data_8VUG # _model_server_result.job_id tc9FhO0hzlXRZqSgmypB3A _model_server_result.datetime_utc '2024-11-15 02:52:42' _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 8vug # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 8VUG # _exptl.entry_id 8VUG _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 90 _cell.entry_id 8VUG _cell.length_a 143.805 _cell.length_b 154.925 _cell.length_c 88.32 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VUG _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 E N N ? 2 H N N ? 2 K N N ? 2 N 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 312 A HIS 328 1_555 E FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc2 B NE2 HIS 312 B HIS 328 1_555 H FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc3 C NE2 HIS 312 C HIS 328 1_555 K FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc4 D NE2 HIS 312 D HIS 328 1_555 N FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? # _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 179 n n CHA C4D HEM doub 180 n n CHA HHA HEM sing 181 n n CHB C4A HEM sing 182 n n CHB C1B HEM doub 183 n n CHB HHB HEM sing 184 n n CHC C4B HEM sing 185 n n CHC C1C HEM doub 186 n n CHC HHC HEM sing 187 n n CHD C4C HEM doub 188 n n CHD C1D HEM sing 189 n n CHD HHD HEM sing 190 n n C1A C2A HEM doub 191 n y C1A NA HEM sing 192 n y C2A C3A HEM sing 193 n y C2A CAA HEM sing 194 n n C3A C4A HEM doub 195 n y C3A CMA HEM sing 196 n n C4A NA HEM sing 197 n y CMA HMA HEM sing 198 n n CMA HMAA HEM sing 199 n n CMA HMAB HEM sing 200 n n CAA CBA HEM sing 201 n n CAA HAA HEM sing 202 n n CAA HAAA HEM sing 203 n n CBA CGA HEM sing 204 n n CBA HBA HEM sing 205 n n CBA HBAA HEM sing 206 n n CGA O1A HEM doub 207 n n CGA O2A HEM sing 208 n n C1B C2B HEM sing 209 n n C1B NB HEM sing 210 n n C2B C3B HEM doub 211 n n C2B CMB HEM sing 212 n n C3B C4B HEM sing 213 n n C3B CAB HEM sing 214 n n C4B NB HEM doub 215 n n CMB HMB HEM sing 216 n n CMB HMBA HEM sing 217 n n CMB HMBB HEM sing 218 n n CAB CBB HEM doub 219 n n CAB HAB HEM sing 220 n n CBB HBB HEM sing 221 n n CBB HBBA HEM sing 222 n n C1C C2C HEM sing 223 n y C1C NC HEM sing 224 n y C2C C3C HEM doub 225 n y C2C CMC HEM sing 226 n n C3C C4C HEM sing 227 n y C3C CAC HEM sing 228 n n C4C NC HEM sing 229 n y CMC HMC HEM sing 230 n n CMC HMCA HEM sing 231 n n CMC HMCB HEM sing 232 n n CAC CBC HEM doub 233 n n CAC HAC HEM sing 234 n n CBC HBC HEM sing 235 n n CBC HBCA HEM sing 236 n n C1D C2D HEM sing 237 n n C1D ND HEM doub 238 n n C2D C3D HEM doub 239 n n C2D CMD HEM sing 240 n n C3D C4D HEM sing 241 n n C3D CAD HEM sing 242 n n C4D ND HEM sing 243 n n CMD HMD HEM sing 244 n n CMD HMDA HEM sing 245 n n CMD HMDB HEM sing 246 n n CAD CBD HEM sing 247 n n CAD HAD HEM sing 248 n n CAD HADA HEM sing 249 n n CBD CGD HEM sing 250 n n CBD HBD HEM sing 251 n n CBD HBDA HEM sing 252 n n CGD O1D HEM doub 253 n n CGD O2D HEM sing 254 n n O2A H2A HEM sing 255 n n O2D H2D HEM sing 256 n n FE NA HEM sing 257 n n FE NB HEM sing 258 n n FE NC HEM sing 259 n n FE ND HEM sing 260 n n # _atom_sites.entry_id 8VUG _atom_sites.fract_transf_matrix[1][1] 0.006954 _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] 0.006455 _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] 0.011322 _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 1 401 401 HEM HEM . F 3 ZIQ A 1 402 402 ZIQ ZIQ . G 4 A1AD1 A 1 403 403 A1AD1 19d . H 2 HEM B 1 401 401 HEM HEM . I 3 ZIQ B 1 402 402 ZIQ ZIQ . J 4 A1AD1 B 1 403 403 A1AD1 19d . K 2 HEM C 1 401 401 HEM HEM . L 3 ZIQ C 1 402 402 ZIQ ZIQ . M 4 A1AD1 C 1 403 403 A1AD1 19d . N 2 HEM D 1 401 401 HEM HEM . O 3 ZIQ D 1 402 402 ZIQ ZIQ . P 4 A1AD1 D 1 403 403 A1AD1 19d . Q 5 HOH A 1 501 109 HOH HOH . Q 5 HOH A 2 502 87 HOH HOH . Q 5 HOH A 3 503 104 HOH HOH . Q 5 HOH A 4 504 117 HOH HOH . Q 5 HOH A 5 505 26 HOH HOH . Q 5 HOH A 6 506 68 HOH HOH . Q 5 HOH A 7 507 73 HOH HOH . Q 5 HOH A 8 508 83 HOH HOH . Q 5 HOH A 9 509 107 HOH HOH . Q 5 HOH A 10 510 45 HOH HOH . Q 5 HOH A 11 511 54 HOH HOH . Q 5 HOH A 12 512 102 HOH HOH . Q 5 HOH A 13 513 123 HOH HOH . Q 5 HOH A 14 514 112 HOH HOH . Q 5 HOH A 15 515 57 HOH HOH . Q 5 HOH A 16 516 51 HOH HOH . Q 5 HOH A 17 517 23 HOH HOH . Q 5 HOH A 18 518 32 HOH HOH . Q 5 HOH A 19 519 48 HOH HOH . Q 5 HOH A 20 520 110 HOH HOH . Q 5 HOH A 21 521 1 HOH HOH . Q 5 HOH A 22 522 120 HOH HOH . Q 5 HOH A 23 523 11 HOH HOH . Q 5 HOH A 24 524 84 HOH HOH . Q 5 HOH A 25 525 3 HOH HOH . Q 5 HOH A 26 526 94 HOH HOH . Q 5 HOH A 27 527 46 HOH HOH . Q 5 HOH A 28 528 10 HOH HOH . Q 5 HOH A 29 529 24 HOH HOH . Q 5 HOH A 30 530 19 HOH HOH . Q 5 HOH A 31 531 27 HOH HOH . Q 5 HOH A 32 532 22 HOH HOH . Q 5 HOH A 33 533 41 HOH HOH . Q 5 HOH A 34 534 49 HOH HOH . Q 5 HOH A 35 535 89 HOH HOH . Q 5 HOH A 36 536 65 HOH HOH . Q 5 HOH A 37 537 108 HOH HOH . Q 5 HOH A 38 538 74 HOH HOH . Q 5 HOH A 39 539 85 HOH HOH . Q 5 HOH A 40 540 55 HOH HOH . Q 5 HOH A 41 541 34 HOH HOH . Q 5 HOH A 42 542 90 HOH HOH . Q 5 HOH A 43 543 2 HOH HOH . Q 5 HOH A 44 544 119 HOH HOH . R 5 HOH B 1 501 18 HOH HOH . R 5 HOH B 2 502 21 HOH HOH . R 5 HOH B 3 503 75 HOH HOH . R 5 HOH B 4 504 31 HOH HOH . R 5 HOH B 5 505 114 HOH HOH . R 5 HOH B 6 506 69 HOH HOH . R 5 HOH B 7 507 8 HOH HOH . R 5 HOH B 8 508 122 HOH HOH . R 5 HOH B 9 509 9 HOH HOH . R 5 HOH B 10 510 76 HOH HOH . R 5 HOH B 11 511 96 HOH HOH . R 5 HOH B 12 512 81 HOH HOH . R 5 HOH B 13 513 82 HOH HOH . R 5 HOH B 14 514 30 HOH HOH . R 5 HOH B 15 515 