data_1Z7Y # _model_server_result.job_id 6EhZY_uo599fngwue06dVQ _model_server_result.datetime_utc '2025-07-14 13:27:01' _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 1z7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 1Z7Y # _exptl.entry_id 1Z7Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 378.338 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE _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 1Z7Y _cell.length_a 105.856 _cell.length_b 105.856 _cell.length_c 100.159 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z7Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 2 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' 8_664 -y+1,-x+1,-z-1/2 0 -1 0 -1 0 0 0 0 -1 105.856 105.856 -50.0795 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C13 H19 N2 O7 P S' _chem_comp.formula_weight 378.338 _chem_comp.id AA5 _chem_comp.mon_nstd_flag . _chem_comp.name N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 AA5 sing 1 n n N C4A AA5 doub 2 n n CA C AA5 sing 3 n n CA CB AA5 sing 4 n n CA HA AA5 sing 5 n n C O1 AA5 doub 6 n n C O2 AA5 sing 7 n n CB CG AA5 sing 8 n n CB HB1 AA5 sing 9 n n CB HB2 AA5 sing 10 n n CG SD AA5 sing 11 n n CG HG1 AA5 sing 12 n n CG HG2 AA5 sing 13 n n SD CE AA5 sing 14 n n CE HE1 AA5 sing 15 n n CE HE2 AA5 sing 16 n n CE HE3 AA5 sing 17 n n O2 HO2 AA5 sing 18 n n C2 C2A AA5 sing 19 n n C2 C3 AA5 doub 20 n y C2 N1 AA5 sing 21 n y C2A H2A1 AA5 sing 22 n n C2A H2A2 AA5 sing 23 n n C2A H2A3 AA5 sing 24 n n C3 C4 AA5 sing 25 n y C3 O3 AA5 sing 26 n n C4 C4A AA5 sing 27 n n C4 C5 AA5 doub 28 n y C4A H4A AA5 sing 29 n n C5 C5A AA5 sing 30 n n C5 C6 AA5 sing 31 n y C5A O4P AA5 sing 32 n n C5A H5A1 AA5 sing 33 n n C5A H5A2 AA5 sing 34 n n C6 N1 AA5 doub 35 n y C6 H6 AA5 sing 36 n n O1P P AA5 doub 37 n n O2P P AA5 sing 38 n n O2P H2P AA5 sing 39 n n O3 HO3 AA5 sing 40 n n O3P P AA5 sing 41 n n O3P H3P AA5 sing 42 n n O4P P AA5 sing 43 n n # _atom_sites.entry_id 1Z7Y _atom_sites.fract_transf_matrix[1][1] 0.009447 _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] 0.009447 _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] 0.009984 _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 AA5 A 1 501 501 AA5 AAA . C 3 HOH A 1 502 1 HOH WAT . C 3 HOH A 2 503 2 HOH WAT . C 3 HOH A 3 504 3 HOH WAT . C 3 HOH A 4 505 4 HOH WAT . C 3 HOH A 5 506 5 HOH WAT . C 3 HOH A 6 507 6 HOH WAT . C 3 HOH A 7 508 7 HOH WAT . C 3 HOH A 8 509 8 HOH WAT . C 3 HOH A 9 510 9 HOH WAT . C 3 HOH A 10 511 10 HOH WAT . C 3 HOH A 11 512 11 HOH WAT . C 3 HOH A 12 513 12 HOH WAT . C 3 HOH A 13 514 13 HOH WAT . C 3 HOH A 14 515 14 HOH WAT . C 3 HOH A 15 516 15 HOH WAT . C 3 HOH A 16 517 16 HOH WAT . C 3 HOH A 17 518 17 HOH WAT . C 3 HOH A 18 519 18 HOH WAT . C 3 HOH A 19 520 19 HOH WAT . C 3 HOH A 20 521 20 HOH WAT . C 3 HOH A 21 522 21 HOH WAT . C 3 HOH A 22 523 22 HOH WAT . C 3 HOH A 23 524 23 HOH WAT . C 3 HOH A 24 525 24 HOH WAT . C 3 HOH A 25 526 25 HOH WAT . C 3 HOH A 26 527 26 HOH WAT . C 3 HOH A 27 528 27 HOH WAT . C 3 HOH A 28 529 28 HOH WAT . C 3 HOH A 29 530 29 HOH WAT . C 3 HOH A 30 531 30 HOH WAT . C 3 HOH A 31 532 31 HOH WAT . C 3 HOH A 32 533 32 HOH WAT . C 3 HOH A 33 534 33 HOH WAT . C 3 HOH A 34 535 34 HOH WAT . C 3 HOH A 35 536 35 HOH WAT . C 3 HOH A 36 537 36 HOH WAT . C 3 HOH A 37 538 37 HOH WAT . C 3 HOH A 38 539 38 HOH WAT . C 3 HOH A 39 540 39 HOH WAT . C 3 HOH A 40 541 40 HOH WAT . C 3 HOH A 41 542 41 HOH WAT . C 3 HOH A 42 543 42 HOH WAT . C 3 HOH A 43 544 43 HOH WAT . C 3 HOH A 44 545 44 HOH WAT . C 3 HOH A 45 546 45 HOH WAT . C 3 HOH A 46 547 46 HOH WAT . C 3 HOH A 47 548 47 HOH WAT . C 3 HOH A 48 549 48 HOH WAT . C 3 HOH A 49 550 49 HOH WAT . C 3 HOH A 50 551 50 HOH WAT . C 3 HOH A 51 552 51 HOH WAT . C 3 HOH A 52 553 52 HOH WAT . C 3 HOH A 53 554 53 HOH WAT . C 3 HOH A 54 555 54 HOH WAT . C 3 HOH A 55 556 55 HOH WAT . C 3 HOH A 56 557 56 HOH WAT . C 3 HOH A 57 558 57 HOH WAT . C 3 HOH A 58 559 58 HOH WAT . C 3 HOH A 59 560 59 HOH WAT . C 3 HOH A 60 561 60 HOH WAT . C 3 HOH A 61 562 61 HOH WAT . C 3 HOH A 62 563 62 HOH WAT . C 3 HOH A 63 564 63 HOH WAT . C 3 HOH A 64 565 64 HOH WAT . C 3 HOH A 65 566 65 HOH WAT . C 3 HOH A 66 567 66 HOH WAT . C 3 HOH A 67 568 67 HOH WAT . C 3 HOH A 68 569 68 HOH WAT . C 3 HOH A 69 570 69 HOH WAT . C 3 HOH A 70 571 70 HOH WAT . C 3 HOH A 71 572 71 HOH WAT . C 3 HOH A 72 573 72 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 N AA5 . . . B 2 78.97 42.589 -14.487 1 50.39 ? N AA5 501 A 1 HETATM 2 C CA AA5 . . . B 2 78.869 43.096 -13.076 1 53.52 ? CA AA5 501 A 1 HETATM 3 C C AA5 . . . B 2 77.366 43.35 -12.68 1 53.97 ? C AA5 501 A 1 HETATM 4 O O1 AA5 . . . B 2 77.013 43.256 -11.48 1 56.16 ? O1 AA5 501 A 1 HETATM 5 C CB AA5 . . . B 2 79.712 44.412 -12.871 1 55.59 ? CB AA5 501 A 1 HETATM 6 C CG AA5 . . . B 2 79.058 45.715 -13.373 1 59.29 ? CG AA5 501 A 1 HETATM 7 S SD AA5 . . . B 2 80.014 47.238 -13.102 1 65.9 ? SD AA5 501 A 1 HETATM 8 C CE AA5 . . . B 2 78.713 48.334 -12.46 1 62.85 ? CE AA5 501 A 1 HETATM 9 O O2 AA5 . . . B 2 76.542 43.669 -13.564 1 55.09 ? O2 AA5 501 A 1 HETATM 10 C C2 AA5 . . . B 2 79.506 43.279 -18.782 1 40.55 ? C2 AA5 501 A 1 HETATM 11 C C2A AA5 . . . B 2 78.415 43.17 -19.833 1 32.92 ? C2A AA5 501 A 1 HETATM 12 C C3 AA5 . . . B 2 79.299 42.763 -17.502 1 43.82 ? C3 AA5 501 A 1 HETATM 13 C C4 AA5 . . . B 2 80.34 42.879 -16.5 1 45.82 ? C4 AA5 501 A 1 HETATM 14 C C4A AA5 . . . B 2 80.088 42.303 -15.07 1 46.56 ? C4A AA5 501 A 1 HETATM 15 C C5 AA5 . . . B 2 81.579 43.506 -16.828 1 45.67 ? C5 AA5 501 A 1 HETATM 16 C C5A AA5 . . . B 2 82.72 43.684 -15.785 1 46.62 ? C5A AA5 501 A 1 HETATM 17 C C6 AA5 . . . B 2 81.75 44.007 -18.129 1 46.42 ? C6 AA5 501 A 1 HETATM 18 N N1 AA5 . . . B 2 80.725 43.885 -19.095 1 43.37 ? N1 AA5 501 A 1 HETATM 19 O O1P AA5 . . . B 2 85.757 41.666 -14.301 1 43.01 ? O1P AA5 501 A 1 HETATM 20 O O2P AA5 . . . B 2 85.594 44.097 -14.593 1 45.82 ? O2P AA5 501 A 1 HETATM 21 O O3 AA5 . . . B 2 78.083 42.171 -17.217 1 40.88 ? O3 AA5 501 A 1 HETATM 22 O O3P AA5 . . . B 2 83.888 42.986 -13.15 1 45.07 ? O3P AA5 501 A 1 HETATM 23 O O4P AA5 . . . B 2 83.761 42.675 -15.691 1 46.92 ? O4P AA5 501 A 1 HETATM 24 P P AA5 . . . B 2 84.745 42.745 -14.361 1 46.96 ? P AA5 501 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #