data_4LB2 # _model_server_result.job_id iwJ2M4J4p2WuoWhDtOLtww _model_server_result.datetime_utc '2024-11-23 07:37:40' _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 4lb2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 4LB2 # _exptl.entry_id 4LB2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 497.494 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description IDARUBICIN _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 74.74 _cell.angle_beta 88.63 _cell.angle_gamma 76.58 _cell.entry_id 4LB2 _cell.length_a 57.952 _cell.length_b 58.199 _cell.length_c 96.085 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LB2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,G 1 1 B,E,F,H 2 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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F 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 disulf ? disulf1 A SG CYS 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf4 A SG CYS 124 A CYS 124 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 168 A CYS 168 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 200 A CYS 200 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 245 A CYS 245 1_555 A SG CYS 253 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 A SG CYS 265 A CYS 265 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 A SG CYS 278 A CYS 278 1_555 A SG CYS 289 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 A SG CYS 316 A CYS 316 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 A SG CYS 360 A CYS 360 1_555 A SG CYS 369 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 A SG CYS 392 A CYS 392 1_555 A SG CYS 438 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf13 A SG CYS 437 A CYS 437 1_555 A SG CYS 448 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 A SG CYS 461 A CYS 461 1_555 A SG CYS 477 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf15 A SG CYS 476 A CYS 476 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 A SG CYS 514 A CYS 514 1_555 A SG CYS 559 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf17 A SG CYS 558 A CYS 558 1_555 A SG CYS 567 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 B SG CYS 53 B CYS 53 1_555 B SG CYS 62 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 B SG CYS 75 B CYS 75 1_555 B SG CYS 91 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf20 B SG CYS 90 B CYS 90 1_555 B SG CYS 101 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 B SG CYS 124 B CYS 124 1_555 B SG CYS 169 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf22 B SG CYS 168 B CYS 168 1_555 B SG CYS 177 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf23 B SG CYS 200 B CYS 200 1_555 B SG CYS 246 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf24 B SG CYS 245 B CYS 245 1_555 B SG CYS 253 B CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf25 B SG CYS 265 B CYS 265 1_555 B SG CYS 279 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf26 B SG CYS 278 B CYS 278 1_555 B SG CYS 289 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf27 B SG CYS 316 B CYS 316 1_555 B SG CYS 361 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf28 B SG CYS 360 B CYS 360 1_555 B SG CYS 369 B CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf29 B SG CYS 392 B CYS 392 1_555 B SG CYS 438 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf30 B SG CYS 437 B CYS 437 1_555 B SG CYS 448 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf31 B SG CYS 461 B CYS 461 1_555 B SG CYS 477 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf32 B SG CYS 476 B CYS 476 1_555 B SG CYS 487 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf33 B SG CYS 514 B CYS 514 1_555 B SG CYS 559 B CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf34 B SG CYS 558 B CYS 558 1_555 B SG CYS 567 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C26 H27 N O9' _chem_comp.formula_weight 497.494 _chem_comp.id DM5 _chem_comp.mon_nstd_flag . _chem_comp.name IDARUBICIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 4-DEMETHOXY-DAUNORUBICIN # _atom_sites.entry_id 4LB2 _atom_sites.fract_transf_matrix[1][1] 0.017256 _atom_sites.fract_transf_matrix[1][2] -0.004117 _atom_sites.fract_transf_matrix[1][3] 0.000704 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017665 _atom_sites.fract_transf_matrix[2][3] -0.004853 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010796 _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 2 DM5 A 1 601 601 DM5 DM5 . D 2 DM5 A 1 602 601 DM5 DM5 . E 2 DM5 B 1 601 602 DM5 DM5 . F 2 DM5 B 1 602 602 DM5 DM5 . G 3 HOH A 1 701 1 HOH HOH . G 3 HOH A 2 702 2 HOH HOH . G 3 HOH A 3 703 3 HOH HOH . G 3 HOH A 4 704 5 HOH HOH . G 3 HOH A 5 705 8 HOH HOH . G 3 HOH A 6 706 11 HOH HOH . G 3 HOH A 7 707 14 HOH HOH . G 3 HOH A 8 708 15 HOH HOH . G 3 HOH A 9 709 18 HOH HOH . G 3 HOH A 10 710 19 HOH HOH . G 3 HOH A 11 711 23 HOH HOH . G 3 HOH A 12 712 24 HOH HOH . G 3 HOH A 13 713 25 HOH HOH . G 3 HOH A 14 714 27 HOH HOH . G 3 HOH A 15 715 29 HOH HOH . G 3 HOH A 16 716 32 HOH HOH . G 3 HOH A 17 717 35 HOH HOH . G 3 HOH A 18 718 38 HOH HOH . G 3 HOH A 19 719 39 HOH HOH . G 3 HOH A 20 720 40 HOH HOH . G 3 HOH A 21 721 42 HOH HOH . G 3 HOH A 22 722 44 HOH HOH . G 3 HOH A 23 723 45 HOH HOH . G 3 HOH A 24 724 47 HOH HOH . G 3 HOH A 25 725 48 HOH HOH . G 3 HOH A 26 726 51 HOH HOH . G 3 HOH A 27 727 54 HOH HOH . G 3 HOH A 28 728 55 HOH HOH . G 3 HOH A 29 729 58 HOH HOH . G 3 HOH A 30 730 60 HOH HOH . G 3 HOH A 31 731 61 HOH HOH . G 3 HOH A 32 732 64 HOH HOH . G 3 HOH A 33 733 65 HOH HOH . G 3 HOH A 34 734 67 HOH HOH . G 3 HOH A 35 735 68 HOH HOH . G 3 HOH A 36 736 69 HOH HOH . G 3 HOH A 37 737 71 HOH HOH . G 3 HOH A 38 738 72 HOH HOH . H 3 HOH B 1 701 4 HOH HOH . H 3 HOH B 2 702 6 HOH HOH . H 3 HOH B 3 703 7 HOH HOH . H 3 HOH B 4 704 9 HOH HOH . H 3 HOH B 5 705 10 HOH HOH . H 3 HOH B 6 706 12 HOH HOH . H 3 HOH B 7 707 13 HOH HOH . H 3 HOH B 8 708 16 HOH HOH . H 3 HOH B 9 709 17 HOH HOH . H 3 HOH B 10 710 20 HOH HOH . H 3 HOH B 11 711 21 HOH HOH . H 3 HOH B 12 712 22 HOH HOH . H 3 HOH B 13 713 26 HOH HOH . H 3 HOH B 14 714 28 HOH HOH . H 3 HOH B 15 715 30 HOH HOH . H 3 HOH B 16 716 31 HOH HOH . H 3 HOH B 17 717 33 HOH HOH . H 3 HOH B 18 718 34 HOH HOH . H 3 HOH B 19 719 36 HOH HOH . H 3 HOH B 20 720 37 HOH HOH . H 3 HOH B 21 721 41 HOH HOH . H 3 HOH B 22 722 43 HOH HOH . H 3 HOH B 23 723 46 HOH HOH . H 3 HOH B 24 724 49 HOH HOH . H 3 HOH B 25 725 50 HOH HOH . H 3 HOH B 26 726 52 HOH HOH . H 3 HOH B 27 727 53 HOH HOH . H 3 HOH B 28 728 56 HOH HOH . H 3 HOH B 29 729 57 HOH HOH . H 3 HOH B 30 730 59 HOH HOH . H 3 HOH B 31 731 62 HOH HOH . H 3 HOH B 32 732 63 HOH HOH . H 3 HOH B 33 733 66 HOH HOH . H 3 HOH B 34 734 70 HOH HOH . H 3 HOH B 35 735 73 HOH HOH . H 3 HOH B 36 736 74 HOH HOH . H 3 HOH B 37 737 75 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 DM5 . . . D 2 -10.976 -14.171 8.81 1 45.16 ? C1 DM5 602 A 1 HETATM 2 C C2 DM5 . . . D 2 -10.49 -13.138 9.644 1 47.62 ? C2 DM5 602 A 1 HETATM 3 C C3 DM5 . . . D 2 -11.276 -12.636 10.679 1 49.09 ? C3 DM5 602 A 1 HETATM 4 C C4 DM5 . . . D 2 -12.574 -13.161 10.91 1 52.29 ? C4 DM5 602 A 1 HETATM 5 C C5 DM5 . . . D 2 -13.074 -14.204 10.08 1 49.99 ? C5 DM5 602 A 1 HETATM 6 C C6 DM5 . . . D 2 -14.457 -14.775 10.319 1 52.28 ? C6 DM5 602 A 1 HETATM 7 O O6 DM5 . . . D 2 -15.127 -14.346 11.206 1 57.33 ? O6 DM5 602 A 1 HETATM 8 C C7 DM5 . . . D 2 -15.001 -15.891 9.433 1 56.87 ? C7 DM5 602 A 1 HETATM 9 C C8 DM5 . . . D 2 -16.276 -16.426 9.646 1 66.3 ? C8 DM5 602 A 1 HETATM 10 O O8 DM5 . . . D 2 -17.084 -15.925 10.701 1 60.87 ? O8 DM5 602 A 1 HETATM 11 C C9 DM5 . . . D 2 -16.771 -17.454 8.804 1 77.35 ? C9 DM5 602 A 1 HETATM 12 C C10 DM5 . . . D 2 -18.133 -18.007 9.101 1 82.67 ? C10 DM5 602 A 1 HETATM 13 O O10 DM5 . . . D 2 -19.262 -17.221 8.651 1 85.16 ? O10 DM5 602 A 1 HETATM 14 C C11 DM5 . . . D 2 -18.253 -19.447 8.625 1 82.77 ? C11 DM5 602 A 1 HETATM 15 C C12 DM5 . . . D 2 -17.71 -19.765 7.195 1 80.04 ? C12 DM5 602 A 1 HETATM 16 O O12 DM5 . . . D 2 -18.423 -18.726 6.603 1 84.85 ? O12 DM5 602 A 1 HETATM 17 C C13 DM5 . . . D 2 -18.484 -20.459 6.082 1 91.41 ? C13 DM5 602 A 1 HETATM 18 O O13 DM5 . . . D 2 -17.877 -21.185 5.321 1 94.75 ? O13 DM5 602 A 1 HETATM 19 C C14 DM5 . . . D 2 -19.994 -20.301 5.901 1 88.3 ? C14 DM5 602 A 1 HETATM 20 C C15 DM5 . . . D 2 -16.406 -19.014 6.886 1 68.35 ? C15 DM5 602 A 1 HETATM 21 C C16 DM5 . . . D 2 -16.003 -17.934 7.822 1 69.32 ? C16 DM5 602 A 1 HETATM 22 C C17 DM5 . . . D 2 -14.724 -17.407 7.599 1 61.69 ? C17 DM5 602 A 1 HETATM 23 O O17 DM5 . . . D 2 -13.942 -17.911 6.556 1 61.2 ? O17 DM5 602 A 1 HETATM 24 C C18 DM5 . . . D 2 -14.219 -16.386 8.398 1 54.77 ? C18 DM5 602 A 1 HETATM 25 C C19 DM5 . . . D 2 -12.837 -15.83 8.147 1 55.89 ? C19 DM5 602 A 1 HETATM 26 O O19 DM5 . . . D 2 -12.159 -16.275 7.234 1 51.05 ? O19 DM5 602 A 1 HETATM 27 C C20 DM5 . . . D 2 -12.284 -14.705 9.037 1 54.26 ? C20 DM5 602 A 1 HETATM 28 C C1' DM5 . . . D 2 -20.292 -17.133 9.703 1 85.81 ? C1' DM5 602 A 1 HETATM 29 C C2' DM5 . . . D 2 -21.69 -17.271 9.083 1 97.05 ? C2' DM5 602 A 1 HETATM 30 C C3' DM5 . . . D 2 -22.235 -18.685 9.175 1 97.5 ? C3' DM5 602 A 1 HETATM 31 N N3' DM5 . . . D 2 -23.589 -18.719 8.698 1 88.06 ? N3' DM5 602 A 1 HETATM 32 C C4' DM5 . . . D 2 -22.188 -19.083 10.605 1 93.8 ? C4' DM5 602 A 1 HETATM 33 O O4' DM5 . . . D 2 -22.861 -18.124 11.414 1 100 ? O4' DM5 602 A 1 HETATM 34 C C5' DM5 . . . D 2 -20.728 -19.141 10.989 1 87.2 ? C5' DM5 602 A 1 HETATM 35 O O5' DM5 . . . D 2 -20.039 -17.912 10.823 1 84.98 ? O5' DM5 602 A 1 HETATM 36 C C6' DM5 . . . D 2 -20.61 -19.596 12.433 1 79.56 ? C6' DM5 602 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #