537 44 HOH HOH . I 7 HOH B 38 538 36 HOH HOH . I 7 HOH B 39 539 86 HOH HOH . I 7 HOH B 40 540 7 HOH HOH . I 7 HOH B 41 541 4 HOH HOH . I 7 HOH B 42 542 19 HOH HOH . I 7 HOH B 43 543 8 HOH HOH . I 7 HOH B 44 544 108 HOH HOH . I 7 HOH B 45 545 119 HOH HOH . I 7 HOH B 46 546 58 HOH HOH . I 7 HOH B 47 547 83 HOH HOH . I 7 HOH B 48 548 30 HOH HOH . I 7 HOH B 49 549 28 HOH HOH . I 7 HOH B 50 550 2 HOH HOH . I 7 HOH B 51 551 32 HOH HOH . I 7 HOH B 52 552 129 HOH HOH . I 7 HOH B 53 553 115 HOH HOH . I 7 HOH B 54 554 70 HOH HOH . I 7 HOH B 55 555 22 HOH HOH . I 7 HOH B 56 556 33 HOH HOH . I 7 HOH B 57 557 29 HOH HOH . I 7 HOH B 58 558 131 HOH HOH . I 7 HOH B 59 559 80 HOH HOH . I 7 HOH B 60 560 110 HOH HOH . I 7 HOH B 61 561 101 HOH HOH . I 7 HOH B 62 562 1 HOH HOH . I 7 HOH B 63 563 121 HOH HOH . I 7 HOH B 64 564 97 HOH HOH . I 7 HOH B 65 565 23 HOH HOH . I 7 HOH B 66 566 46 HOH HOH . I 7 HOH B 67 567 31 HOH HOH . I 7 HOH B 68 568 87 HOH HOH . I 7 HOH B 69 569 102 HOH HOH . I 7 HOH B 70 570 84 HOH HOH . I 7 HOH B 71 571 47 HOH HOH . I 7 HOH B 72 572 93 HOH HOH . I 7 HOH B 73 573 99 HOH HOH . I 7 HOH B 74 574 43 HOH HOH . I 7 HOH B 75 575 89 HOH HOH . I 7 HOH B 76 576 111 HOH HOH . I 7 HOH B 77 577 77 HOH HOH . I 7 HOH B 78 578 15 HOH HOH . I 7 HOH B 79 579 94 HOH HOH . I 7 HOH B 80 580 53 HOH HOH . I 7 HOH B 81 581 120 HOH HOH . I 7 HOH B 82 582 109 HOH HOH . I 7 HOH B 83 583 113 HOH HOH . I 7 HOH B 84 584 20 HOH HOH . I 7 HOH B 85 585 67 HOH HOH . I 7 HOH B 86 586 76 HOH HOH . I 7 HOH B 87 587 100 HOH HOH . I 7 HOH B 88 588 98 HOH HOH . I 7 HOH B 89 589 114 HOH HOH . I 7 HOH B 90 590 112 HOH HOH . I 7 HOH B 91 591 96 HOH HOH . I 7 HOH B 92 592 103 HOH HOH . I 7 HOH B 93 593 117 HOH HOH . I 7 HOH B 94 594 133 HOH HOH . I 7 HOH B 95 595 128 HOH HOH . I 7 HOH B 96 596 127 HOH HOH . I 7 HOH B 97 597 126 HOH HOH . I 7 HOH B 98 598 130 HOH HOH . I 7 HOH B 99 599 138 HOH HOH . I 7 HOH B 100 600 132 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 N PLS . . . E 5 80.07 16.965 10.038 1 41.5 ? N PLS 402 B 1 HETATM 2 C CA PLS . . . E 5 78.633 17.234 10.039 1 43.79 ? CA PLS 402 B 1 HETATM 3 C CB PLS . . . E 5 78.247 18.043 11.275 1 46.1 ? CB PLS 402 B 1 HETATM 4 O OG PLS . . . E 5 78.358 19.406 10.979 1 48.39 ? OG PLS 402 B 1 HETATM 5 C C PLS . . . E 5 78.217 17.994 8.778 1 46.56 ? C PLS 402 B 1 HETATM 6 O O PLS . . . E 5 79.099 18.352 7.954 1 48.81 ? O PLS 402 B 1 HETATM 7 O OXT PLS . . . E 5 77.001 18.254 8.558 1 47.51 ? OXT PLS 402 B 1 HETATM 8 N N1 PLS . . . E 5 84.001 14.054 11.564 1 27.53 ? N1 PLS 402 B 1 HETATM 9 C C2 PLS . . . E 5 83.784 14.841 10.49 1 29.32 ? C2 PLS 402 B 1 HETATM 10 C C2A PLS . . . E 5 84.825 14.903 9.381 1 29.44 ? C2A PLS 402 B 1 HETATM 11 C C3 PLS . . . E 5 82.62 15.588 10.389 1 29.5 ? C3 PLS 402 B 1 HETATM 12 O O3 PLS . . . E 5 82.408 16.4 9.268 1 27.45 ? O3 PLS 402 B 1 HETATM 13 C C4 PLS . . . E 5 81.689 15.532 11.375 1 30 ? C4 PLS 402 B 1 HETATM 14 C C4A PLS . . . E 5 80.39 16.345 11.314 1 32.83 ? C4A PLS 402 B 1 HETATM 15 C C5 PLS . . . E 5 81.917 14.739 12.456 1 29.94 ? C5 PLS 402 B 1 HETATM 16 C C6 PLS . . . E 5 83.081 13.996 12.549 1 29.47 ? C6 PLS 402 B 1 HETATM 17 C C5A PLS . . . E 5 80.897 14.659 13.59 1 24.87 ? C5A PLS 402 B 1 HETATM 18 O O4P PLS . . . E 5 79.781 13.917 13.197 1 23.46 ? O4P PLS 402 B 1 HETATM 19 P P PLS . . . E 5 79.368 12.616 14.114 1 24.81 ? P PLS 402 B 1 HETATM 20 O O1P PLS . . . E 5 80.134 11.396 13.66 1 27.42 ? O1P PLS 402 B 1 HETATM 21 O O2P PLS . . . E 5 79.692 12.909 15.557 1 31.48 -1 O2P PLS 402 B 1 HETATM 22 O O3P PLS . . . E 5 77.88 12.39 13.965 1 33.79 ? O3P PLS 402 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #