data_5VXI # _model_server_result.job_id W-MSR_2M7RD2ws01nEpblg _model_server_result.datetime_utc '2024-11-06 17:39:17' _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 5vxi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5VXI # _exptl.entry_id 5VXI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 225.284 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S,3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE _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 5VXI _cell.length_a 89.765 _cell.length_b 89.765 _cell.length_c 69.509 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VXI _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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 _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' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 23.169667 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 ND1 HIS 38 A HIS 38 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc2 A OD1 ASP 76 A ASP 76 1_555 B MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc3 B MN MN . A MN 401 1_555 D O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc4 B MN MN . A MN 401 1_555 D O HOH . A HOH 506 2_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc5 B MN MN . A MN 401 1_555 D O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc6 B MN MN . A MN 401 1_555 D O HOH . A HOH 521 2_654 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? # _chem_comp.formula 'C12 H19 N O3' _chem_comp.formula_weight 225.284 _chem_comp.id CER _chem_comp.mon_nstd_flag . _chem_comp.name '(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CERULENIN # 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 C1 N1 CER sing 70 n n C1 C2 CER sing 71 n n C1 O2 CER doub 72 n n N1 HN11 CER sing 73 n n N1 HN12 CER sing 74 n n O1 C4 CER doub 75 n n C2 C3 CER sing 76 n n C2 H21 CER sing 77 n n C2 H22 CER sing 78 n n C3 O3 CER sing 79 n n C3 C4 CER sing 80 n n C3 H31 CER sing 81 n n O3 HO3 CER sing 82 n n C4 C5 CER sing 83 n n C5 C6 CER sing 84 n n C5 H51 CER sing 85 n n C5 H52 CER sing 86 n n C6 C7 CER sing 87 n n C6 H61 CER sing 88 n n C6 H62 CER sing 89 n n C7 C8 CER doub 90 e n C7 H71 CER sing 91 n n C8 C9 CER sing 92 n n C8 H81 CER sing 93 n n C9 C10 CER sing 94 n n C9 H91 CER sing 95 n n C9 H92 CER sing 96 n n C10 C11 CER doub 97 e n C10 H101 CER sing 98 n n C11 C12 CER sing 99 n n C11 H111 CER sing 100 n n C12 H121 CER sing 101 n n C12 H122 CER sing 102 n n C12 H123 CER sing 103 n n # _atom_sites.entry_id 5VXI _atom_sites.fract_transf_matrix[1][1] 0.01114 _atom_sites.fract_transf_matrix[1][2] 0.006432 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012864 _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] 0.014387 _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 MN A 1 401 1 MN MN . C 3 CER A 1 402 1 CER CER . D 4 HOH A 1 501 25 HOH HOH . D 4 HOH A 2 502 14 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 42 HOH HOH . D 4 HOH A 5 505 17 HOH HOH . D 4 HOH A 6 506 44 HOH HOH . D 4 HOH A 7 507 35 HOH HOH . D 4 HOH A 8 508 22 HOH HOH . D 4 HOH A 9 509 9 HOH HOH . D 4 HOH A 10 510 37 HOH HOH . D 4 HOH A 11 511 46 HOH HOH . D 4 HOH A 12 512 34 HOH HOH . D 4 HOH A 13 513 38 HOH HOH . D 4 HOH A 14 514 15 HOH HOH . D 4 HOH A 15 515 8 HOH HOH . D 4 HOH A 16 516 24 HOH HOH . D 4 HOH A 17 517 33 HOH HOH . D 4 HOH A 18 518 27 HOH HOH . D 4 HOH A 19 519 19 HOH HOH . D 4 HOH A 20 520 13 HOH HOH . D 4 HOH A 21 521 43 HOH HOH . D 4 HOH A 22 522 32 HOH HOH . D 4 HOH A 23 523 21 HOH HOH . D 4 HOH A 24 524 16 HOH HOH . D 4 HOH A 25 525 6 HOH HOH . D 4 HOH A 26 526 28 HOH HOH . D 4 HOH A 27 527 11 HOH HOH . D 4 HOH A 28 528 30 HOH HOH . D 4 HOH A 29 529 39 HOH HOH . D 4 HOH A 30 530 20 HOH HOH . D 4 HOH A 31 531 10 HOH HOH . D 4 HOH A 32 532 4 HOH HOH . D 4 HOH A 33 533 5 HOH HOH . D 4 HOH A 34 534 40 HOH HOH . D 4 HOH A 35 535 31 HOH HOH . D 4 HOH A 36 536 7 HOH HOH . D 4 HOH A 37 537 1 HOH HOH . D 4 HOH A 38 538 12 HOH HOH . D 4 HOH A 39 539 41 HOH HOH . D 4 HOH A 40 540 29 HOH HOH . D 4 HOH A 41 541 23 HOH HOH . D 4 HOH A 42 542 26 HOH HOH . D 4 HOH A 43 543 18 HOH HOH . D 4 HOH A 44 544 45 HOH HOH . D 4 HOH A 45 545 36 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 C C1 CER . . . C 3 52.709 -6.266 -0.76 1 67.74 ? C1 CER 402 A 1 HETATM 2 N N1 CER . . . C 3 53.707 -6.523 0.087 1 80.42 ? N1 CER 402 A 1 HETATM 3 O O1 CER . . . C 3 55.54 -7.832 -2.064 1 70.05 ? O1 CER 402 A 1 HETATM 4 C C2 CER . . . C 3 53.059 -5.556 -2.033 1 67.81 ? C2 CER 402 A 1 HETATM 5 O O2 CER . . . C 3 51.541 -6.513 -0.554 1 45.24 ? O2 CER 402 A 1 HETATM 6 C C3 CER . . . C 3 54.269 -6.007 -2.777 1 67.1 ? C3 CER 402 A 1 HETATM 7 O O3 CER . . . C 3 53.974 -5.628 -4.123 1 55.85 ? O3 CER 402 A 1 HETATM 8 C C4 CER . . . C 3 54.457 -7.466 -2.499 1 62.51 ? C4 CER 402 A 1 HETATM 9 C C5 CER . . . C 3 53.313 -8.422 -2.663 1 67.62 ? C5 CER 402 A 1 HETATM 10 C C6 CER . . . C 3 53.78 -9.605 -3.467 1 69.37 ? C6 CER 402 A 1 HETATM 11 C C7 CER . . . C 3 52.586 -10.464 -3.751 1 66.16 ? C7 CER 402 A 1 HETATM 12 C C8 CER . . . C 3 52.638 -11.239 -4.819 1 66.02 ? C8 CER 402 A 1 HETATM 13 C C9 CER . . . C 3 51.465 -12.117 -5.108 1 70.32 ? C9 CER 402 A 1 HETATM 14 C C10 CER . . . C 3 51.317 -12.5 -6.555 1 66.96 ? C10 CER 402 A 1 HETATM 15 C C11 CER . . . C 3 50.238 -12.062 -7.207 1 74.66 ? C11 CER 402 A 1 HETATM 16 C C12 CER . . . C 3 49.922 -12.403 -8.643 1 77 ? C12 CER 402 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 16 #