64 HOH HOH . R 5 HOH B 16 516 116 HOH HOH . R 5 HOH B 17 517 86 HOH HOH . R 5 HOH B 18 518 70 HOH HOH . R 5 HOH B 19 519 100 HOH HOH . R 5 HOH B 20 520 101 HOH HOH . R 5 HOH B 21 521 56 HOH HOH . R 5 HOH B 22 522 77 HOH HOH . R 5 HOH B 23 523 93 HOH HOH . R 5 HOH B 24 524 95 HOH HOH . R 5 HOH B 25 525 52 HOH HOH . R 5 HOH B 26 526 16 HOH HOH . R 5 HOH B 27 527 13 HOH HOH . R 5 HOH B 28 528 58 HOH HOH . R 5 HOH B 29 529 50 HOH HOH . R 5 HOH B 30 530 79 HOH HOH . R 5 HOH B 31 531 15 HOH HOH . R 5 HOH B 32 532 72 HOH HOH . R 5 HOH B 33 533 91 HOH HOH . S 5 HOH C 1 501 111 HOH HOH . S 5 HOH C 2 502 7 HOH HOH . S 5 HOH C 3 503 12 HOH HOH . S 5 HOH C 4 504 25 HOH HOH . S 5 HOH C 5 505 40 HOH HOH . S 5 HOH C 6 506 17 HOH HOH . S 5 HOH C 7 507 37 HOH HOH . S 5 HOH C 8 508 103 HOH HOH . S 5 HOH C 9 509 59 HOH HOH . S 5 HOH C 10 510 80 HOH HOH . S 5 HOH C 11 511 35 HOH HOH . S 5 HOH C 12 512 78 HOH HOH . S 5 HOH C 13 513 71 HOH HOH . S 5 HOH C 14 514 99 HOH HOH . S 5 HOH C 15 515 67 HOH HOH . S 5 HOH C 16 516 42 HOH HOH . S 5 HOH C 17 517 62 HOH HOH . S 5 HOH C 18 518 66 HOH HOH . S 5 HOH C 19 519 4 HOH HOH . S 5 HOH C 20 520 125 HOH HOH . T 5 HOH D 1 501 115 HOH HOH . T 5 HOH D 2 502 118 HOH HOH . T 5 HOH D 3 503 5 HOH HOH . T 5 HOH D 4 504 43 HOH HOH . T 5 HOH D 5 505 113 HOH HOH . T 5 HOH D 6 506 106 HOH HOH . T 5 HOH D 7 507 14 HOH HOH . T 5 HOH D 8 508 33 HOH HOH . T 5 HOH D 9 509 28 HOH HOH . T 5 HOH D 10 510 47 HOH HOH . T 5 HOH D 11 511 105 HOH HOH . T 5 HOH D 12 512 20 HOH HOH . T 5 HOH D 13 513 36 HOH HOH . T 5 HOH D 14 514 97 HOH HOH . T 5 HOH D 15 515 98 HOH HOH . T 5 HOH D 16 516 60 HOH HOH . T 5 HOH D 17 517 44 HOH HOH . T 5 HOH D 18 518 121 HOH HOH . T 5 HOH D 19 519 63 HOH HOH . T 5 HOH D 20 520 53 HOH HOH . T 5 HOH D 21 521 61 HOH HOH . T 5 HOH D 22 522 29 HOH HOH . T 5 HOH D 23 523 39 HOH HOH . T 5 HOH D 24 524 38 HOH HOH . T 5 HOH D 25 525 6 HOH HOH . T 5 HOH D 26 526 88 HOH HOH . T 5 HOH D 27 527 92 HOH HOH . T 5 HOH D 28 528 124 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 . . . N 2 2.717 39.957 -11.364 1 60.22 ? CHA HEM 401 D 1 HETATM 2 C CHB HEM . . . N 2 2.454 37.042 -15.178 1 61.44 ? CHB HEM 401 D 1 HETATM 3 C CHC HEM . . . N 2 -2.239 38.137 -15.624 1 55.63 ? CHC HEM 401 D 1 HETATM 4 C CHD HEM . . . N 2 -1.725 41.635 -12.324 1 54.74 ? CHD HEM 401 D 1 HETATM 5 C C1A HEM . . . N 2 3.022 39.064 -12.363 1 55.69 ? C1A HEM 401 D 1 HETATM 6 C C2A HEM . . . N 2 4.264 38.416 -12.492 1 63.52 ? C2A HEM 401 D 1 HETATM 7 C C3A HEM . . . N 2 4.193 37.601 -13.548 1 64.12 ? C3A HEM 401 D 1 HETATM 8 C C4A HEM . . . N 2 2.897 37.723 -14.088 1 60.18 ? C4A HEM 401 D 1 HETATM 9 C CMA HEM . . . N 2 5.289 36.708 -14.04 1 66.81 ? CMA HEM 401 D 1 HETATM 10 C CAA HEM . . . N 2 5.469 38.556 -11.607 1 66.88 ? CAA HEM 401 D 1 HETATM 11 C CBA HEM . . . N 2 6.184 39.845 -11.974 1 72.59 ? CBA HEM 401 D 1 HETATM 12 C CGA HEM . . . N 2 6.999 39.62 -13.219 1 76.1 ? CGA HEM 401 D 1 HETATM 13 O O1A HEM . . . N 2 6.771 40.28 -14.246 1 76.01 ? O1A HEM 401 D 1 HETATM 14 O O2A HEM . . . N 2 7.894 38.748 -13.226 1 86.25 ? O2A HEM 401 D 1 HETATM 15 C C1B HEM . . . N 2 1.109 37.098 -15.595 1 63.5 ? C1B HEM 401 D 1 HETATM 16 C C2B HEM . . . N 2 0.643 36.297 -16.658 1 56.57 ? C2B HEM 401 D 1 HETATM 17 C C3B HEM . . . N 2 -0.681 36.552 -16.786 1 58.67 ? C3B HEM 401 D 1 HETATM 18 C C4B HEM . . . N 2 -0.995 37.571 -15.776 1 55.55 ? C4B HEM 401 D 1 HETATM 19 C CMB HEM . . . N 2 1.485 35.341 -17.44 1 61.49 ? CMB HEM 401 D 1 HETATM 20 C CAB HEM . . . N 2 -1.649 36.06 -17.783 1 59.36 ? CAB HEM 401 D 1 HETATM 21 C CBB HEM . . . N 2 -1.254 35.579 -18.966 1 56.83 ? CBB HEM 401 D 1 HETATM 22 C C1C HEM . . . N 2 -2.524 39.211 -14.799 1 58.12 ? C1C HEM 401 D 1 HETATM 23 C C2C HEM . . . N 2 -3.742 39.906 -14.73 1 56.87 ? C2C HEM 401 D 1 HETATM 24 C C3C HEM . . . N 2 -3.598 40.916 -13.797 1 55.43 ? C3C HEM 401 D 1 HETATM 25 C C4C HEM . . . N 2 -2.259 40.833 -13.298 1 58.81 ? C4C HEM 401 D 1 HETATM 26 C CMC HEM . . . N 2 -4.971 39.604 -15.548 1 55.62 ? CMC HEM 401 D 1 HETATM 27 C CAC HEM . . . N 2 -4.622 41.904 -13.509 1 54.54 ? CAC HEM 401 D 1 HETATM 28 C CBC HEM . . . N 2 -4.325 43.163 -13.174 1 52.91 ? CBC HEM 401 D 1 HETATM 29 C C1D HEM . . . N 2 -0.461 41.405 -11.811 1 61.76 ? C1D HEM 401 D 1 HETATM 30 C C2D HEM . . . N 2 0.033 42.171 -10.688 1 59.18 ? C2D HEM 401 D 1 HETATM 31 C C3D HEM . . . N 2 1.263 41.712 -10.425 1 58.24 ? C3D HEM 401 D 1 HETATM 32 C C4D HEM . . . N 2 1.511 40.648 -11.358 1 57.12 ? C4D HEM 401 D 1 HETATM 33 C CMD HEM . . . N 2 -0.633 43.299 -9.954 1 59.73 ? CMD HEM 401 D 1 HETATM 34 C CAD HEM . . . N 2 2.154 42.186 -9.308 1 58.52 ? CAD HEM 401 D 1 HETATM 35 C CBD HEM . . . N 2 1.758 41.277 -8.111 1 54.61 ? CBD HEM 401 D 1 HETATM 36 C CGD HEM . . . N 2 2.583 41.461 -6.857 1 58.46 ? CGD HEM 401 D 1 HETATM 37 O O1D HEM . . . N 2 3.738 42.036 -6.87 1 55.69 ? O1D HEM 401 D 1 HETATM 38 O O2D HEM . . . N 2 2.13 40.981 -5.776 1 54.64 ? O2D HEM 401 D 1 HETATM 39 N NA HEM . . . N 2 2.193 38.611 -13.352 1 56.12 ? NA HEM 401 D 1 HETATM 40 N NB HEM . . . N 2 0.106 37.815 -15.097 1 59.09 ? NB HEM 401 D 1 HETATM 41 N NC HEM . . . N 2 -1.649 39.782 -13.925 1 55.75 ? NC HEM 401 D 1 HETATM 42 N ND HEM . . . N 2 0.455 40.488 -12.17 1 61.44 ? ND HEM 401 D 1 HETATM 43 FE FE HEM . . . N 2 0.256 39.117 -13.476 1 56.12 ? FE HEM 401 D 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 432 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #