data_1VF5 # _model_server_result.job_id MjNIPR5JbK5pkM6sQ1Xk4A _model_server_result.datetime_utc '2024-11-22 04:46:22' _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 1vf5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":301}' # _entry.id 1VF5 # _exptl.entry_id 1VF5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 8 _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 1VF5 _cell.length_a 157.536 _cell.length_b 157.536 _cell.length_c 360.347 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VF5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 ? 9 Q N N ? 9 R N N ? 9 S N N ? 9 X N N ? 9 BA N N ? 9 CA N N ? 9 DA N N ? 9 HA 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 D SG CYS 113 D CYS 113 1_555 D SG CYS 128 D CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 L SG CYS 113 Q CYS 113 1_555 L SG CYS 128 Q CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A SG CYS 35 A CYS 35 1_555 S CAB HEM . A HEM 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.787 ? covale ? covale2 C SG CYS 22 C CYS 22 1_555 X CAB HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.84 ? covale ? covale3 C SG CYS 25 C CYS 25 1_555 X CAC HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? covale ? covale4 C SG CYS 25 C CYS 25 1_555 X CBC HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? covale ? covale5 I SG CYS 35 N CYS 35 1_555 DA CAB HEM . N HEM 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.827 ? covale ? covale6 K SG CYS 22 P CYS 22 1_555 HA CAB HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? covale ? covale7 K SG CYS 25 P CYS 25 1_555 HA CAC HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? covale ? covale8 K SG CYS 25 P CYS 25 1_555 HA CBC HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? metalc ? metalc1 A NE2 HIS 86 A HIS 86 1_555 Q FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc2 A NE2 HIS 100 A HIS 100 1_555 R FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc3 A NE2 HIS 187 A HIS 187 1_555 Q FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc4 A NE2 HIS 202 A HIS 202 1_555 R FE HEM . A HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc5 S FE HEM . A HEM 303 1_555 MA O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc6 C N TYR 1 C TYR 1 1_555 X FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc7 C NE2 HIS 26 C HIS 26 1_555 X FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc8 D SG CYS 108 D CYS 108 1_555 Z FE1 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc9 D ND1 HIS 110 D HIS 110 1_555 Z FE2 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc10 D SG CYS 126 D CYS 126 1_555 Z FE1 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc11 D ND1 HIS 129 D HIS 129 1_555 Z FE2 FES . D FES 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc12 I NE2 HIS 86 N HIS 86 1_555 BA FE HEM . N HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc13 I NE2 HIS 100 N HIS 100 1_555 CA FE HEM . N HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc14 I NE2 HIS 187 N HIS 187 1_555 BA FE HEM . N HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc15 I NE2 HIS 202 N HIS 202 1_555 CA FE HEM . N HEM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc16 DA FE HEM . N HEM 303 1_555 NA O HOH . N HOH 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc17 K N TYR 1 P TYR 1 1_555 HA FE HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc18 K NE2 HIS 26 P HIS 26 1_555 HA FE HEM . P HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc19 L SG CYS 108 Q CYS 108 1_555 KA FE1 FES . Q FES 1200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc20 L ND1 HIS 110 Q HIS 110 1_555 KA FE2 FES . Q FES 1200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc21 L SG CYS 126 Q CYS 126 1_555 KA FE1 FES . Q FES 1200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc22 L ND1 HIS 129 Q HIS 129 1_555 KA FE2 FES . Q FES 1200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? # _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 375 n n CHA C4D HEM doub 376 n n CHA HHA HEM sing 377 n n CHB C4A HEM sing 378 n n CHB C1B HEM doub 379 n n CHB HHB HEM sing 380 n n CHC C4B HEM sing 381 n n CHC C1C HEM doub 382 n n CHC HHC HEM sing 383 n n CHD C4C HEM doub 384 n n CHD C1D HEM sing 385 n n CHD HHD HEM sing 386 n n C1A C2A HEM doub 387 n y C1A NA HEM sing 388 n y C2A C3A HEM sing 389 n y C2A CAA HEM sing 390 n n C3A C4A HEM doub 391 n y C3A CMA HEM sing 392 n n C4A NA HEM sing 393 n y CMA HMA HEM sing 394 n n CMA HMAA HEM sing 395 n n CMA HMAB HEM sing 396 n n CAA CBA HEM sing 397 n n CAA HAA HEM sing 398 n n CAA HAAA HEM sing 399 n n CBA CGA HEM sing 400 n n CBA HBA HEM sing 401 n n CBA HBAA HEM sing 402 n n CGA O1A HEM doub 403 n n CGA O2A HEM sing 404 n n C1B C2B HEM sing 405 n n C1B NB HEM sing 406 n n C2B C3B HEM doub 407 n n C2B CMB HEM sing 408 n n C3B C4B HEM sing 409 n n C3B CAB HEM sing 410 n n C4B NB HEM doub 411 n n CMB HMB HEM sing 412 n n CMB HMBA HEM sing 413 n n CMB HMBB HEM sing 414 n n CAB CBB HEM doub 415 n n CAB HAB HEM sing 416 n n CBB HBB HEM sing 417 n n CBB HBBA HEM sing 418 n n C1C C2C HEM sing 419 n y C1C NC HEM sing 420 n y C2C C3C HEM doub 421 n y C2C CMC HEM sing 422 n n C3C C4C HEM sing 423 n y C3C CAC HEM sing 424 n n C4C NC HEM sing 425 n y CMC HMC HEM sing 426 n n CMC HMCA HEM sing 427 n n CMC HMCB HEM sing 428 n n CAC CBC HEM doub 429 n n CAC HAC HEM sing 430 n n CBC HBC HEM sing 431 n n CBC HBCA HEM sing 432 n n C1D C2D HEM sing 433 n n C1D ND HEM doub 434 n n C2D C3D HEM doub 435 n n C2D CMD HEM sing 436 n n C3D C4D HEM sing 437 n n C3D CAD HEM sing 438 n n C4D ND HEM sing 439 n n CMD HMD HEM sing 440 n n CMD HMDA HEM sing 441 n n CMD HMDB HEM sing 442 n n CAD CBD HEM sing 443 n n CAD HAD HEM sing 444 n n CAD HADA HEM sing 445 n n CBD CGD HEM sing 446 n n CBD HBD HEM sing 447 n n CBD HBDA HEM sing 448 n n CGD O1D HEM doub 449 n n CGD O2D HEM sing 450 n n O2A H2A HEM sing 451 n n O2D H2D HEM sing 452 n n FE NA HEM sing 453 n n FE NB HEM sing 454 n n FE NC HEM sing 455 n n FE ND HEM sing 456 n n # _atom_sites.entry_id 1VF5 _atom_sites.fract_transf_matrix[1][1] 0.006348 _atom_sites.fract_transf_matrix[1][2] 0.003665 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00733 _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] 0.002775 _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 Q 9 HEM A 1 301 301 HEM HEM . R 9 HEM A 1 302 302 HEM HEM . S 9 HEM A 1 303 303 HEM HEM . T 10 TDS A 1 304 304 TDS TDS . U 11 PL9 A 1 305 305 PL9 PL9 . V 12 OPC B 1 307 307 OPC OPC . W 13 CLA B 1 201 201 CLA CLA . X 9 HEM C 1 301 301 HEM HEM . Y 12 OPC D 1 306 306 OPC OPC . Z 14 FES D 1 200 200 FES FES . AA 15 BCR E 1 101 101 BCR BCR . BA 9 HEM N 1 301 301 HEM HEM . CA 9 HEM N 1 302 302 HEM HEM . DA 9 HEM N 1 303 303 HEM HEM . EA 10 TDS N 1 1304 1304 TDS TDS . FA 12 OPC N 1 1306 1306 OPC OPC . GA 13 CLA O 1 1201 1201 CLA CLA . HA 9 HEM P 1 301 301 HEM HEM . IA 11 PL9 Q 1 1305 1305 PL9 PL9 . JA 12 OPC Q 1 1307 1307 OPC OPC . KA 14 FES Q 1 1200 1200 FES FES . LA 15 BCR R 1 1101 1101 BCR BCR . MA 16 HOH A 1 306 1 HOH HOH . NA 16 HOH N 1 1307 2 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 CHA HEM . . . X 9 85.039 -41.254 56.829 1 83.23 ? CHA HEM 301 C 1 HETATM 2 C CHB HEM . . . X 9 82 -38.096 59.033 1 83.23 ? CHB HEM 301 C 1 HETATM 3 C CHC HEM . . . X 9 83.853 -39.218 63.346 1 83.23 ? CHC HEM 301 C 1 HETATM 4 C CHD HEM . . . X 9 86.909 -42.353 61.203 1 83.23 ? CHD HEM 301 C 1 HETATM 5 C C1A HEM . . . X 9 84.01 -40.285 57.019 1 83.23 ? C1A HEM 301 C 1 HETATM 6 C C2A HEM . . . X 9 83.15 -39.689 55.992 1 83.23 ? C2A HEM 301 C 1 HETATM 7 C C3A HEM . . . X 9 82.309 -38.807 56.616 1 83.23 ? C3A HEM 301 C 1 HETATM 8 C C4A HEM . . . X 9 82.618 -38.837 58.059 1 83.23 ? C4A HEM 301 C 1 HETATM 9 C CMA HEM . . . X 9 81.261 -37.99 55.821 1 83.23 ? CMA HEM 301 C 1 HETATM 10 C CAA HEM . . . X 9 83.068 -39.895 54.478 1 83.23 ? CAA HEM 301 C 1 HETATM 11 C CBA HEM . . . X 9 84.186 -39.177 53.715 1 83.23 ? CBA HEM 301 C 1 HETATM 12 C CGA HEM . . . X 9 84.15 -39.35 52.182 1 83.23 ? CGA HEM 301 C 1 HETATM 13 O O1A HEM . . . X 9 83.561 -40.344 51.669 1 83.23 ? O1A HEM 301 C 1 HETATM 14 O O2A HEM . . . X 9 84.709 -38.493 51.431 1 83.23 ? O2A HEM 301 C 1 HETATM 15 C C1B HEM . . . X 9 82.237 -38.101 60.387 1 83.23 ? C1B HEM 301 C 1 HETATM 16 C C2B HEM . . . X 9 81.551 -37.283 61.362 1 83.23 ? C2B HEM 301 C 1 HETATM 17 C C3B HEM . . . X 9 82.055 -37.584 62.601 1 83.23 ? C3B HEM 301 C 1 HETATM 18 C C4B HEM . . . X 9 83.074 -38.616 62.353 1 83.23 ? C4B HEM 301 C 1 HETATM 19 C CMB HEM . . . X 9 80.474 -36.285 61.03 1 83.23 ? CMB HEM 301 C 1 HETATM 20 C CAB HEM . . . X 9 81.619 -36.961 63.871 1 83.23 ? CAB HEM 301 C 1 HETATM 21 C CBB HEM . . . X 9 80.693 -37.418 64.698 1 83.23 ? CBB HEM 301 C 1 HETATM 22 C C1C HEM . . . X 9 84.852 -40.182 63.167 1 83.23 ? C1C HEM 301 C 1 HETATM 23 C C2C HEM . . . X 9 85.636 -40.79 64.221 1 83.23 ? C2C HEM 301 C 1 HETATM 24 C C3C HEM . . . X 9 86.506 -41.677 63.629 1 83.23 ? C3C HEM 301 C 1 HETATM 25 C C4C HEM . . . X 9 86.243 -41.611 62.176 1 83.23 ? C4C HEM 301 C 1 HETATM 26 C CMC HEM . . . X 9 85.511 -40.489 65.695 1 83.23 ? CMC HEM 301 C 1 HETATM 27 C CAC HEM . . . X 9 87.576 -42.595 64.298 1 83.23 ? CAC HEM 301 C 1 HETATM 28 C CBC HEM . . . X 9 88.684 -42.203 65.305 1 83.23 ? CBC HEM 301 C 1 HETATM 29 C C1D HEM . . . X 9 86.674 -42.319 59.832 1 83.23 ? C1D HEM 301 C 1 HETATM 30 C C2D HEM . . . X 9 87.403 -43.126 58.846 1 83.23 ? C2D HEM 301 C 1 HETATM 31 C C3D HEM . . . X 9 86.854 -42.802 57.602 1 83.23 ? C3D HEM 301 C 1 HETATM 32 C C4D HEM . . . X 9 85.816 -41.808 57.875 1 83.23 ? C4D HEM 301 C 1 HETATM 33 C CMD HEM . . . X 9 88.504 -44.094 59.166 1 83.23 ? CMD HEM 301 C 1 HETATM 34 C CAD HEM . . . X 9 87.271 -43.388 56.248 1 83.23 ? CAD HEM 301 C 1 HETATM 35 C CBD HEM . . . X 9 86.967 -44.917 56.118 1 83.23 ? CBD HEM 301 C 1 HETATM 36 C CGD HEM . . . X 9 87.414 -45.468 54.755 1 83.23 ? CGD HEM 301 C 1 HETATM 37 O O1D HEM . . . X 9 88.621 -45.329 54.397 1 83.23 ? O1D HEM 301 C 1 HETATM 38 O O2D HEM . . . X 9 86.531 -46.067 54.065 1 83.23 ? O2D HEM 301 C 1 HETATM 39 N NA HEM . . . X 9 83.63 -39.737 58.25 1 83.23 ? NA HEM 301 C 1 HETATM 40 N NB HEM . . . X 9 83.162 -38.893 61.006 1 83.23 ? NB HEM 301 C 1 HETATM 41 N NC HEM . . . X 9 85.23 -40.695 61.937 1 83.23 ? NC HEM 301 C 1 HETATM 42 N ND HEM . . . X 9 85.731 -41.535 59.195 1 83.23 ? ND HEM 301 C 1 HETATM 43 FE FE HEM . . . X 9 84.451 -40.212 60.05 1 62.22 ? FE HEM 301 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #