data_6UDM # _model_server_result.job_id 6xBtLqK6PTygctap2IqGSA _model_server_result.datetime_utc '2024-11-24 21:20:47' _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 6udm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 6UDM # _exptl.entry_id 6UDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _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 6UDM _cell.length_a 241.281 _cell.length_b 241.281 _cell.length_c 125.298 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G 1 1 B,H,I 2 1 C,J,K 3 1 D,L,M 4 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 E N N ? 2 H N N ? 2 J N N ? 2 L N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 430 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 457 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 601 _struct_conn.ptnr2_symmetry 1_555 _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 2.67 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # 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 CHA C1A HEM sing 232 n n CHA C4D HEM doub 233 n n CHA HHA HEM sing 234 n n CHB C4A HEM sing 235 n n CHB C1B HEM doub 236 n n CHB HHB HEM sing 237 n n CHC C4B HEM sing 238 n n CHC C1C HEM doub 239 n n CHC HHC HEM sing 240 n n CHD C4C HEM doub 241 n n CHD C1D HEM sing 242 n n CHD HHD HEM sing 243 n n C1A C2A HEM doub 244 n y C1A NA HEM sing 245 n y C2A C3A HEM sing 246 n y C2A CAA HEM sing 247 n n C3A C4A HEM doub 248 n y C3A CMA HEM sing 249 n n C4A NA HEM sing 250 n y CMA HMA HEM sing 251 n n CMA HMAA HEM sing 252 n n CMA HMAB HEM sing 253 n n CAA CBA HEM sing 254 n n CAA HAA HEM sing 255 n n CAA HAAA HEM sing 256 n n CBA CGA HEM sing 257 n n CBA HBA HEM sing 258 n n CBA HBAA HEM sing 259 n n CGA O1A HEM doub 260 n n CGA O2A HEM sing 261 n n C1B C2B HEM sing 262 n n C1B NB HEM sing 263 n n C2B C3B HEM doub 264 n n C2B CMB HEM sing 265 n n C3B C4B HEM sing 266 n n C3B CAB HEM sing 267 n n C4B NB HEM doub 268 n n CMB HMB HEM sing 269 n n CMB HMBA HEM sing 270 n n CMB HMBB HEM sing 271 n n CAB CBB HEM doub 272 n n CAB HAB HEM sing 273 n n CBB HBB HEM sing 274 n n CBB HBBA HEM sing 275 n n C1C C2C HEM sing 276 n y C1C NC HEM sing 277 n y C2C C3C HEM doub 278 n y C2C CMC HEM sing 279 n n C3C C4C HEM sing 280 n y C3C CAC HEM sing 281 n n C4C NC HEM sing 282 n y CMC HMC HEM sing 283 n n CMC HMCA HEM sing 284 n n CMC HMCB HEM sing 285 n n CAC CBC HEM doub 286 n n CAC HAC HEM sing 287 n n CBC HBC HEM sing 288 n n CBC HBCA HEM sing 289 n n C1D C2D HEM sing 290 n n C1D ND HEM doub 291 n n C2D C3D HEM doub 292 n n C2D CMD HEM sing 293 n n C3D C4D HEM sing 294 n n C3D CAD HEM sing 295 n n C4D ND HEM sing 296 n n CMD HMD HEM sing 297 n n CMD HMDA HEM sing 298 n n CMD HMDB HEM sing 299 n n CAD CBD HEM sing 300 n n CAD HAD HEM sing 301 n n CAD HADA HEM sing 302 n n CBD CGD HEM sing 303 n n CBD HBD HEM sing 304 n n CBD HBDA HEM sing 305 n n CGD O1D HEM doub 306 n n CGD O2D HEM sing 307 n n O2A H2A HEM sing 308 n n O2D H2D HEM sing 309 n n FE NA HEM sing 310 n n FE NB HEM sing 311 n n FE NC HEM sing 312 n n FE ND HEM sing 313 n n # _atom_sites.entry_id 6UDM _atom_sites.fract_transf_matrix[1][1] 0.004145 _atom_sites.fract_transf_matrix[1][2] 0.002393 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004786 _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] 0.007981 _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 E 2 HEM A 1 601 601 HEM HEM . F 3 Q4P A 1 602 1 Q4P LIG . G 4 CPS A 1 603 1 CPS CPS . H 2 HEM B 1 601 601 HEM HEM . I 3 Q4P B 1 602 2 Q4P LIG . J 2 HEM C 1 601 601 HEM HEM . K 3 Q4P C 1 602 3 Q4P LIG . L 2 HEM D 1 601 601 HEM HEM . M 3 Q4P D 1 602 4 Q4P LIG . # 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 CHA HEM . . . E 2 -62.955 -63.512 11.059 1 67.59 ? CHA HEM 601 A 1 HETATM 2 C CHB HEM . . . E 2 -67.089 -64.428 13.423 1 63.97 ? CHB HEM 601 A 1 HETATM 3 C CHC HEM . . . E 2 -69.08 -65.901 9.244 1 66.43 ? CHC HEM 601 A 1 HETATM 4 C CHD HEM . . . E 2 -64.951 -64.985 6.895 1 70.22 ? CHD HEM 601 A 1 HETATM 5 C C1A HEM . . . E 2 -63.884 -63.657 12.064 1 65.98 ? C1A HEM 601 A 1 HETATM 6 C C2A HEM . . . E 2 -63.654 -63.39 13.467 1 64.7 ? C2A HEM 601 A 1 HETATM 7 C C3A HEM . . . E 2 -64.787 -63.645 14.127 1 64.18 ? C3A HEM 601 A 1 HETATM 8 C C4A HEM . . . E 2 -65.783 -64.072 13.162 1 64.3 ? C4A HEM 601 A 1 HETATM 9 C CMA HEM . . . E 2 -65.003 -63.504 15.651 1 63.16 ? CMA HEM 601 A 1 HETATM 10 C CAA HEM . . . E 2 -62.306 -62.919 14.055 1 65.31 ? CAA HEM 601 A 1 HETATM 11 C CBA HEM . . . E 2 -62.435 -61.5 14.594 1 67.2 ? CBA HEM 601 A 1 HETATM 12 C CGA HEM . . . E 2 -61.081 -61.007 15.034 1 67.02 ? CGA HEM 601 A 1 HETATM 13 O O1A HEM . . . E 2 -61.001 -59.861 15.555 1 67.63 ? O1A HEM 601 A 1 HETATM 14 O O2A HEM . . . E 2 -60.086 -61.756 14.847 1 64.87 ? O2A HEM 601 A 1 HETATM 15 C C1B HEM . . . E 2 -67.983 -64.929 12.497 1 64.35 ? C1B HEM 601 A 1 HETATM 16 C C2B HEM . . . E 2 -69.329 -65.395 12.772 1 63.37 ? C2B HEM 601 A 1 HETATM 17 C C3B HEM . . . E 2 -69.87 -65.809 11.617 1 63.27 ? C3B HEM 601 A 1 HETATM 18 C C4B HEM . . . E 2 -68.89 -65.606 10.575 1 64.59 ? C4B HEM 601 A 1 HETATM 19 C CMB HEM . . . E 2 -69.975 -65.402 14.175 1 63.14 ? CMB HEM 601 A 1 HETATM 20 C CAB HEM . . . E 2 -71.281 -66.383 11.341 1 63.92 ? CAB HEM 601 A 1 HETATM 21 C CBB HEM . . . E 2 -72.28 -66.29 12.222 1 63.67 ? CBB HEM 601 A 1 HETATM 22 C C1C HEM . . . E 2 -68.161 -65.731 8.235 1 67.74 ? C1C HEM 601 A 1 HETATM 23 C C2C HEM . . . E 2 -68.412 -65.901 6.819 1 68.54 ? C2C HEM 601 A 1 HETATM 24 C C3C HEM . . . E 2 -67.271 -65.638 6.164 1 69.18 ? C3C HEM 601 A 1 HETATM 25 C C4C HEM . . . E 2 -66.264 -65.31 7.153 1 69.38 ? C4C HEM 601 A 1 HETATM 26 C CMC HEM . . . E 2 -69.784 -66.298 6.229 1 69.28 ? CMC HEM 601 A 1 HETATM 27 C CAC HEM . . . E 2 -66.984 -65.684 4.643 1 71.36 ? CAC HEM 601 A 1 HETATM 28 C CBC HEM . . . E 2 -67.819 -66.261 3.773 1 72.3 ? CBC HEM 601 A 1 HETATM 29 C C1D HEM . . . E 2 -64.035 -64.557 7.827 1 68.83 ? C1D HEM 601 A 1 HETATM 30 C C2D HEM . . . E 2 -62.627 -64.319 7.589 1 69.8 ? C2D HEM 601 A 1 HETATM 31 C C3D HEM . . . E 2 -62.076 -63.914 8.737 1 69.8 ? C3D HEM 601 A 1 HETATM 32 C C4D HEM . . . E 2 -63.118 -63.88 9.743 1 67.59 ? C4D HEM 601 A 1 HETATM 33 C CMD HEM . . . E 2 -61.905 -64.509 6.238 1 72.04 ? CMD HEM 601 A 1 HETATM 34 C CAD HEM . . . E 2 -60.596 -63.539 8.972 1 70.53 ? CAD HEM 601 A 1 HETATM 35 C CBD HEM . . . E 2 -60.492 -62.021 9.076 1 71.2 ? CBD HEM 601 A 1 HETATM 36 C CGD HEM . . . E 2 -59.075 -61.622 9.389 1 72.29 ? CGD HEM 601 A 1 HETATM 37 O O1D HEM . . . E 2 -58.759 -60.407 9.305 1 72.87 ? O1D HEM 601 A 1 HETATM 38 O O2D HEM . . . E 2 -58.261 -62.519 9.723 1 73.5 ? O2D HEM 601 A 1 HETATM 39 N NA HEM . . . E 2 -65.195 -64.064 11.912 1 65.27 ? NA HEM 601 A 1 HETATM 40 N NB HEM . . . E 2 -67.751 -65.071 11.142 1 64.18 ? NB HEM 601 A 1 HETATM 41 N NC HEM . . . E 2 -66.842 -65.369 8.404 1 67.84 ? NC HEM 601 A 1 HETATM 42 N ND HEM . . . E 2 -64.3 -64.277 9.153 1 66.43 ? ND HEM 601 A 1 HETATM 43 FE FE HEM . . . E 2 -66.075 -64.526 10.107 1 65.78 ? FE HEM 601 A 1 HETATM 44 H HHB HEM . . . E 2 -67.447 -64.192 14.304 1 63.97 ? HHB HEM 601 A 1 HETATM 45 H HHC HEM . . . E 2 -69.957 -66.256 8.989 1 66.43 ? HHC HEM 601 A 1 HETATM 46 H HHD HEM . . . E 2 -64.614 -65.178 5.995 1 70.22 ? HHD HEM 601 A 1 HETATM 47 H HMA HEM . . . E 2 -64.323 -64.026 16.126 1 63.16 ? HMA HEM 601 A 1 HETATM 48 H HMAA HEM . . . E 2 -65.894 -63.837 15.887 1 63.16 ? HMAA HEM 601 A 1 HETATM 49 H HMAB HEM . . . E 2 -64.928 -62.561 15.907 1 63.16 ? HMAB HEM 601 A 1 HETATM 50 H HAA HEM . . . E 2 -61.627 -62.94 13.363 1 65.31 ? HAA HEM 601 A 1 HETATM 51 H HAAA HEM . . . E 2 -62.046 -63.513 14.776 1 65.31 ? HAAA HEM 601 A 1 HETATM 52 H HBA HEM . . . E 2 -63.041 -61.494 15.351 1 67.2 ? HBA HEM 601 A 1 HETATM 53 H HBAA HEM . . . E 2 -62.78 -60.919 13.898 1 67.2 ? HBAA HEM 601 A 1 HETATM 54 H HMB HEM . . . E 2 -69.279 -65.485 14.846 1 63.14 ? HMB HEM 601 A 1 HETATM 55 H HMBA HEM . . . E 2 -70.584 -66.152 14.255 1 63.14 ? HMBA HEM 601 A 1 HETATM 56 H HMBB HEM . . . E 2 -70.455 -64.571 14.315 1 63.14 ? HMBB HEM 601 A 1 HETATM 57 H HAB HEM . . . E 2 -71.443 -66.828 10.506 1 63.92 ? HAB HEM 601 A 1 HETATM 58 H HBB HEM . . . E 2 -73.022 -66.913 12.177 1 63.67 ? HBB HEM 601 A 1 HETATM 59 H HBBA HEM . . . E 2 -72.268 -65.604 12.906 1 63.67 ? HBBA HEM 601 A 1 HETATM 60 H HMC HEM . . . E 2 -69.901 -65.89 5.358 1 69.28 ? HMC HEM 601 A 1 HETATM 61 H HMCA HEM . . . E 2 -70.486 -65.986 6.821 1 69.28 ? HMCA HEM 601 A 1 HETATM 62 H HMCB HEM . . . E 2 -69.839 -67.263 6.153 1 69.28 ? HMCB HEM 601 A 1 HETATM 63 H HAC HEM . . . E 2 -66.177 -65.283 4.313 1 71.36 ? HAC HEM 601 A 1 HETATM 64 H HBC HEM . . . E 2 -67.716 -66.09 2.824 1 72.3 ? HBC HEM 601 A 1 HETATM 65 H HBCA HEM . . . E 2 -68.439 -66.944 4.072 1 72.3 ? HBCA HEM 601 A 1 HETATM 66 H HMD HEM . . . E 2 -60.999 -64.141 6.288 1 72.04 ? HMD HEM 601 A 1 HETATM 67 H HMDA HEM . . . E 2 -62.406 -64.045 5.536 1 72.04 ? HMDA HEM 601 A 1 HETATM 68 H HMDB HEM . . . E 2 -61.86 -65.464 6.024 1 72.04 ? HMDB HEM 601 A 1 HETATM 69 H HAD HEM . . . E 2 -60.052 -63.855 8.235 1 70.53 ? HAD HEM 601 A 1 HETATM 70 H HADA HEM . . . E 2 -60.288 -63.943 9.798 1 70.53 ? HADA HEM 601 A 1 HETATM 71 H HBD HEM . . . E 2 -61.078 -61.706 9.782 1 71.2 ? HBD HEM 601 A 1 HETATM 72 H HBDA HEM . . . E 2 -60.76 -61.622 8.233 1 71.2 ? HBDA HEM 601 A 1 HETATM 73 H HHA HEM . . . E 2 -62.132 -63.029 11.284 1 67.59 ? HHA HEM 601 A 1 # _model_server_stats.io_time_ms 135 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 73 #