data_1JDZ # _model_server_result.job_id cnvtu36mjo6C_jeR7ZHf5Q _model_server_result.datetime_utc '2024-11-25 07:53:57' _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 1jdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":275}' # _entry.id 1JDZ # _exptl.entry_id 1JDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 268.226 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FORMYCIN B' _entity.pdbx_number_of_molecules 3 _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 1JDZ _cell.length_a 102.6 _cell.length_b 176.9 _cell.length_c 87.3 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JDZ _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,E,F,G,H,I,J,K,L _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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 102.6 0 43.65 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I 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 125 A CYS 125 1_555 C SG CYS 125 C CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 B SG CYS 125 B CYS 125 1_555 B SG CYS 125 B CYS 125 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _chem_comp.formula 'C10 H12 N4 O5' _chem_comp.formula_weight 268.226 _chem_comp.id FMB _chem_comp.mon_nstd_flag . _chem_comp.name 'FORMYCIN B' _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 N1 C2 FMB sing 83 n y N1 C6 FMB sing 84 n y N1 HN1 FMB sing 85 n n C2 N3 FMB doub 86 n y C2 H2 FMB sing 87 n n N3 C4 FMB sing 88 n y C4 C5 FMB doub 89 n y C4 C9 FMB sing 90 n y C5 C6 FMB sing 91 n y C5 N7 FMB sing 92 n y C6 O6 FMB doub 93 n n N7 N8 FMB sing 94 n y N7 HN7 FMB sing 95 n n N8 C9 FMB doub 96 n y C9 C1' FMB sing 97 n n C1' C2' FMB sing 98 n n C1' O4' FMB sing 99 n n C1' H1' FMB sing 100 n n C2' O2' FMB sing 101 n n C2' C3' FMB sing 102 n n C2' H2' FMB sing 103 n n O2' HO2 FMB sing 104 n n C3' O3' FMB sing 105 n n C3' C4' FMB sing 106 n n C3' H3' FMB sing 107 n n O3' HO3 FMB sing 108 n n C4' O4' FMB sing 109 n n C4' C5' FMB sing 110 n n C4' H4' FMB sing 111 n n C5' O5' FMB sing 112 n n C5' "H5'1" FMB sing 113 n n C5' "H5'2" FMB sing 114 n n O5' HO5 FMB sing 115 n n # _atom_sites.entry_id 1JDZ _atom_sites.fract_transf_matrix[1][1] 0.009747 _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] 0.005653 _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] 0.011455 _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 D 2 SO4 A 1 250 250 SO4 SO4 . E 3 FMB A 1 270 270 FMB FMB . F 2 SO4 B 1 255 255 SO4 SO4 . G 3 FMB B 1 275 275 FMB FMB . H 2 SO4 C 1 260 260 SO4 SO4 . I 3 FMB C 1 280 280 FMB FMB . J 4 HOH A 1 271 1 HOH HOH . J 4 HOH A 2 272 2 HOH HOH . J 4 HOH A 3 273 4 HOH HOH . J 4 HOH A 4 274 6 HOH HOH . J 4 HOH A 5 275 7 HOH HOH . J 4 HOH A 6 276 8 HOH HOH . J 4 HOH A 7 277 12 HOH HOH . J 4 HOH A 8 278 13 HOH HOH . J 4 HOH A 9 279 16 HOH HOH . J 4 HOH A 10 280 17 HOH HOH . J 4 HOH A 11 281 22 HOH HOH . J 4 HOH A 12 282 26 HOH HOH . J 4 HOH A 13 283 29 HOH HOH . J 4 HOH A 14 284 30 HOH HOH . J 4 HOH A 15 285 35 HOH HOH . J 4 HOH A 16 286 37 HOH HOH . J 4 HOH A 17 287 38 HOH HOH . J 4 HOH A 18 288 39 HOH HOH . J 4 HOH A 19 289 46 HOH HOH . J 4 HOH A 20 290 50 HOH HOH . J 4 HOH A 21 291 52 HOH HOH . J 4 HOH A 22 292 54 HOH HOH . J 4 HOH A 23 293 56 HOH HOH . J 4 HOH A 24 294 57 HOH HOH . J 4 HOH A 25 295 63 HOH HOH . J 4 HOH A 26 296 64 HOH HOH . J 4 HOH A 27 297 66 HOH HOH . J 4 HOH A 28 298 70 HOH HOH . J 4 HOH A 29 299 72 HOH HOH . J 4 HOH A 30 300 78 HOH HOH . J 4 HOH A 31 301 79 HOH HOH . J 4 HOH A 32 302 85 HOH HOH . J 4 HOH A 33 303 87 HOH HOH . J 4 HOH A 34 304 91 HOH HOH . J 4 HOH A 35 305 96 HOH HOH . J 4 HOH A 36 306 98 HOH HOH . J 4 HOH A 37 307 102 HOH HOH . J 4 HOH A 38 308 103 HOH HOH . J 4 HOH A 39 309 105 HOH HOH . J 4 HOH A 40 310 106 HOH HOH . J 4 HOH A 41 311 112 HOH HOH . J 4 HOH A 42 312 120 HOH HOH . J 4 HOH A 43 313 121 HOH HOH . J 4 HOH A 44 314 122 HOH HOH . J 4 HOH A 45 315 123 HOH HOH . J 4 HOH A 46 316 124 HOH HOH . J 4 HOH A 47 317 125 HOH HOH . J 4 HOH A 48 318 127 HOH HOH . J 4 HOH A 49 319 130 HOH HOH . J 4 HOH A 50 320 138 HOH HOH . J 4 HOH A 51 321 140 HOH HOH . J 4 HOH A 52 322 145 HOH HOH . K 4 HOH B 1 276 11 HOH HOH . K 4 HOH B 2 277 14 HOH HOH . K 4 HOH B 3 278 19 HOH HOH . K 4 HOH B 4 279 20 HOH HOH . K 4 HOH B 5 280 23 HOH HOH . K 4 HOH B 6 281 24 HOH HOH . K 4 HOH B 7 282 31 HOH HOH . K 4 HOH B 8 283 32 HOH HOH . K 4 HOH B 9 284 34 HOH HOH . K 4 HOH B 10 285 36 HOH HOH . K 4 HOH B 11 286 41 HOH HOH . K 4 HOH B 12 287 42 HOH HOH . K 4 HOH B 13 288 48 HOH HOH . K 4 HOH B 14 289 49 HOH HOH . K 4 HOH B 15 290 51 HOH HOH . K 4 HOH B 16 291 59 HOH HOH . K 4 HOH B 17 292 60 HOH HOH . K 4 HOH B 18 293 61 HOH HOH . K 4 HOH B 19 294 62 HOH HOH . K 4 HOH B 20 295 68 HOH HOH . K 4 HOH B 21 296 71 HOH HOH . K 4 HOH B 22 297 73 HOH HOH . K 4 HOH B 23 298 74 HOH HOH . K 4 HOH B 24 299 75 HOH HOH . K 4 HOH B 25 300 76 HOH HOH . K 4 HOH B 26 301 77 HOH HOH . K 4 HOH B 27 302 80 HOH HOH . K 4 HOH B 28 303 81 HOH HOH . K 4 HOH B 29 304 82 HOH HOH . K 4 HOH B 30 305 83 HOH HOH . K 4 HOH B 31 306 84 HOH HOH . K 4 HOH B 32 307 86 HOH HOH . K 4 HOH B 33 308 90 HOH HOH . K 4 HOH B 34 309 93 HOH HOH . K 4 HOH B 35 310 99 HOH HOH . K 4 HOH B 36 311 101 HOH HOH . K 4 HOH B 37 312 107 HOH HOH . K 4 HOH B 38 313 108 HOH HOH . K 4 HOH B 39 314 111 HOH HOH . K 4 HOH B 40 315 114 HOH HOH . K 4 HOH B 41 316 115 HOH HOH . K 4 HOH B 42 317 118 HOH HOH . K 4 HOH B 43 318 126 HOH HOH . K 4 HOH B 44 319 128 HOH HOH . K 4 HOH B 45 320 129 HOH HOH . K 4 HOH B 46 321 131 HOH HOH . K 4 HOH B 47 322 133 HOH HOH . K 4 HOH B 48 323 134 HOH HOH . K 4 HOH B 49 324 136 HOH HOH . K 4 HOH B 50 325 139 HOH HOH . K 4 HOH B 51 326 142 HOH HOH . K 4 HOH B 52 327 143 HOH HOH . L 4 HOH C 1 281 3 HOH HOH . L 4 HOH C 2 282 5 HOH HOH . L 4 HOH C 3 283 9 HOH HOH . L 4 HOH C 4 284 10 HOH HOH . L 4 HOH C 5 285 15 HOH HOH . L 4 HOH C 6 286 18 HOH HOH . L 4 HOH C 7 287 21 HOH HOH . L 4 HOH C 8 288 25 HOH HOH . L 4 HOH C 9 289 27 HOH HOH . L 4 HOH C 10 290 28 HOH HOH . L 4 HOH C 11 291 33 HOH HOH . L 4 HOH C 12 292 40 HOH HOH . L 4 HOH C 13 293 43 HOH HOH . L 4 HOH C 14 294 44 HOH HOH . L 4 HOH C 15 295 45 HOH HOH . L 4 HOH C 16 296 47 HOH HOH . L 4 HOH C 17 297 53 HOH HOH . L 4 HOH C 18 298 55 HOH HOH . L 4 HOH C 19 299 58 HOH HOH . L 4 HOH C 20 300 65 HOH HOH . L 4 HOH C 21 301 67 HOH HOH . L 4 HOH C 22 302 69 HOH HOH . L 4 HOH C 23 303 88 HOH HOH . L 4 HOH C 24 304 89 HOH HOH . L 4 HOH C 25 305 92 HOH HOH . L 4 HOH C 26 306 94 HOH HOH . L 4 HOH C 27 307 95 HOH HOH . L 4 HOH C 28 308 97 HOH HOH . L 4 HOH C 29 309 100 HOH HOH . L 4 HOH C 30 310 104 HOH HOH . L 4 HOH C 31 311 109 HOH HOH . L 4 HOH C 32 312 110 HOH HOH . L 4 HOH C 33 313 113 HOH HOH . L 4 HOH C 34 314 116 HOH HOH . L 4 HOH C 35 315 117 HOH HOH . L 4 HOH C 36 316 119 HOH HOH . L 4 HOH C 37 317 132 HOH HOH . L 4 HOH C 38 318 135 HOH HOH . L 4 HOH C 39 319 137 HOH HOH . L 4 HOH C 40 320 141 HOH HOH . L 4 HOH C 41 321 144 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 N N1 FMB . . . G 3 65.712 109.429 37.371 1 30.67 ? N1 FMB 275 B 1 HETATM 2 C C2 FMB . . . G 3 66.587 108.486 36.832 1 30.61 ? C2 FMB 275 B 1 HETATM 3 N N3 FMB . . . G 3 67.12 108.594 35.596 1 30.2 ? N3 FMB 275 B 1 HETATM 4 C C4 FMB . . . G 3 66.707 109.72 34.939 1 30.57 ? C4 FMB 275 B 1 HETATM 5 C C5 FMB . . . G 3 65.835 110.72 35.388 1 30.07 ? C5 FMB 275 B 1 HETATM 6 C C6 FMB . . . G 3 65.277 110.6 36.695 1 30.51 ? C6 FMB 275 B 1 HETATM 7 O O6 FMB . . . G 3 64.504 111.371 37.258 1 32.09 ? O6 FMB 275 B 1 HETATM 8 N N7 FMB . . . G 3 65.664 111.703 34.422 1 30.2 ? N7 FMB 275 B 1 HETATM 9 N N8 FMB . . . G 3 66.426 111.297 33.416 1 29.21 ? N8 FMB 275 B 1 HETATM 10 C C9 FMB . . . G 3 67.09 110.093 33.669 1 30.63 ? C9 FMB 275 B 1 HETATM 11 C C1' FMB . . . G 3 67.949 109.704 32.499 1 30.19 ? C1' FMB 275 B 1 HETATM 12 C C2' FMB . . . G 3 67.81 110.57 31.251 1 30.82 ? C2' FMB 275 B 1 HETATM 13 O O2' FMB . . . G 3 67.626 109.719 30.152 1 30.46 ? O2' FMB 275 B 1 HETATM 14 C C3' FMB . . . G 3 69.095 111.422 31.2 1 30.88 ? C3' FMB 275 B 1 HETATM 15 O O3' FMB . . . G 3 69.758 111.4 29.911 1 28.75 ? O3' FMB 275 B 1 HETATM 16 C C4' FMB . . . G 3 70.013 110.877 32.289 1 31.3 ? C4' FMB 275 B 1 HETATM 17 O O4' FMB . . . G 3 69.316 109.742 32.903 1 29.95 ? O4' FMB 275 B 1 HETATM 18 C C5' FMB . . . G 3 70.358 111.917 33.37 1 32.75 ? C5' FMB 275 B 1 HETATM 19 O O5' FMB . . . G 3 70.707 111.34 34.645 1 32.9 ? O5' FMB 275 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 19 #