data_1Z9K # _model_server_result.job_id WOIgDn7WARCXx9LDtMF0iQ _model_server_result.datetime_utc '2024-11-12 20:53:30' _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 1z9k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":855}' # _entry.id 1Z9K # _exptl.entry_id 1Z9K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 889.215 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BACTERIOPHEOPHYTIN A' _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 1Z9K _cell.length_a 207.8 _cell.length_b 207.8 _cell.length_c 107.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z9K _symmetry.cell_setting ? _symmetry.Int_Tables_number 93 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 2 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 PISA trimeric 3 author_and_software_defined_assembly 1 PISA hexameric 6 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,D,E,F,G,H,I,J,K,L,M 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M 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' 6_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 207.8 107.5 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 K 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 NE2 HIS 153 A HIS 153 1_555 J MG BCL . B BCL 853 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.011 ? metalc ? metalc2 A NE2 HIS 173 A HIS 173 1_555 E MG BCL . A BCL 851 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc3 A NE2 HIS 190 A HIS 190 1_555 H FE FE . B FE 858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc4 A NE2 HIS 230 A HIS 230 1_555 H FE FE . B FE 858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc5 D MG BCL . A BCL 850 1_555 B NE2 HIS 182 B HIS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc6 B NE2 HIS 202 B HIS 202 1_555 I MG BCL . B BCL 852 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc7 B NE2 HIS 219 B HIS 219 1_555 H FE FE . B FE 858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? metalc ? metalc8 B OE2 GLU 234 B GLU 234 1_555 H FE FE . B FE 858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc9 B OE1 GLU 234 B GLU 234 1_555 H FE FE . B FE 858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc10 C NE2 HIS 128 C HIS 128 1_555 M MN MN . C MN 860 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc11 C NE2 HIS 128 C HIS 128 6_566 M MN MN . C MN 860 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? # _chem_comp.formula 'C55 H76 N4 O6' _chem_comp.formula_weight 889.215 _chem_comp.id BPH _chem_comp.mon_nstd_flag . _chem_comp.name 'BACTERIOPHEOPHYTIN A' _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 O1D CGD BPH doub 218 n n CGD O2D BPH sing 219 n n CGD CBD BPH sing 220 n n O2D CED BPH sing 221 n n CBD CHA BPH sing 222 n n CBD CAD BPH sing 223 n n CHA C4D BPH doub 224 n y CHA C1A BPH sing 225 n y C4D C3D BPH sing 226 n y C4D ND BPH sing 227 n y C3D CAD BPH sing 228 n n C3D C2D BPH doub 229 n y CAD OBD BPH doub 230 n n C2D CMD BPH sing 231 n n C2D C1D BPH sing 232 n y C1D ND BPH sing 233 n y C1D CHD BPH doub 234 n y CHD C4C BPH sing 235 n y C4C C3C BPH sing 236 n n C4C NC BPH doub 237 n y C3C CAC BPH sing 238 n n C3C C2C BPH sing 239 n n CAC CBC BPH sing 240 n n C2C CMC BPH sing 241 n n C2C C1C BPH sing 242 n n C1C NC BPH sing 243 n y C1C CHC BPH doub 244 n y CHC C4B BPH sing 245 n y C4B C3B BPH doub 246 n y C4B NB BPH sing 247 n y C3B CAB BPH sing 248 n n C3B C2B BPH sing 249 n y CAB CBB BPH sing 250 n n CAB OBB BPH doub 251 n n C2B CMB BPH sing 252 n n C2B C1B BPH doub 253 n y C1B NB BPH sing 254 n y C1B CHB BPH sing 255 n y CHB C4A BPH doub 256 n y C4A C3A BPH sing 257 n n C4A NA BPH sing 258 n y C3A CMA BPH sing 259 n n C3A C2A BPH sing 260 n n C2A C1A BPH sing 261 n n C2A CAA BPH sing 262 n n C1A NA BPH doub 263 n y CAA CBA BPH sing 264 n n CBA CGA BPH sing 265 n n CGA O1A BPH doub 266 n n CGA O2A BPH sing 267 n n O2A C1 BPH sing 268 n n C1 C2 BPH sing 269 n n C2 C3 BPH doub 270 e n C3 C4 BPH sing 271 n n C3 C5 BPH sing 272 n n C5 C6 BPH sing 273 n n C6 C7 BPH sing 274 n n C7 C8 BPH sing 275 n n C8 C9 BPH sing 276 n n C8 C10 BPH sing 277 n n C10 C11 BPH sing 278 n n C11 C12 BPH sing 279 n n C12 C13 BPH sing 280 n n C13 C14 BPH sing 281 n n C13 C15 BPH sing 282 n n C15 C16 BPH sing 283 n n C16 C17 BPH sing 284 n n C17 C18 BPH sing 285 n n C18 C19 BPH sing 286 n n C18 C20 BPH sing 287 n n CED HED1 BPH sing 288 n n CED HED2 BPH sing 289 n n CED HED3 BPH sing 290 n n CBD HBD BPH sing 291 n n CMD HMD1 BPH sing 292 n n CMD HMD2 BPH sing 293 n n CMD HMD3 BPH sing 294 n n ND HD BPH sing 295 n n CHD HHD BPH sing 296 n n C3C H3C BPH sing 297 n n CAC HAC1 BPH sing 298 n n CAC HAC2 BPH sing 299 n n CBC HBC1 BPH sing 300 n n CBC HBC2 BPH sing 301 n n CBC HBC3 BPH sing 302 n n C2C H2C BPH sing 303 n n CMC HMC1 BPH sing 304 n n CMC HMC2 BPH sing 305 n n CMC HMC3 BPH sing 306 n n CHC HHC BPH sing 307 n n CBB HBB1 BPH sing 308 n n CBB HBB2 BPH sing 309 n n CBB HBB3 BPH sing 310 n n CMB HMB1 BPH sing 311 n n CMB HMB2 BPH sing 312 n n CMB HMB3 BPH sing 313 n n NB HB BPH sing 314 n n CHB HHB BPH sing 315 n n C3A H3A BPH sing 316 n n CMA HMA1 BPH sing 317 n n CMA HMA2 BPH sing 318 n n CMA HMA3 BPH sing 319 n n C2A H2A BPH sing 320 n n CAA HAA1 BPH sing 321 n n CAA HAA2 BPH sing 322 n n CBA HBA1 BPH sing 323 n n CBA HBA2 BPH sing 324 n n C1 H1C1 BPH sing 325 n n C1 H1C2 BPH sing 326 n n C2 H2 BPH sing 327 n n C4 H4C1 BPH sing 328 n n C4 H4C2 BPH sing 329 n n C4 H4C3 BPH sing 330 n n C5 H5C1 BPH sing 331 n n C5 H5C2 BPH sing 332 n n C6 H6C1 BPH sing 333 n n C6 H6C2 BPH sing 334 n n C7 H7C1 BPH sing 335 n n C7 H7C2 BPH sing 336 n n C8 H8 BPH sing 337 n n C9 H9C1 BPH sing 338 n n C9 H9C2 BPH sing 339 n n C9 H9C3 BPH sing 340 n n C10 H101 BPH sing 341 n n C10 H102 BPH sing 342 n n C11 H111 BPH sing 343 n n C11 H112 BPH sing 344 n n C12 H121 BPH sing 345 n n C12 H122 BPH sing 346 n n C13 H13 BPH sing 347 n n C14 H141 BPH sing 348 n n C14 H142 BPH sing 349 n n C14 H143 BPH sing 350 n n C15 H151 BPH sing 351 n n C15 H152 BPH sing 352 n n C16 H161 BPH sing 353 n n C16 H162 BPH sing 354 n n C17 H171 BPH sing 355 n n C17 H172 BPH sing 356 n n C18 H18 BPH sing 357 n n C19 H191 BPH sing 358 n n C19 H192 BPH sing 359 n n C19 H193 BPH sing 360 n n C20 H201 BPH sing 361 n n C20 H202 BPH sing 362 n n C20 H203 BPH sing 363 n n # _atom_sites.entry_id 1Z9K _atom_sites.fract_transf_matrix[1][1] 0.004812 _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] 0.004812 _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] 0.009302 _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 4 BCL A 1 850 850 BCL BCL . E 4 BCL A 1 851 851 BCL BCL . F 5 BPH A 1 855 855 BPH BPH . G 6 U10 A 1 857 857 U10 U10 . H 7 FE B 1 858 858 FE FE . I 4 BCL B 1 852 852 BCL BCL . J 4 BCL B 1 853 853 BCL BCL . K 5 BPH B 1 854 854 BPH BPH . L 6 U10 B 1 856 856 U10 U10 . M 8 MN C 1 860 860 MN MN . # 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 O O1D BPH . . . F 5 20.412 68.653 25.778 1 90 ? O1D BPH 855 A 1 HETATM 2 C CGD BPH . . . F 5 21.339 68.742 26.585 1 90 ? CGD BPH 855 A 1 HETATM 3 O O2D BPH . . . F 5 21.209 68.768 27.87 1 90 ? O2D BPH 855 A 1 HETATM 4 C CED BPH . . . F 5 19.927 68.697 28.519 1 90 ? CED BPH 855 A 1 HETATM 5 C CBD BPH . . . F 5 22.782 68.807 26.057 1 90 ? CBD BPH 855 A 1 HETATM 6 C CHA BPH . . . F 5 23.74 67.94 26.865 1 90 ? CHA BPH 855 A 1 HETATM 7 C C4D BPH . . . F 5 24.61 68.852 27.478 1 90 ? C4D BPH 855 A 1 HETATM 8 C C3D BPH . . . F 5 24.375 70.196 27.187 1 90 ? C3D BPH 855 A 1 HETATM 9 C CAD BPH . . . F 5 23.264 70.199 26.324 1 90 ? CAD BPH 855 A 1 HETATM 10 O OBD BPH . . . F 5 22.735 71.213 25.836 1 90 ? OBD BPH 855 A 1 HETATM 11 C C2D BPH . . . F 5 25.429 70.857 27.956 1 90 ? C2D BPH 855 A 1 HETATM 12 C CMD BPH . . . F 5 25.661 72.4 28.014 1 90 ? CMD BPH 855 A 1 HETATM 13 C C1D BPH . . . F 5 26.147 69.866 28.599 1 90 ? C1D BPH 855 A 1 HETATM 14 N ND BPH . . . F 5 25.654 68.616 28.316 1 90 ? ND BPH 855 A 1 HETATM 15 C CHD BPH . . . F 5 27.229 70.153 29.431 1 90 ? CHD BPH 855 A 1 HETATM 16 C C4C BPH . . . F 5 27.982 69.249 30.128 1 90 ? C4C BPH 855 A 1 HETATM 17 C C3C BPH . . . F 5 29.143 69.567 31.01 1 90 ? C3C BPH 855 A 1 HETATM 18 C CAC BPH . . . F 5 30.332 70.199 30.264 1 90 ? CAC BPH 855 A 1 HETATM 19 C CBC BPH . . . F 5 31.035 71.273 31.028 1 90 ? CBC BPH 855 A 1 HETATM 20 C C2C BPH . . . F 5 29.569 68.213 31.52 1 90 ? C2C BPH 855 A 1 HETATM 21 C CMC BPH . . . F 5 29.528 68.082 33.041 1 90 ? CMC BPH 855 A 1 HETATM 22 C C1C BPH . . . F 5 28.589 67.261 30.846 1 90 ? C1C BPH 855 A 1 HETATM 23 N NC BPH . . . F 5 27.704 67.903 30.064 1 90 ? NC BPH 855 A 1 HETATM 24 C CHC BPH . . . F 5 28.578 65.904 30.985 1 90 ? CHC BPH 855 A 1 HETATM 25 C C4B BPH . . . F 5 27.829 64.778 30.491 1 90 ? C4B BPH 855 A 1 HETATM 26 C C3B BPH . . . F 5 27.971 63.336 30.766 1 90 ? C3B BPH 855 A 1 HETATM 27 C CAB BPH . . . F 5 28.944 62.556 31.663 1 90 ? CAB BPH 855 A 1 HETATM 28 C CBB BPH . . . F 5 30.222 63.285 32.12 1 90 ? CBB BPH 855 A 1 HETATM 29 O OBB BPH . . . F 5 28.683 61.391 31.999 1 90 ? OBB BPH 855 A 1 HETATM 30 C C2B BPH . . . F 5 26.906 62.756 29.939 1 90 ? C2B BPH 855 A 1 HETATM 31 C CMB BPH . . . F 5 26.402 61.28 29.676 1 90 ? CMB BPH 855 A 1 HETATM 32 C C1B BPH . . . F 5 26.261 63.83 29.292 1 90 ? C1B BPH 855 A 1 HETATM 33 N NB BPH . . . F 5 26.809 65.033 29.618 1 90 ? NB BPH 855 A 1 HETATM 34 C CHB BPH . . . F 5 25.184 63.663 28.427 1 90 ? CHB BPH 855 A 1 HETATM 35 C C4A BPH . . . F 5 24.441 64.601 27.726 1 90 ? C4A BPH 855 A 1 HETATM 36 C C3A BPH . . . F 5 23.284 64.258 26.837 1 90 ? C3A BPH 855 A 1 HETATM 37 C CMA BPH . . . F 5 22.153 63.561 27.594 1 90 ? CMA BPH 855 A 1 HETATM 38 C C2A BPH . . . F 5 22.787 65.566 26.306 1 90 ? C2A BPH 855 A 1 HETATM 39 C C1A BPH . . . F 5 23.736 66.555 26.973 1 90 ? C1A BPH 855 A 1 HETATM 40 N NA BPH . . . F 5 24.666 65.948 27.77 1 90 ? NA BPH 855 A 1 HETATM 41 C CAA BPH . . . F 5 22.81 65.65 24.764 1 90 ? CAA BPH 855 A 1 HETATM 42 C CBA BPH . . . F 5 21.808 64.709 24.102 1 90 ? CBA BPH 855 A 1 HETATM 43 C CGA BPH . . . F 5 21.906 64.535 22.588 1 90 ? CGA BPH 855 A 1 HETATM 44 O O1A BPH . . . F 5 22.776 65.122 21.926 1 90 ? O1A BPH 855 A 1 HETATM 45 O O2A BPH . . . F 5 21.021 63.762 22.079 1 90 ? O2A BPH 855 A 1 HETATM 46 C C1 BPH . . . F 5 20.752 63.352 20.679 1 90 ? C1 BPH 855 A 1 HETATM 47 C C2 BPH . . . F 5 21.694 62.231 20.542 1 90 ? C2 BPH 855 A 1 HETATM 48 C C3 BPH . . . F 5 21.417 60.913 20.153 1 90 ? C3 BPH 855 A 1 HETATM 49 C C4 BPH . . . F 5 19.978 60.455 19.8 1 90 ? C4 BPH 855 A 1 HETATM 50 C C5 BPH . . . F 5 22.632 59.979 20.106 1 90 ? C5 BPH 855 A 1 HETATM 51 C C6 BPH . . . F 5 22.508 58.485 19.694 1 90 ? C6 BPH 855 A 1 HETATM 52 C C7 BPH . . . F 5 23.831 57.916 19.141 1 90 ? C7 BPH 855 A 1 HETATM 53 C C8 BPH . . . F 5 23.901 56.431 18.701 1 90 ? C8 BPH 855 A 1 HETATM 54 C C9 BPH . . . F 5 22.592 55.693 18.915 1 90 ? C9 BPH 855 A 1 HETATM 55 C C10 BPH . . . F 5 25.011 55.578 19.428 1 90 ? C10 BPH 855 A 1 HETATM 56 C C11 BPH . . . F 5 25.563 56.069 20.808 1 90 ? C11 BPH 855 A 1 HETATM 57 C C12 BPH . . . F 5 27.111 56.206 20.811 1 90 ? C12 BPH 855 A 1 HETATM 58 C C13 BPH . . . F 5 27.852 56.452 22.164 1 90 ? C13 BPH 855 A 1 HETATM 59 C C14 BPH . . . F 5 29.358 56.567 21.888 1 90 ? C14 BPH 855 A 1 HETATM 60 C C15 BPH . . . F 5 27.566 55.28 23.146 1 90 ? C15 BPH 855 A 1 HETATM 61 C C16 BPH . . . F 5 28.244 55.391 24.514 1 90 ? C16 BPH 855 A 1 HETATM 62 C C17 BPH . . . F 5 27.908 54.21 25.422 1 90 ? C17 BPH 855 A 1 HETATM 63 C C18 BPH . . . F 5 28.554 54.239 26.824 1 90 ? C18 BPH 855 A 1 HETATM 64 C C19 BPH . . . F 5 30.088 54.26 26.765 1 90 ? C19 BPH 855 A 1 HETATM 65 C C20 BPH . . . F 5 28.113 53.016 27.613 1 90 ? C20 BPH 855 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 65 #