data_5VVN # _model_server_result.job_id -2rth_pOjmqdf1TIEMF5DQ _model_server_result.datetime_utc '2024-11-13 07:30:15' _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 5vvn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5VVN # _exptl.entry_id 5VVN _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 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 5VVN _cell.length_a 58.093 _cell.length_b 106.388 _cell.length_c 156.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VVN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 J 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 covale ? covale1 A C VAL 344 A VAL 383 1_555 A N CAS 345 A CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C CAS 345 A CAS 384 1_555 A N MET 346 A MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 B C VAL 344 B VAL 383 1_555 B N CAS 345 B CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 B C CAS 345 B CAS 384 1_555 B N MET 346 B MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 A SG CYS 57 A CYS 96 1_555 I ZN ZN . A ZN 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc2 A SG CYS 62 A CYS 101 1_555 I ZN ZN . A ZN 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc3 A SG CYS 147 A CYS 186 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc4 I ZN ZN . A ZN 507 1_555 B SG CYS 57 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc5 I ZN ZN . A ZN 507 1_555 B SG CYS 62 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc6 B SG CYS 147 B CYS 186 1_555 J FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? # _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 202 n n CHA C4D HEM doub 203 n n CHA HHA HEM sing 204 n n CHB C4A HEM sing 205 n n CHB C1B HEM doub 206 n n CHB HHB HEM sing 207 n n CHC C4B HEM sing 208 n n CHC C1C HEM doub 209 n n CHC HHC HEM sing 210 n n CHD C4C HEM doub 211 n n CHD C1D HEM sing 212 n n CHD HHD HEM sing 213 n n C1A C2A HEM doub 214 n y C1A NA HEM sing 215 n y C2A C3A HEM sing 216 n y C2A CAA HEM sing 217 n n C3A C4A HEM doub 218 n y C3A CMA HEM sing 219 n n C4A NA HEM sing 220 n y CMA HMA HEM sing 221 n n CMA HMAA HEM sing 222 n n CMA HMAB HEM sing 223 n n CAA CBA HEM sing 224 n n CAA HAA HEM sing 225 n n CAA HAAA HEM sing 226 n n CBA CGA HEM sing 227 n n CBA HBA HEM sing 228 n n CBA HBAA HEM sing 229 n n CGA O1A HEM doub 230 n n CGA O2A HEM sing 231 n n C1B C2B HEM sing 232 n n C1B NB HEM sing 233 n n C2B C3B HEM doub 234 n n C2B CMB HEM sing 235 n n C3B C4B HEM sing 236 n n C3B CAB HEM sing 237 n n C4B NB HEM doub 238 n n CMB HMB HEM sing 239 n n CMB HMBA HEM sing 240 n n CMB HMBB HEM sing 241 n n CAB CBB HEM doub 242 n n CAB HAB HEM sing 243 n n CBB HBB HEM sing 244 n n CBB HBBA HEM sing 245 n n C1C C2C HEM sing 246 n y C1C NC HEM sing 247 n y C2C C3C HEM doub 248 n y C2C CMC HEM sing 249 n n C3C C4C HEM sing 250 n y C3C CAC HEM sing 251 n n C4C NC HEM sing 252 n y CMC HMC HEM sing 253 n n CMC HMCA HEM sing 254 n n CMC HMCB HEM sing 255 n n CAC CBC HEM doub 256 n n CAC HAC HEM sing 257 n n CBC HBC HEM sing 258 n n CBC HBCA HEM sing 259 n n C1D C2D HEM sing 260 n n C1D ND HEM doub 261 n n C2D C3D HEM doub 262 n n C2D CMD HEM sing 263 n n C3D C4D HEM sing 264 n n C3D CAD HEM sing 265 n n C4D ND HEM sing 266 n n CMD HMD HEM sing 267 n n CMD HMDA HEM sing 268 n n CMD HMDB HEM sing 269 n n CAD CBD HEM sing 270 n n CAD HAD HEM sing 271 n n CAD HADA HEM sing 272 n n CBD CGD HEM sing 273 n n CBD HBD HEM sing 274 n n CBD HBDA HEM sing 275 n n CGD O1D HEM doub 276 n n CGD O2D HEM sing 277 n n O2A H2A HEM sing 278 n n O2D H2D HEM sing 279 n n FE NA HEM sing 280 n n FE NB HEM sing 281 n n FE NC HEM sing 282 n n FE ND HEM sing 283 n n # _atom_sites.entry_id 5VVN _atom_sites.fract_transf_matrix[1][1] 0.017214 _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] 0.0094 _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] 0.006409 _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 HEM A 1 501 500 HEM HEM . D 3 H4B A 1 502 600 H4B BH4 . E 4 P94 A 1 503 800 P94 P94 . F 5 ACT A 1 504 860 ACT ACT . G 5 ACT A 1 505 861 ACT ACT . H 6 GOL A 1 506 880 GOL GOL . I 7 ZN A 1 507 900 ZN ZN . J 2 HEM B 1 501 500 HEM HEM . K 3 H4B B 1 502 600 H4B BH4 . L 4 P94 B 1 503 800 P94 P94 . M 5 ACT B 1 504 860 ACT ACT . N 5 ACT B 1 505 861 ACT ACT . O 6 GOL B 1 506 880 GOL GOL . P 8 HOH A 1 601 16 HOH HOH . P 8 HOH A 2 602 49 HOH HOH . P 8 HOH A 3 603 61 HOH HOH . P 8 HOH A 4 604 48 HOH HOH . P 8 HOH A 5 605 24 HOH HOH . P 8 HOH A 6 606 56 HOH HOH . P 8 HOH A 7 607 66 HOH HOH . P 8 HOH A 8 608 13 HOH HOH . P 8 HOH A 9 609 35 HOH HOH . P 8 HOH A 10 610 9 HOH HOH . P 8 HOH A 11 611 72 HOH HOH . P 8 HOH A 12 612 42 HOH HOH . P 8 HOH A 13 613 19 HOH HOH . P 8 HOH A 14 614 28 HOH HOH . P 8 HOH A 15 615 29 HOH HOH . P 8 HOH A 16 616 73 HOH HOH . P 8 HOH A 17 617 34 HOH HOH . P 8 HOH A 18 618 47 HOH HOH . P 8 HOH A 19 619 82 HOH HOH . P 8 HOH A 20 620 11 HOH HOH . P 8 HOH A 21 621 36 HOH HOH . P 8 HOH A 22 622 78 HOH HOH . P 8 HOH A 23 623 31 HOH HOH . P 8 HOH A 24 624 67 HOH HOH . P 8 HOH A 25 625 77 HOH HOH . P 8 HOH A 26 626 38 HOH HOH . P 8 HOH A 27 627 71 HOH HOH . P 8 HOH A 28 628 33 HOH HOH . P 8 HOH A 29 629 5 HOH HOH . P 8 HOH A 30 630 70 HOH HOH . P 8 HOH A 31 631 37 HOH HOH . P 8 HOH A 32 632 46 HOH HOH . P 8 HOH A 33 633 64 HOH HOH . P 8 HOH A 34 634 14 HOH HOH . P 8 HOH A 35 635 4 HOH HOH . P 8 HOH A 36 636 63 HOH HOH . P 8 HOH A 37 637 76 HOH HOH . P 8 HOH A 38 638 80 HOH HOH . P 8 HOH A 39 639 2 HOH HOH . P 8 HOH A 40 640 17 HOH HOH . P 8 HOH A 41 641 65 HOH HOH . P 8 HOH A 42 642 62 HOH HOH . P 8 HOH A 43 643 81 HOH HOH . P 8 HOH A 44 644 74 HOH HOH . P 8 HOH A 45 645 22 HOH HOH . P 8 HOH A 46 646 75 HOH HOH . P 8 HOH A 47 647 20 HOH HOH . P 8 HOH A 48 648 18 HOH HOH . P 8 HOH A 49 649 23 HOH HOH . P 8 HOH A 50 650 79 HOH HOH . P 8 HOH A 51 651 39 HOH HOH . P 8 HOH A 52 652 43 HOH HOH . P 8 HOH A 53 653 45 HOH HOH . P 8 HOH A 54 654 55 HOH HOH . P 8 HOH A 55 655 68 HOH HOH . P 8 HOH A 56 656 3 HOH HOH . P 8 HOH A 57 657 40 HOH HOH . Q 8 HOH B 1 601 83 HOH HOH . Q 8 HOH B 2 602 50 HOH HOH . Q 8 HOH B 3 603 6 HOH HOH . Q 8 HOH B 4 604 91 HOH HOH . Q 8 HOH B 5 605 30 HOH HOH . Q 8 HOH B 6 606 69 HOH HOH . Q 8 HOH B 7 607 44 HOH HOH . Q 8 HOH B 8 608 7 HOH HOH . Q 8 HOH B 9 609 93 HOH HOH . Q 8 HOH B 10 610 88 HOH HOH . Q 8 HOH B 11 611 85 HOH HOH . Q 8 HOH B 12 612 32 HOH HOH . Q 8 HOH B 13 613 51 HOH HOH . Q 8 HOH B 14 614 41 HOH HOH . Q 8 HOH B 15 615 8 HOH HOH . Q 8 HOH B 16 616 21 HOH HOH . Q 8 HOH B 17 617 90 HOH HOH . Q 8 HOH B 18 618 54 HOH HOH . Q 8 HOH B 19 619 10 HOH HOH . Q 8 HOH B 20 620 84 HOH HOH . Q 8 HOH B 21 621 12 HOH HOH . Q 8 HOH B 22 622 1 HOH HOH . Q 8 HOH B 23 623 53 HOH HOH . Q 8 HOH B 24 624 26 HOH HOH . Q 8 HOH B 25 625 57 HOH HOH . Q 8 HOH B 26 626 15 HOH HOH . Q 8 HOH B 27 627 27 HOH HOH . Q 8 HOH B 28 628 86 HOH HOH . Q 8 HOH B 29 629 52 HOH HOH . Q 8 HOH B 30 630 89 HOH HOH . Q 8 HOH B 31 631 25 HOH HOH . Q 8 HOH B 32 632 59 HOH HOH . Q 8 HOH B 33 633 58 HOH HOH . Q 8 HOH B 34 634 92 HOH HOH . Q 8 HOH B 35 635 60 HOH HOH . Q 8 HOH B 36 636 87 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 . . . C 2 9.108 8.933 35.137 1 35.66 ? CHA HEM 501 A 1 HETATM 2 C CHB HEM . . . C 2 4.567 9.11 33.612 1 34.63 ? CHB HEM 501 A 1 HETATM 3 C CHC HEM . . . C 2 6.099 7.468 29.306 1 30.82 ? CHC HEM 501 A 1 HETATM 4 C CHD HEM . . . C 2 10.544 6.752 30.98 1 30.71 ? CHD HEM 501 A 1 HETATM 5 C C1A HEM . . . C 2 7.777 9.289 35.054 1 39.27 ? C1A HEM 501 A 1 HETATM 6 C C2A HEM . . . C 2 7.016 10.182 35.949 1 39.36 ? C2A HEM 501 A 1 HETATM 7 C C3A HEM . . . C 2 5.758 10.209 35.505 1 38.15 ? C3A HEM 501 A 1 HETATM 8 C C4A HEM . . . C 2 5.679 9.35 34.345 1 38.08 ? C4A HEM 501 A 1 HETATM 9 C CMA HEM . . . C 2 4.577 10.985 36.107 1 38.42 ? CMA HEM 501 A 1 HETATM 10 C CAA HEM . . . C 2 7.526 10.984 37.18 1 43.95 ? CAA HEM 501 A 1 HETATM 11 C CBA HEM . . . C 2 8.657 11.925 36.748 1 48.51 ? CBA HEM 501 A 1 HETATM 12 C CGA HEM . . . C 2 8.831 13.153 37.625 1 55.24 ? CGA HEM 501 A 1 HETATM 13 O O1A HEM . . . C 2 8.005 13.422 38.549 1 52.84 ? O1A HEM 501 A 1 HETATM 14 O O2A HEM . . . C 2 9.828 13.887 37.377 1 58.44 ? O2A HEM 501 A 1 HETATM 15 C C1B HEM . . . C 2 4.63 8.682 32.32 1 34.25 ? C1B HEM 501 A 1 HETATM 16 C C2B HEM . . . C 2 3.475 8.636 31.463 1 34.14 ? C2B HEM 501 A 1 HETATM 17 C C3B HEM . . . C 2 3.873 8.18 30.277 1 38.09 ? C3B HEM 501 A 1 HETATM 18 C C4B HEM . . . C 2 5.314 7.927 30.345 1 32.67 ? C4B HEM 501 A 1 HETATM 19 C CMB HEM . . . C 2 2.056 9.049 31.903 1 34.3 ? CMB HEM 501 A 1 HETATM 20 C CAB HEM . . . C 2 2.954 7.973 29.054 1 45.7 ? CAB HEM 501 A 1 HETATM 21 C CBB HEM . . . C 2 3.277 7.06 28.128 1 45.16 ? CBB HEM 501 A 1 HETATM 22 C C1C HEM . . . C 2 7.435 7.182 29.353 1 28.71 ? C1C HEM 501 A 1 HETATM 23 C C2C HEM . . . C 2 8.268 6.74 28.25 1 31.33 ? C2C HEM 501 A 1 HETATM 24 C C3C HEM . . . C 2 9.51 6.562 28.723 1 32.09 ? C3C HEM 501 A 1 HETATM 25 C C4C HEM . . . C 2 9.473 6.851 30.131 1 31.15 ? C4C HEM 501 A 1 HETATM 26 C CMC HEM . . . C 2 7.776 6.571 26.797 1 33.22 ? CMC HEM 501 A 1 HETATM 27 C CAC HEM . . . C 2 10.804 6.082 28.027 1 38.88 ? CAC HEM 501 A 1 HETATM 28 C CBC HEM . . . C 2 10.821 5.223 27.007 1 44.15 ? CBC HEM 501 A 1 HETATM 29 C C1D HEM . . . C 2 10.561 7.258 32.256 1 31.3 ? C1D HEM 501 A 1 HETATM 30 C C2D HEM . . . C 2 11.738 7.25 33.1 1 33.4 ? C2D HEM 501 A 1 HETATM 31 C C3D HEM . . . C 2 11.29 7.936 34.387 1 29.08 ? C3D HEM 501 A 1 HETATM 32 C C4D HEM . . . C 2 9.89 8.282 34.197 1 29.15 ? C4D HEM 501 A 1 HETATM 33 C CMD HEM . . . C 2 13.146 6.684 32.774 1 36.01 ? CMD HEM 501 A 1 HETATM 34 C CAD HEM . . . C 2 12.176 8.192 35.622 1 44.22 ? CAD HEM 501 A 1 HETATM 35 C CBD HEM . . . C 2 12.285 9.716 35.744 1 60.48 ? CBD HEM 501 A 1 HETATM 36 C CGD HEM . . . C 2 13.652 10.099 36.219 1 67.52 ? CGD HEM 501 A 1 HETATM 37 O O1D HEM . . . C 2 14.348 9.198 36.76 1 71.89 ? O1D HEM 501 A 1 HETATM 38 O O2D HEM . . . C 2 14.051 11.289 36.073 1 67.53 ? O2D HEM 501 A 1 HETATM 39 N NA HEM . . . C 2 6.916 8.806 34.089 1 39.76 ? NA HEM 501 A 1 HETATM 40 N NB HEM . . . C 2 5.75 8.23 31.629 1 25.95 ? NB HEM 501 A 1 HETATM 41 N NC HEM . . . C 2 8.198 7.237 30.489 1 28.91 ? NC HEM 501 A 1 HETATM 42 N ND HEM . . . C 2 9.478 7.855 32.926 1 21.45 ? ND HEM 501 A 1 HETATM 43 FE FE HEM . . . C 2 7.547 7.8 32.399 1 39.15 ? FE HEM 501 A 1 # _model_server_stats.io_time_ms 97 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #