data_5YLS # _model_server_result.job_id jiHo0dbSgi3i-Eu2TKTdFw _model_server_result.datetime_utc '2024-10-19 22:31:05' _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 5yls # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":504}' # _entry.id 5YLS # _exptl.entry_id 5YLS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 365.422 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description E-3-(3-azanyl-4-methoxy-phenyl)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)prop-2-en-1-one _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 90 _cell.angle_gamma 90 _cell.entry_id 5YLS _cell.length_a 105.767 _cell.length_b 159.054 _cell.length_c 183.151 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLS _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y _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 ? 11 N N N ? 11 T 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.15 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc9 H MG MG . A MG 502 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc12 H MG MG . A MG 502 1_555 V O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc13 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc14 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc15 L MG MG . B MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc16 L MG MG . B MG 502 1_555 W O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc17 L MG MG . B MG 502 1_555 W O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc18 L MG MG . B MG 502 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc19 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc20 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc21 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc22 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc23 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc24 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc25 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc26 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc27 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc28 P MG MG . C MG 502 1_555 X O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc29 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc30 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc31 P MG MG . C MG 502 1_555 X O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? # _chem_comp.formula 'C22 H23 N O4' _chem_comp.formula_weight 365.422 _chem_comp.id Y50 _chem_comp.mon_nstd_flag . _chem_comp.name E-3-(3-azanyl-4-methoxy-phenyl)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)prop-2-en-1-one _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 C16 O15 Y50 sing 560 n n O15 C14 Y50 sing 561 n n C13 C14 Y50 doub 562 n y C13 C12 Y50 sing 563 n y C14 C17 Y50 sing 564 n y C12 C11 Y50 doub 565 n y C17 C18 Y50 sing 566 n n C17 C24 Y50 doub 567 n y C18 C19 Y50 doub 568 n n C11 C24 Y50 sing 569 n y C11 C9 Y50 sing 570 n n C24 O23 Y50 sing 571 n n C19 C20 Y50 sing 572 n n O10 C9 Y50 doub 573 n n C22 C20 Y50 sing 574 n n C20 O23 Y50 sing 575 n n C20 C21 Y50 sing 576 n n C9 C8 Y50 sing 577 n n C8 C7 Y50 doub 578 e n C7 C6 Y50 sing 579 n n C5 C6 Y50 doub 580 n y C5 C4 Y50 sing 581 n y C6 C25 Y50 sing 582 n y C4 C3 Y50 doub 583 n y C25 C26 Y50 doub 584 n y C3 C26 Y50 sing 585 n y C3 O2 Y50 sing 586 n n C26 N27 Y50 sing 587 n n O2 C1 Y50 sing 588 n n C1 H1 Y50 sing 589 n n C1 H2 Y50 sing 590 n n C1 H3 Y50 sing 591 n n C4 H4 Y50 sing 592 n n C5 H5 Y50 sing 593 n n C7 H6 Y50 sing 594 n n C8 H7 Y50 sing 595 n n C12 H8 Y50 sing 596 n n C13 H9 Y50 sing 597 n n C16 H10 Y50 sing 598 n n C16 H11 Y50 sing 599 n n C16 H12 Y50 sing 600 n n C18 H13 Y50 sing 601 n n C19 H14 Y50 sing 602 n n C21 H15 Y50 sing 603 n n C21 H16 Y50 sing 604 n n C21 H17 Y50 sing 605 n n C22 H18 Y50 sing 606 n n C22 H19 Y50 sing 607 n n C22 H20 Y50 sing 608 n n C25 H21 Y50 sing 609 n n N27 H22 Y50 sing 610 n n N27 H23 Y50 sing 611 n n # _atom_sites.entry_id 5YLS _atom_sites.fract_transf_matrix[1][1] 0.009455 _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] 0.006287 _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] 0.00546 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GOL A 1 504 601 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 505 MES MES . N 11 Y50 B 1 504 1 Y50 Y50 . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 504 CA CA . R 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 11 Y50 D 1 503 2 Y50 Y50 . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 11 HOH HOH . V 13 HOH A 2 602 2 HOH HOH . V 13 HOH A 3 603 1 HOH HOH . V 13 HOH A 4 604 3 HOH HOH . V 13 HOH A 5 605 4 HOH HOH . W 13 HOH B 1 601 17 HOH HOH . W 13 HOH B 2 602 18 HOH HOH . W 13 HOH B 3 603 10 HOH HOH . W 13 HOH B 4 604 12 HOH HOH . W 13 HOH B 5 605 15 HOH HOH . W 13 HOH B 6 606 16 HOH HOH . W 13 HOH B 7 607 13 HOH HOH . X 13 HOH C 1 601 5 HOH HOH . X 13 HOH C 2 602 6 HOH HOH . X 13 HOH C 3 603 7 HOH HOH . X 13 HOH C 4 604 8 HOH HOH . X 13 HOH C 5 605 14 HOH HOH . Y 13 HOH D 1 601 9 HOH HOH . Y 13 HOH D 2 602 19 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 Y50 . . . N 11 16.971 221.866 47.492 1 55.68 ? C1 Y50 504 B 1 HETATM 2 O O2 Y50 . . . N 11 16.603 223.268 47.477 1 54 ? O2 Y50 504 B 1 HETATM 3 C C3 Y50 . . . N 11 17.003 224.02 46.352 1 53.44 ? C3 Y50 504 B 1 HETATM 4 C C4 Y50 . . . N 11 16.775 223.53 45.049 1 52.88 ? C4 Y50 504 B 1 HETATM 5 C C5 Y50 . . . N 11 17.169 224.293 43.933 1 54.54 ? C5 Y50 504 B 1 HETATM 6 C C6 Y50 . . . N 11 17.79 225.55 44.114 1 55.38 ? C6 Y50 504 B 1 HETATM 7 C C7 Y50 . . . N 11 18.197 226.347 42.786 1 56.59 ? C7 Y50 504 B 1 HETATM 8 C C8 Y50 . . . N 11 18.477 227.653 42.733 1 62.52 ? C8 Y50 504 B 1 HETATM 9 C C9 Y50 . . . N 11 18.793 228.259 41.386 1 67.59 ? C9 Y50 504 B 1 HETATM 10 O O10 Y50 . . . N 11 19.612 229.093 41.294 1 72.5 ? O10 Y50 504 B 1 HETATM 11 C C11 Y50 . . . N 11 18.036 227.796 40.126 1 68.36 ? C11 Y50 504 B 1 HETATM 12 C C12 Y50 . . . N 11 18.74 227.656 38.901 1 68.9 ? C12 Y50 504 B 1 HETATM 13 C C13 Y50 . . . N 11 18.063 227.222 37.718 1 69.1 ? C13 Y50 504 B 1 HETATM 14 C C14 Y50 . . . N 11 16.673 226.917 37.757 1 70.01 ? C14 Y50 504 B 1 HETATM 15 O O15 Y50 . . . N 11 16.012 226.475 36.558 1 70.89 ? O15 Y50 504 B 1 HETATM 16 C C16 Y50 . . . N 11 16.174 225.102 36.321 1 72.18 ? C16 Y50 504 B 1 HETATM 17 C C17 Y50 . . . N 11 15.943 227.05 39.001 1 71.14 ? C17 Y50 504 B 1 HETATM 18 C C18 Y50 . . . N 11 14.531 226.758 39.093 1 72.18 ? C18 Y50 504 B 1 HETATM 19 C C19 Y50 . . . N 11 13.744 227.356 40.158 1 72.6 ? C19 Y50 504 B 1 HETATM 20 C C20 Y50 . . . N 11 14.468 228.05 41.343 1 72.86 ? C20 Y50 504 B 1 HETATM 21 C C21 Y50 . . . N 11 13.731 227.833 42.664 1 74.47 ? C21 Y50 504 B 1 HETATM 22 C C22 Y50 . . . N 11 14.496 229.562 41.297 1 73.05 ? C22 Y50 504 B 1 HETATM 23 O O23 Y50 . . . N 11 15.881 227.622 41.457 1 72.49 ? O23 Y50 504 B 1 HETATM 24 C C24 Y50 . . . N 11 16.628 227.486 40.158 1 70.72 ? C24 Y50 504 B 1 HETATM 25 C C25 Y50 . . . N 11 18.003 226.066 45.43 1 54.98 ? C25 Y50 504 B 1 HETATM 26 C C26 Y50 . . . N 11 17.619 225.291 46.543 1 54.35 ? C26 Y50 504 B 1 HETATM 27 N N27 Y50 . . . N 11 17.838 225.795 47.885 1 54.29 ? N27 Y50 504 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #