data_1RFT
#
_model_server_result.job_id            BxAAw09kpXVCghD2EpTmew 
_model_server_result.datetime_utc      '2024-11-28 19:37:27' 
_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          1rft 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":402}' 
#
_entry.id    1RFT 
#
_exptl.entry_id    1RFT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              168.193 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL 
_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         120 
_cell.entry_id            1RFT 
_cell.length_a            103.687 
_cell.length_b            103.687 
_cell.length_c            58.604 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RFT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 A OD2 ASP 113 A ASP 113 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.394 ? 
metalc ? metalc2 A O THR 148 A THR 148 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc3 A OG1 THR 186 A THR 186 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.453 ? 
metalc ? metalc4 D O2G ACP . A ACP 401 1_555 B ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? 
metalc ? metalc5 D O1B ACP . A ACP 401 1_555 B ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc6 D O1B ACP . A ACP 401 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? 
metalc ? metalc7 C K K . A K 404 1_555 F O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? 
#
_chem_comp.formula           'C8 H12 N2 O2' 
_chem_comp.formula_weight    168.193 
_chem_comp.id                PXM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     PYRIDOXAMINE 
#
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 PXM doub 328 n y 
N1 C6 PXM sing 329 n y 
C2 C2A PXM sing 330 n n 
C2 C3 PXM sing 331 n y 
C2A H2A1 PXM sing 332 n n 
C2A H2A2 PXM sing 333 n n 
C2A H2A3 PXM sing 334 n n 
C3 O3 PXM sing 335 n n 
C3 C4 PXM doub 336 n y 
O3 HO3 PXM sing 337 n n 
C4 C5 PXM sing 338 n y 
C4 C4A PXM sing 339 n n 
C5 C5A PXM sing 340 n n 
C5 C6 PXM doub 341 n y 
C5A O5 PXM sing 342 n n 
C5A H5A1 PXM sing 343 n n 
C5A H5A2 PXM sing 344 n n 
O5 HO5 PXM sing 345 n n 
C6 H6 PXM sing 346 n n 
C4A N4 PXM sing 347 n n 
C4A H4A1 PXM sing 348 n n 
C4A H4A2 PXM sing 349 n n 
N4 HN41 PXM sing 350 n n 
N4 HN42 PXM sing 351 n n 
#
_atom_sites.entry_id                     1RFT 
_atom_sites.fract_transf_matrix[1][1]    0.009644 
_atom_sites.fract_transf_matrix[1][2]    0.005568 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011136 
_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]    0.017064 
_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
B 2 ZN A 1 403 403 ZN ZN2 . 
C 3 K A 1 404 404 K K1 . 
D 4 ACP A 1 401 401 ACP ACP . 
E 5 PXM A 1 402 402 PXM PYM . 
F 6 HOH A 1 405 1 HOH WAT . 
F 6 HOH A 2 406 2 HOH WAT . 
F 6 HOH A 3 407 3 HOH WAT . 
F 6 HOH A 4 408 4 HOH WAT . 
F 6 HOH A 5 409 5 HOH WAT . 
F 6 HOH A 6 410 6 HOH WAT . 
F 6 HOH A 7 411 7 HOH WAT . 
F 6 HOH A 8 412 8 HOH WAT . 
F 6 HOH A 9 413 9 HOH WAT . 
F 6 HOH A 10 414 10 HOH WAT . 
F 6 HOH A 11 415 11 HOH WAT . 
F 6 HOH A 12 416 12 HOH WAT . 
F 6 HOH A 13 417 13 HOH WAT . 
F 6 HOH A 14 418 14 HOH WAT . 
F 6 HOH A 15 419 15 HOH WAT . 
F 6 HOH A 16 420 16 HOH WAT . 
F 6 HOH A 17 421 17 HOH WAT . 
F 6 HOH A 18 422 18 HOH WAT . 
F 6 HOH A 19 423 19 HOH WAT . 
F 6 HOH A 20 424 20 HOH WAT . 
F 6 HOH A 21 425 21 HOH WAT . 
F 6 HOH A 22 426 22 HOH WAT . 
F 6 HOH A 23 427 23 HOH WAT . 
F 6 HOH A 24 428 24 HOH WAT . 
F 6 HOH A 25 429 25 HOH WAT . 
F 6 HOH A 26 430 26 HOH WAT . 
F 6 HOH A 27 431 27 HOH WAT . 
F 6 HOH A 28 432 28 HOH WAT . 
F 6 HOH A 29 433 29 HOH WAT . 
F 6 HOH A 30 434 30 HOH WAT . 
F 6 HOH A 31 435 31 HOH WAT . 
F 6 HOH A 32 436 32 HOH WAT . 
F 6 HOH A 33 437 33 HOH WAT . 
F 6 HOH A 34 438 34 HOH WAT . 
F 6 HOH A 35 439 35 HOH WAT . 
F 6 HOH A 36 440 36 HOH WAT . 
F 6 HOH A 37 441 37 HOH WAT . 
F 6 HOH A 38 442 38 HOH WAT . 
F 6 HOH A 39 443 39 HOH WAT . 
F 6 HOH A 40 444 40 HOH WAT . 
F 6 HOH A 41 445 41 HOH WAT . 
F 6 HOH A 42 446 42 HOH WAT . 
F 6 HOH A 43 447 43 HOH WAT . 
F 6 HOH A 44 448 44 HOH WAT . 
F 6 HOH A 45 449 45 HOH WAT . 
F 6 HOH A 46 450 46 HOH WAT . 
F 6 HOH A 47 451 47 HOH WAT . 
F 6 HOH A 48 452 48 HOH WAT . 
F 6 HOH A 49 453 49 HOH WAT . 
F 6 HOH A 50 454 50 HOH WAT . 
F 6 HOH A 51 455 51 HOH WAT . 
F 6 HOH A 52 456 52 HOH WAT . 
F 6 HOH A 53 457 53 HOH WAT . 
F 6 HOH A 54 458 54 HOH WAT . 
F 6 HOH A 55 459 55 HOH WAT . 
F 6 HOH A 56 460 56 HOH WAT . 
F 6 HOH A 57 461 57 HOH WAT . 
F 6 HOH A 58 462 58 HOH WAT . 
F 6 HOH A 59 463 59 HOH WAT . 
F 6 HOH A 60 464 60 HOH WAT . 
F 6 HOH A 61 465 61 HOH WAT . 
F 6 HOH A 62 466 62 HOH WAT . 
F 6 HOH A 63 467 63 HOH WAT . 
F 6 HOH A 64 468 64 HOH WAT . 
F 6 HOH A 65 469 65 HOH WAT . 
F 6 HOH A 66 470 66 HOH WAT . 
F 6 HOH A 67 471 67 HOH WAT . 
F 6 HOH A 68 472 68 HOH WAT . 
F 6 HOH A 69 473 69 HOH WAT . 
F 6 HOH A 70 474 70 HOH WAT . 
F 6 HOH A 71 475 71 HOH WAT . 
F 6 HOH A 72 476 72 HOH WAT . 
F 6 HOH A 73 477 73 HOH WAT . 
F 6 HOH A 74 478 74 HOH WAT . 
F 6 HOH A 75 479 75 HOH WAT . 
F 6 HOH A 76 480 76 HOH WAT . 
F 6 HOH A 77 481 77 HOH WAT . 
F 6 HOH A 78 482 78 HOH WAT . 
F 6 HOH A 79 483 79 HOH WAT . 
F 6 HOH A 80 484 80 HOH WAT . 
F 6 HOH A 81 485 81 HOH WAT . 
F 6 HOH A 82 486 82 HOH WAT . 
F 6 HOH A 83 487 83 HOH WAT . 
F 6 HOH A 84 488 84 HOH WAT . 
F 6 HOH A 85 489 85 HOH WAT . 
F 6 HOH A 86 490 86 HOH WAT . 
F 6 HOH A 87 491 87 HOH WAT . 
F 6 HOH A 88 492 88 HOH WAT . 
F 6 HOH A 89 493 89 HOH WAT . 
F 6 HOH A 90 494 90 HOH WAT . 
F 6 HOH A 91 495 91 HOH WAT . 
F 6 HOH A 92 496 92 HOH WAT . 
F 6 HOH A 93 497 93 HOH WAT . 
F 6 HOH A 94 498 94 HOH WAT . 
F 6 HOH A 95 499 95 HOH WAT . 
F 6 HOH A 96 500 96 HOH WAT . 
F 6 HOH A 97 501 97 HOH WAT . 
F 6 HOH A 98 502 98 HOH WAT . 
F 6 HOH A 99 503 99 HOH WAT . 
F 6 HOH A 100 504 100 HOH WAT . 
F 6 HOH A 101 505 101 HOH WAT . 
F 6 HOH A 102 506 102 HOH WAT . 
F 6 HOH A 103 507 103 HOH WAT . 
F 6 HOH A 104 508 104 HOH WAT . 
F 6 HOH A 105 509 105 HOH WAT . 
F 6 HOH A 106 510 106 HOH WAT . 
F 6 HOH A 107 511 107 HOH WAT . 
F 6 HOH A 108 512 108 HOH WAT . 
F 6 HOH A 109 513 109 HOH WAT . 
F 6 HOH A 110 514 110 HOH WAT . 
F 6 HOH A 111 515 111 HOH WAT . 
F 6 HOH A 112 516 112 HOH WAT . 
F 6 HOH A 113 517 113 HOH WAT . 
F 6 HOH A 114 518 114 HOH WAT . 
F 6 HOH A 115 519 115 HOH WAT . 
F 6 HOH A 116 520 116 HOH WAT . 
F 6 HOH A 117 521 117 HOH WAT . 
F 6 HOH A 118 522 118 HOH WAT . 
F 6 HOH A 119 523 119 HOH WAT . 
F 6 HOH A 120 524 120 HOH WAT . 
F 6 HOH A 121 525 121 HOH WAT . 
F 6 HOH A 122 526 122 HOH WAT . 
F 6 HOH A 123 527 123 HOH WAT . 
F 6 HOH A 124 528 124 HOH WAT . 
F 6 HOH A 125 529 125 HOH WAT . 
F 6 HOH A 126 530 126 HOH WAT . 
#
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 PXM . . . E 5 40.289 45.598 -2.272 1 35.91 ? N1 PXM 402 A 1 
HETATM 2 C C2 PXM . . . E 5 40.459 44.689 -1.247 1 35.75 ? C2 PXM 402 A 1 
HETATM 3 C C2A PXM . . . E 5 39.239 44.118 -0.547 1 34.93 ? C2A PXM 402 A 1 
HETATM 4 C C3 PXM . . . E 5 41.796 44.296 -0.937 1 36.15 ? C3 PXM 402 A 1 
HETATM 5 O O3 PXM . . . E 5 41.943 43.389 0.052 1 37.22 ? O3 PXM 402 A 1 
HETATM 6 C C4 PXM . . . E 5 42.904 44.835 -1.673 1 35.83 ? C4 PXM 402 A 1 
HETATM 7 C C5 PXM . . . E 5 42.625 45.75 -2.797 1 35.82 ? C5 PXM 402 A 1 
HETATM 8 C C5A PXM . . . E 5 43.819 46.24 -3.657 1 35.85 ? C5A PXM 402 A 1 
HETATM 9 O O5 PXM . . . E 5 43.394 47.089 -4.68 1 35.02 ? O5 PXM 402 A 1 
HETATM 10 C C6 PXM . . . E 5 41.302 46.147 -3.065 1 36.37 ? C6 PXM 402 A 1 
HETATM 11 C C4A PXM . . . E 5 44.239 44.425 -1.331 1 35.68 ? C4A PXM 402 A 1 
HETATM 12 N N4 PXM . . . E 5 44.426 43.183 -2.102 1 35.27 ? N4 PXM 402 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           341 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           12 
#