data_4KMM # _model_server_result.job_id kVYQ05diP62HAqv4tgIOCA _model_server_result.datetime_utc '2024-11-20 04:32:46' _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 4kmm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 4KMM # _exptl.entry_id 4KMM _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 4KMM _cell.length_a 88.138 _cell.length_b 93.418 _cell.length_c 110.219 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KMM _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 _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 H 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 SG CYS 143 A CYS 196 1_555 D FE2 FES . A FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc2 A SG CYS 350 A CYS 403 1_555 D FE2 FES . A FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc3 A SG CYS 353 A CYS 406 1_555 D FE1 FES . A FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc4 A SG CYS 358 A CYS 411 1_555 D FE1 FES . A FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc5 B SG CYS 143 B CYS 196 1_555 I FE2 FES . B FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc6 B SG CYS 350 B CYS 403 1_555 I FE2 FES . B FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc7 B SG CYS 353 B CYS 406 1_555 I FE1 FES . B FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc8 B SG CYS 358 B CYS 411 1_555 I FE1 FES . B FES 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? # _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 205 n n CHA C4D HEM doub 206 n n CHA HHA HEM sing 207 n n CHB C4A HEM sing 208 n n CHB C1B HEM doub 209 n n CHB HHB HEM sing 210 n n CHC C4B HEM sing 211 n n CHC C1C HEM doub 212 n n CHC HHC HEM sing 213 n n CHD C4C HEM doub 214 n n CHD C1D HEM sing 215 n n CHD HHD HEM sing 216 n n C1A C2A HEM doub 217 n y C1A NA HEM sing 218 n y C2A C3A HEM sing 219 n y C2A CAA HEM sing 220 n n C3A C4A HEM doub 221 n y C3A CMA HEM sing 222 n n C4A NA HEM sing 223 n y CMA HMA HEM sing 224 n n CMA HMAA HEM sing 225 n n CMA HMAB HEM sing 226 n n CAA CBA HEM sing 227 n n CAA HAA HEM sing 228 n n CAA HAAA HEM sing 229 n n CBA CGA HEM sing 230 n n CBA HBA HEM sing 231 n n CBA HBAA HEM sing 232 n n CGA O1A HEM doub 233 n n CGA O2A HEM sing 234 n n C1B C2B HEM sing 235 n n C1B NB HEM sing 236 n n C2B C3B HEM doub 237 n n C2B CMB HEM sing 238 n n C3B C4B HEM sing 239 n n C3B CAB HEM sing 240 n n C4B NB HEM doub 241 n n CMB HMB HEM sing 242 n n CMB HMBA HEM sing 243 n n CMB HMBB HEM sing 244 n n CAB CBB HEM doub 245 n n CAB HAB HEM sing 246 n n CBB HBB HEM sing 247 n n CBB HBBA HEM sing 248 n n C1C C2C HEM sing 249 n y C1C NC HEM sing 250 n y C2C C3C HEM doub 251 n y C2C CMC HEM sing 252 n n C3C C4C HEM sing 253 n y C3C CAC HEM sing 254 n n C4C NC HEM sing 255 n y CMC HMC HEM sing 256 n n CMC HMCA HEM sing 257 n n CMC HMCB HEM sing 258 n n CAC CBC HEM doub 259 n n CAC HAC HEM sing 260 n n CBC HBC HEM sing 261 n n CBC HBCA HEM sing 262 n n C1D C2D HEM sing 263 n n C1D ND HEM doub 264 n n C2D C3D HEM doub 265 n n C2D CMD HEM sing 266 n n C3D C4D HEM sing 267 n n C3D CAD HEM sing 268 n n C4D ND HEM sing 269 n n CMD HMD HEM sing 270 n n CMD HMDA HEM sing 271 n n CMD HMDB HEM sing 272 n n CAD CBD HEM sing 273 n n CAD HAD HEM sing 274 n n CAD HADA HEM sing 275 n n CBD CGD HEM sing 276 n n CBD HBD HEM sing 277 n n CBD HBDA HEM sing 278 n n CGD O1D HEM doub 279 n n CGD O2D HEM sing 280 n n O2A H2A HEM sing 281 n n O2D H2D HEM sing 282 n n FE NA HEM sing 283 n n FE NB HEM sing 284 n n FE NC HEM sing 285 n n FE ND HEM sing 286 n n # _atom_sites.entry_id 4KMM _atom_sites.fract_transf_matrix[1][1] 0.011346 _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] 0.010705 _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] 0.009073 _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 1 HEM HEM . D 3 FES A 1 502 1 FES FES . E 4 CHD A 1 503 1 CHD CHD . F 4 CHD A 1 504 2 CHD CHD . G 5 CL A 1 505 1 CL CL . H 2 HEM B 1 501 2 HEM HEM . I 3 FES B 1 502 2 FES FES . J 4 CHD B 1 503 3 CHD CHD . K 4 CHD B 1 504 4 CHD CHD . L 5 CL B 1 505 2 CL CL . M 6 HOH A 1 601 1 HOH HOH . M 6 HOH A 2 602 2 HOH HOH . M 6 HOH A 3 603 3 HOH HOH . M 6 HOH A 4 604 4 HOH HOH . M 6 HOH A 5 605 5 HOH HOH . M 6 HOH A 6 606 6 HOH HOH . M 6 HOH A 7 607 7 HOH HOH . M 6 HOH A 8 608 8 HOH HOH . M 6 HOH A 9 609 9 HOH HOH . M 6 HOH A 10 610 10 HOH HOH . M 6 HOH A 11 611 11 HOH HOH . M 6 HOH A 12 612 13 HOH HOH . M 6 HOH A 13 613 15 HOH HOH . M 6 HOH A 14 614 16 HOH HOH . M 6 HOH A 15 615 17 HOH HOH . M 6 HOH A 16 616 18 HOH HOH . M 6 HOH A 17 617 19 HOH HOH . M 6 HOH A 18 618 30 HOH HOH . M 6 HOH A 19 619 31 HOH HOH . M 6 HOH A 20 620 32 HOH HOH . M 6 HOH A 21 621 33 HOH HOH . M 6 HOH A 22 622 34 HOH HOH . M 6 HOH A 23 623 35 HOH HOH . M 6 HOH A 24 624 36 HOH HOH . M 6 HOH A 25 625 37 HOH HOH . M 6 HOH A 26 626 38 HOH HOH . M 6 HOH A 27 627 39 HOH HOH . M 6 HOH A 28 628 40 HOH HOH . M 6 HOH A 29 629 41 HOH HOH . M 6 HOH A 30 630 42 HOH HOH . M 6 HOH A 31 631 43 HOH HOH . M 6 HOH A 32 632 44 HOH HOH . M 6 HOH A 33 633 45 HOH HOH . M 6 HOH A 34 634 46 HOH HOH . M 6 HOH A 35 635 57 HOH HOH . M 6 HOH A 36 636 60 HOH HOH . M 6 HOH A 37 637 65 HOH HOH . M 6 HOH A 38 638 66 HOH HOH . M 6 HOH A 39 639 67 HOH HOH . M 6 HOH A 40 640 68 HOH HOH . M 6 HOH A 41 641 69 HOH HOH . M 6 HOH A 42 642 70 HOH HOH . M 6 HOH A 43 643 71 HOH HOH . M 6 HOH A 44 644 72 HOH HOH . M 6 HOH A 45 645 77 HOH HOH . M 6 HOH A 46 646 79 HOH HOH . M 6 HOH A 47 647 81 HOH HOH . M 6 HOH A 48 648 84 HOH HOH . M 6 HOH A 49 649 85 HOH HOH . M 6 HOH A 50 650 89 HOH HOH . M 6 HOH A 51 651 94 HOH HOH . M 6 HOH A 52 652 95 HOH HOH . M 6 HOH A 53 653 97 HOH HOH . M 6 HOH A 54 654 99 HOH HOH . M 6 HOH A 55 655 102 HOH HOH . M 6 HOH A 56 656 103 HOH HOH . M 6 HOH A 57 657 107 HOH HOH . M 6 HOH A 58 658 108 HOH HOH . M 6 HOH A 59 659 109 HOH HOH . N 6 HOH B 1 601 12 HOH HOH . N 6 HOH B 2 602 14 HOH HOH . N 6 HOH B 3 603 20 HOH HOH . N 6 HOH B 4 604 21 HOH HOH . N 6 HOH B 5 605 22 HOH HOH . N 6 HOH B 6 606 23 HOH HOH . N 6 HOH B 7 607 24 HOH HOH . N 6 HOH B 8 608 25 HOH HOH . N 6 HOH B 9 609 26 HOH HOH . N 6 HOH B 10 610 27 HOH HOH . N 6 HOH B 11 611 28 HOH HOH . N 6 HOH B 12 612 29 HOH HOH . N 6 HOH B 13 613 47 HOH HOH . N 6 HOH B 14 614 48 HOH HOH . N 6 HOH B 15 615 49 HOH HOH . N 6 HOH B 16 616 50 HOH HOH . N 6 HOH B 17 617 51 HOH HOH . N 6 HOH B 18 618 52 HOH HOH . N 6 HOH B 19 619 53 HOH HOH . N 6 HOH B 20 620 54 HOH HOH . N 6 HOH B 21 621 55 HOH HOH . N 6 HOH B 22 622 56 HOH HOH . N 6 HOH B 23 623 58 HOH HOH . N 6 HOH B 24 624 59 HOH HOH . N 6 HOH B 25 625 61 HOH HOH . N 6 HOH B 26 626 62 HOH HOH . N 6 HOH B 27 627 63 HOH HOH . N 6 HOH B 28 628 64 HOH HOH . N 6 HOH B 29 629 73 HOH HOH . N 6 HOH B 30 630 74 HOH HOH . N 6 HOH B 31 631 75 HOH HOH . N 6 HOH B 32 632 76 HOH HOH . N 6 HOH B 33 633 78 HOH HOH . N 6 HOH B 34 634 80 HOH HOH . N 6 HOH B 35 635 82 HOH HOH . N 6 HOH B 36 636 83 HOH HOH . N 6 HOH B 37 637 86 HOH HOH . N 6 HOH B 38 638 87 HOH HOH . N 6 HOH B 39 639 88 HOH HOH . N 6 HOH B 40 640 90 HOH HOH . N 6 HOH B 41 641 91 HOH HOH . N 6 HOH B 42 642 92 HOH HOH . N 6 HOH B 43 643 93 HOH HOH . N 6 HOH B 44 644 96 HOH HOH . N 6 HOH B 45 645 98 HOH HOH . N 6 HOH B 46 646 100 HOH HOH . N 6 HOH B 47 647 101 HOH HOH . N 6 HOH B 48 648 104 HOH HOH . N 6 HOH B 49 649 105 HOH HOH . N 6 HOH B 50 650 106 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 . . . H 2 4.504 12.831 18.425 0.5 54.33 ? CHA HEM 501 B 1 HETATM 2 C CHB HEM . . . H 2 6.783 16.569 16.313 0.5 53.94 ? CHB HEM 501 B 1 HETATM 3 C CHC HEM . . . H 2 8.298 18.073 20.733 0.5 53.49 ? CHC HEM 501 B 1 HETATM 4 C CHD HEM . . . H 2 6.095 14.282 22.855 0.5 54.09 ? CHD HEM 501 B 1 HETATM 5 C C1A HEM . . . H 2 5.064 13.651 17.46 0.5 54.5 ? C1A HEM 501 B 1 HETATM 6 C C2A HEM . . . H 2 5.101 13.435 16.025 0.5 53.25 ? C2A HEM 501 B 1 HETATM 7 C C3A HEM . . . H 2 5.727 14.457 15.45 0.5 53.48 ? C3A HEM 501 B 1 HETATM 8 C C4A HEM . . . H 2 6.113 15.383 16.484 0.5 54.38 ? C4A HEM 501 B 1 HETATM 9 C CMA HEM . . . H 2 5.989 14.628 13.947 0.5 53.44 ? CMA HEM 501 B 1 HETATM 10 C CAA HEM . . . H 2 4.533 12.218 15.288 0.5 51.83 ? CAA HEM 501 B 1 HETATM 11 C CBA HEM . . . H 2 5.495 11.082 15.58 0.5 50.09 ? CBA HEM 501 B 1 HETATM 12 C CGA HEM . . . H 2 5.666 10.344 14.296 0.5 48.6 ? CGA HEM 501 B 1 HETATM 13 O O1A HEM . . . H 2 4.732 10.436 13.468 0.5 47.29 ? O1A HEM 501 B 1 HETATM 14 O O2A HEM . . . H 2 6.715 9.68 14.113 0.5 48.7 ? O2A HEM 501 B 1 HETATM 15 C C1B HEM . . . H 2 7.308 17.326 17.335 0.5 54.81 ? C1B HEM 501 B 1 HETATM 16 C C2B HEM . . . H 2 7.837 18.653 17.198 0.5 54.41 ? C2B HEM 501 B 1 HETATM 17 C C3B HEM . . . H 2 8.252 19.076 18.384 0.5 54.69 ? C3B HEM 501 B 1 HETATM 18 C C4B HEM . . . H 2 8.007 18.033 19.371 0.5 54.69 ? C4B HEM 501 B 1 HETATM 19 C CMB HEM . . . H 2 7.919 19.464 15.898 0.5 53.89 ? CMB HEM 501 B 1 HETATM 20 C CAB HEM . . . H 2 8.869 20.475 18.588 0.5 55.19 ? CAB HEM 501 B 1 HETATM 21 C CBB HEM . . . H 2 8.452 21.483 17.807 0.5 54.94 ? CBB HEM 501 B 1 HETATM 22 C C1C HEM . . . H 2 8.008 17.104 21.679 0.5 53.4 ? C1C HEM 501 B 1 HETATM 23 C C2C HEM . . . H 2 8.66 16.847 22.958 0.5 52.41 ? C2C HEM 501 B 1 HETATM 24 C C3C HEM . . . H 2 8.044 15.8 23.541 0.5 52.83 ? C3C HEM 501 B 1 HETATM 25 C C4C HEM . . . H 2 6.98 15.338 22.657 0.5 53.93 ? C4C HEM 501 B 1 HETATM 26 C CMC HEM . . . H 2 9.851 17.622 23.57 0.5 50.73 ? CMC HEM 501 B 1 HETATM 27 C CAC HEM . . . H 2 8.413 15.191 24.917 0.5 51.61 ? CAC HEM 501 B 1 HETATM 28 C CBC HEM . . . H 2 7.78 14.107 25.376 0.5 49.88 ? CBC HEM 501 B 1 HETATM 29 C C1D HEM . . . H 2 5.561 13.46 21.864 0.5 55.01 ? C1D HEM 501 B 1 HETATM 30 C C2D HEM . . . H 2 5.119 12.082 22.026 0.5 54.9 ? C2D HEM 501 B 1 HETATM 31 C C3D HEM . . . H 2 4.626 11.667 20.64 0.5 54.42 ? C3D HEM 501 B 1 HETATM 32 C C4D HEM . . . H 2 4.815 12.796 19.771 0.5 54.36 ? C4D HEM 501 B 1 HETATM 33 C CMD HEM . . . H 2 5.117 11.2 23.294 0.5 54.63 ? CMD HEM 501 B 1 HETATM 34 C CAD HEM . . . H 2 4.047 10.325 20.19 0.5 54.47 ? CAD HEM 501 B 1 HETATM 35 C CBD HEM . . . H 2 4.267 10.324 18.684 0.5 54.97 ? CBD HEM 501 B 1 HETATM 36 C CGD HEM . . . H 2 4.115 8.914 18.208 0.5 55.09 ? CGD HEM 501 B 1 HETATM 37 O O1D HEM . . . H 2 4.528 8.612 17.054 0.5 55.94 ? O1D HEM 501 B 1 HETATM 38 O O2D HEM . . . H 2 3.57 8.108 19.003 0.5 54.19 ? O2D HEM 501 B 1 HETATM 39 N NA HEM . . . H 2 5.687 14.86 17.693 1 55.57 ? NA HEM 501 B 1 HETATM 40 N NB HEM . . . H 2 7.423 16.981 18.674 1 55.72 ? NB HEM 501 B 1 HETATM 41 N NC HEM . . . H 2 6.996 16.168 21.547 1 55.14 ? NC HEM 501 B 1 HETATM 42 N ND HEM . . . H 2 5.351 13.821 20.526 1 54.62 ? ND HEM 501 B 1 HETATM 43 FE FE HEM . . . H 2 6.263 15.469 19.633 0.5 57.16 ? FE HEM 501 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #