data_3L70 # _model_server_result.job_id 39TiBDdLGUcLq-S0PSB1RA _model_server_result.datetime_utc '2024-11-27 17:31:30' _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 3l70 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"KA","auth_seq_id":502}' # _entry.id 3L70 # _exptl.entry_id 3L70 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 12 _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 3L70 _cell.length_a 169.614 _cell.length_b 181.993 _cell.length_c 240.54 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L70 _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 eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB _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 ? 12 V N N ? 12 W N N ? 12 JA N N ? 12 KA 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 E SG CYS 144 E CYS 144 1_555 E SG CYS 160 E CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 H SG CYS 23 H CYS 24 1_555 H SG CYS 67 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 H SG CYS 39 H CYS 40 1_555 H SG CYS 53 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf4 O SG CYS 144 R CYS 144 1_555 O SG CYS 160 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 R SG CYS 23 U CYS 24 1_555 R SG CYS 67 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf6 R SG CYS 39 U CYS 40 1_555 R SG CYS 53 U CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc1 C NE2 HIS 84 C HIS 84 1_555 V FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc2 C NE2 HIS 98 C HIS 98 1_555 W FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 V FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 W FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc5 D NE2 HIS 41 D HIS 41 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc6 D SD MET 160 D MET 160 1_555 CA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc7 E SG CYS 139 E CYS 139 1_555 GA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc8 E ND1 HIS 141 E HIS 141 1_555 GA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc9 E SG CYS 158 E CYS 158 1_555 GA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc10 E ND1 HIS 161 E HIS 161 1_555 GA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc11 M NE2 HIS 84 P HIS 84 1_555 JA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc12 M NE2 HIS 98 P HIS 98 1_555 KA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc13 M NE2 HIS 183 P HIS 183 1_555 JA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc14 M NE2 HIS 197 P HIS 197 1_555 KA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc15 N NE2 HIS 41 Q HIS 41 1_555 RA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc16 N SD MET 160 Q MET 160 1_555 RA FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc17 O SG CYS 139 R CYS 139 1_555 VA FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc18 O ND1 HIS 141 R HIS 141 1_555 VA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc19 O SG CYS 158 R CYS 158 1_555 VA FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc20 O ND1 HIS 161 R HIS 161 1_555 VA FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _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 533 n n CHA C4D HEM doub 534 n n CHA HHA HEM sing 535 n n CHB C4A HEM sing 536 n n CHB C1B HEM doub 537 n n CHB HHB HEM sing 538 n n CHC C4B HEM sing 539 n n CHC C1C HEM doub 540 n n CHC HHC HEM sing 541 n n CHD C4C HEM doub 542 n n CHD C1D HEM sing 543 n n CHD HHD HEM sing 544 n n C1A C2A HEM doub 545 n y C1A NA HEM sing 546 n y C2A C3A HEM sing 547 n y C2A CAA HEM sing 548 n n C3A C4A HEM doub 549 n y C3A CMA HEM sing 550 n n C4A NA HEM sing 551 n y CMA HMA HEM sing 552 n n CMA HMAA HEM sing 553 n n CMA HMAB HEM sing 554 n n CAA CBA HEM sing 555 n n CAA HAA HEM sing 556 n n CAA HAAA HEM sing 557 n n CBA CGA HEM sing 558 n n CBA HBA HEM sing 559 n n CBA HBAA HEM sing 560 n n CGA O1A HEM doub 561 n n CGA O2A HEM sing 562 n n C1B C2B HEM sing 563 n n C1B NB HEM sing 564 n n C2B C3B HEM doub 565 n n C2B CMB HEM sing 566 n n C3B C4B HEM sing 567 n n C3B CAB HEM sing 568 n n C4B NB HEM doub 569 n n CMB HMB HEM sing 570 n n CMB HMBA HEM sing 571 n n CMB HMBB HEM sing 572 n n CAB CBB HEM doub 573 n n CAB HAB HEM sing 574 n n CBB HBB HEM sing 575 n n CBB HBBA HEM sing 576 n n C1C C2C HEM sing 577 n y C1C NC HEM sing 578 n y C2C C3C HEM doub 579 n y C2C CMC HEM sing 580 n n C3C C4C HEM sing 581 n y C3C CAC HEM sing 582 n n C4C NC HEM sing 583 n y CMC HMC HEM sing 584 n n CMC HMCA HEM sing 585 n n CMC HMCB HEM sing 586 n n CAC CBC HEM doub 587 n n CAC HAC HEM sing 588 n n CBC HBC HEM sing 589 n n CBC HBCA HEM sing 590 n n C1D C2D HEM sing 591 n n C1D ND HEM doub 592 n n C2D C3D HEM doub 593 n n C2D CMD HEM sing 594 n n C3D C4D HEM sing 595 n n C3D CAD HEM sing 596 n n C4D ND HEM sing 597 n n CMD HMD HEM sing 598 n n CMD HMDA HEM sing 599 n n CMD HMDB HEM sing 600 n n CAD CBD HEM sing 601 n n CAD HAD HEM sing 602 n n CAD HADA HEM sing 603 n n CBD CGD HEM sing 604 n n CBD HBD HEM sing 605 n n CBD HBDA HEM sing 606 n n CGD O1D HEM doub 607 n n CGD O2D HEM sing 608 n n O2A H2A HEM sing 609 n n O2D H2D HEM sing 610 n n FE NA HEM sing 611 n n FE NB HEM sing 612 n n FE NC HEM sing 613 n n FE ND HEM sing 614 n n # _atom_sites.entry_id 3L70 _atom_sites.fract_transf_matrix[1][1] 0.005896 _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] 0.005495 _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] 0.004157 _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 U 11 PEE A 1 2008 2008 PEE PEE . V 12 HEM C 1 501 501 HEM HEM . W 12 HEM C 1 502 502 HEM HEM . X 13 JZV C 1 2001 2001 JZV JZV . Y 14 UQ C 1 2002 2002 UQ UQ . Z 15 CDL C 1 2004 2004 CDL CDL . AA 11 PEE C 1 2007 2007 PEE PEE . BA 16 GOL C 1 2011 2011 GOL GOL . CA 17 HEC D 1 501 501 HEC HEC . DA 15 CDL D 1 2003 2003 CDL CDL . EA 18 BOG D 1 2009 2009 BOG BOG . FA 18 BOG D 1 2091 2091 BOG BOG . GA 19 FES E 1 501 501 FES FES . HA 11 PEE E 1 2005 2005 PEE PEE . IA 11 PEE N 1 3008 3008 PEE PEE . JA 12 HEM P 1 501 501 HEM HEM . KA 12 HEM P 1 502 502 HEM HEM . LA 18 BOG P 1 2010 2010 BOG BOG . MA 13 JZV P 1 3001 3001 JZV JZV . NA 14 UQ P 1 3002 3002 UQ UQ . OA 15 CDL P 1 3004 3004 CDL CDL . PA 11 PEE P 1 3007 3007 PEE PEE . QA 16 GOL P 1 3011 3011 GOL GOL . RA 17 HEC Q 1 501 501 HEC HEC . SA 15 CDL Q 1 3003 3003 CDL CDL . TA 18 BOG Q 1 3009 3009 BOG BOG . UA 18 BOG Q 1 3091 3091 BOG BOG . VA 19 FES R 1 501 501 FES FES . WA 11 PEE R 1 3005 3005 PEE PEE . XA 20 HOH C 1 381 2 HOH HOH . XA 20 HOH C 2 382 4 HOH HOH . XA 20 HOH C 3 383 108 HOH HOH . XA 20 HOH C 4 384 119 HOH HOH . XA 20 HOH C 5 385 168 HOH HOH . XA 20 HOH C 6 386 222 HOH HOH . XA 20 HOH C 7 1008 1008 HOH HOH . XA 20 HOH C 8 1238 1238 HOH HOH . YA 20 HOH E 1 1289 1289 HOH HOH . ZA 20 HOH P 1 381 1 HOH HOH . ZA 20 HOH P 2 382 5 HOH HOH . ZA 20 HOH P 3 383 6 HOH HOH . ZA 20 HOH P 4 384 28 HOH HOH . ZA 20 HOH P 5 385 35 HOH HOH . ZA 20 HOH P 6 386 109 HOH HOH . ZA 20 HOH P 7 387 214 HOH HOH . ZA 20 HOH P 8 959 959 HOH HOH . ZA 20 HOH P 9 1239 1239 HOH HOH . AB 20 HOH R 1 1230 1230 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 . . . KA 12 48.631 118.742 96.771 1 42.4 ? CHA HEM 502 P 1 HETATM 2 C CHB HEM . . . KA 12 44.852 121.641 96.349 1 41.69 ? CHB HEM 502 P 1 HETATM 3 C CHC HEM . . . KA 12 47.738 124.984 94.511 1 40.59 ? CHC HEM 502 P 1 HETATM 4 C CHD HEM . . . KA 12 51.296 121.852 94.4 1 38.77 ? CHD HEM 502 P 1 HETATM 5 C C1A HEM . . . KA 12 47.396 119.287 96.925 1 40.82 ? C1A HEM 502 P 1 HETATM 6 C C2A HEM . . . KA 12 46.309 118.69 97.719 1 41.04 ? C2A HEM 502 P 1 HETATM 7 C C3A HEM . . . KA 12 45.238 119.512 97.551 1 41.61 ? C3A HEM 502 P 1 HETATM 8 C C4A HEM . . . KA 12 45.684 120.611 96.729 1 41.37 ? C4A HEM 502 P 1 HETATM 9 C CMA HEM . . . KA 12 43.838 119.313 98.117 1 40.55 ? CMA HEM 502 P 1 HETATM 10 C CAA HEM . . . KA 12 46.343 117.496 98.676 1 41.65 ? CAA HEM 502 P 1 HETATM 11 C CBA HEM . . . KA 12 46.677 117.82 100.151 1 43.25 ? CBA HEM 502 P 1 HETATM 12 C CGA HEM . . . KA 12 48.027 118.549 100.317 1 45.7 ? CGA HEM 502 P 1 HETATM 13 O O1A HEM . . . KA 12 48.02 119.766 100.625 1 44.47 ? O1A HEM 502 P 1 HETATM 14 O O2A HEM . . . KA 12 49.094 117.912 100.124 1 45.46 ? O2A HEM 502 P 1 HETATM 15 C C1B HEM . . . KA 12 45.266 122.808 95.703 1 41.57 ? C1B HEM 502 P 1 HETATM 16 C C2B HEM . . . KA 12 44.389 123.961 95.431 1 39.58 ? C2B HEM 502 P 1 HETATM 17 C C3B HEM . . . KA 12 45.237 124.909 95.007 1 40.58 ? C3B HEM 502 P 1 HETATM 18 C C4B HEM . . . KA 12 46.607 124.339 95.004 1 40.96 ? C4B HEM 502 P 1 HETATM 19 C CMB HEM . . . KA 12 42.903 124.085 95.743 1 38.3 ? CMB HEM 502 P 1 HETATM 20 C CAB HEM . . . KA 12 44.993 126.212 94.603 1 40.76 ? CAB HEM 502 P 1 HETATM 21 C CBB HEM . . . KA 12 43.681 126.858 94.358 1 41.73 ? CBB HEM 502 P 1 HETATM 22 C C1C HEM . . . KA 12 48.943 124.406 94.256 1 38.43 ? C1C HEM 502 P 1 HETATM 23 C C2C HEM . . . KA 12 50.131 125.153 93.911 1 37.47 ? C2C HEM 502 P 1 HETATM 24 C C3C HEM . . . KA 12 51.183 124.241 93.877 1 36.23 ? C3C HEM 502 P 1 HETATM 25 C C4C HEM . . . KA 12 50.573 123 94.257 1 38.12 ? C4C HEM 502 P 1 HETATM 26 C CMC HEM . . . KA 12 50.15 126.662 93.641 1 35.5 ? CMC HEM 502 P 1 HETATM 27 C CAC HEM . . . KA 12 52.508 124.359 93.473 1 30.74 ? CAC HEM 502 P 1 HETATM 28 C CBC HEM . . . KA 12 53.029 125.516 92.688 1 29.04 ? CBC HEM 502 P 1 HETATM 29 C C1D HEM . . . KA 12 50.829 120.686 94.89 1 40.73 ? C1D HEM 502 P 1 HETATM 30 C C2D HEM . . . KA 12 51.624 119.526 94.973 1 43.32 ? C2D HEM 502 P 1 HETATM 31 C C3D HEM . . . KA 12 50.987 118.666 95.798 1 44.73 ? C3D HEM 502 P 1 HETATM 32 C C4D HEM . . . KA 12 49.66 119.287 96.031 1 43.21 ? C4D HEM 502 P 1 HETATM 33 C CMD HEM . . . KA 12 52.98 119.325 94.265 1 45.62 ? CMD HEM 502 P 1 HETATM 34 C CAD HEM . . . KA 12 51.636 117.385 96.343 1 47.92 ? CAD HEM 502 P 1 HETATM 35 C CBD HEM . . . KA 12 51.615 117.281 97.868 1 54.17 ? CBD HEM 502 P 1 HETATM 36 C CGD HEM . . . KA 12 52.548 116.197 98.404 1 57.21 ? CGD HEM 502 P 1 HETATM 37 O O1D HEM . . . KA 12 53.79 116.383 98.363 1 59.29 ? O1D HEM 502 P 1 HETATM 38 O O2D HEM . . . KA 12 52.034 115.154 98.862 1 57.66 ? O2D HEM 502 P 1 HETATM 39 N NA HEM . . . KA 12 47.036 120.505 96.391 1 40.33 ? NA HEM 502 P 1 HETATM 40 N NB HEM . . . KA 12 46.604 123.045 95.366 1 40.71 ? NB HEM 502 P 1 HETATM 41 N NC HEM . . . KA 12 49.221 123.115 94.528 1 38.22 ? NC HEM 502 P 1 HETATM 42 N ND HEM . . . KA 12 49.574 120.509 95.405 1 41.39 ? ND HEM 502 P 1 HETATM 43 FE FE HEM . . . KA 12 48.119 121.817 95.396 1 41.57 ? FE HEM 502 P 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #