data_3H1L # _model_server_result.job_id cNLULOQoqVTpS747KuTngw _model_server_result.datetime_utc '2024-11-05 06:52:36' _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 3h1l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":502}' # _entry.id 3H1L # _exptl.entry_id 3H1L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 13 _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 3H1L _cell.length_a 174.139 _cell.length_b 182.364 _cell.length_c 241.626 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H1L _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,BB,CB,DB,EB,FB,GB,HB,IB,JB _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 ? 13 W N N ? 13 X N N ? 13 NA N N ? 13 OA 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 H SG CYS 23 H CYS 24 1_555 H SG CYS 67 H CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 H SG CYS 39 H CYS 40 1_555 H SG CYS 53 H CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf4 O SG CYS 144 R CYS 144 1_555 O SG CYS 160 R CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 R SG CYS 23 U CYS 24 1_555 R SG CYS 67 U CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 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 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc2 C NE2 HIS 98 C HIS 98 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc3 C NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc4 C NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc5 D NE2 HIS 41 D HIS 41 1_555 HA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc6 D SD MET 160 D MET 160 1_555 HA FE HEC . D HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc7 E SG CYS 139 E CYS 139 1_555 JA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc8 E ND1 HIS 141 E HIS 141 1_555 JA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc9 E SG CYS 158 E CYS 158 1_555 JA FE1 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc10 E ND1 HIS 161 E HIS 161 1_555 JA FE2 FES . E FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc11 M NE2 HIS 84 P HIS 84 1_555 NA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc12 M NE2 HIS 98 P HIS 98 1_555 OA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc13 M NE2 HIS 183 P HIS 183 1_555 NA FE HEM . P HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc14 M NE2 HIS 197 P HIS 197 1_555 OA FE HEM . P HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc15 N NE2 HIS 41 Q HIS 41 1_555 AB FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc16 N SD MET 160 Q MET 160 1_555 AB FE HEC . Q HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc17 O SG CYS 139 R CYS 139 1_555 BB FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc18 O ND1 HIS 141 R HIS 141 1_555 BB FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc19 O SG CYS 158 R CYS 158 1_555 BB FE1 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc20 O ND1 HIS 161 R HIS 161 1_555 BB FE2 FES . R FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? # _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 591 n n CHA C4D HEM doub 592 n n CHA HHA HEM sing 593 n n CHB C4A HEM sing 594 n n CHB C1B HEM doub 595 n n CHB HHB HEM sing 596 n n CHC C4B HEM sing 597 n n CHC C1C HEM doub 598 n n CHC HHC HEM sing 599 n n CHD C4C HEM doub 600 n n CHD C1D HEM sing 601 n n CHD HHD HEM sing 602 n n C1A C2A HEM doub 603 n y C1A NA HEM sing 604 n y C2A C3A HEM sing 605 n y C2A CAA HEM sing 606 n n C3A C4A HEM doub 607 n y C3A CMA HEM sing 608 n n C4A NA HEM sing 609 n y CMA HMA HEM sing 610 n n CMA HMAA HEM sing 611 n n CMA HMAB HEM sing 612 n n CAA CBA HEM sing 613 n n CAA HAA HEM sing 614 n n CAA HAAA HEM sing 615 n n CBA CGA HEM sing 616 n n CBA HBA HEM sing 617 n n CBA HBAA HEM sing 618 n n CGA O1A HEM doub 619 n n CGA O2A HEM sing 620 n n C1B C2B HEM sing 621 n n C1B NB HEM sing 622 n n C2B C3B HEM doub 623 n n C2B CMB HEM sing 624 n n C3B C4B HEM sing 625 n n C3B CAB HEM sing 626 n n C4B NB HEM doub 627 n n CMB HMB HEM sing 628 n n CMB HMBA HEM sing 629 n n CMB HMBB HEM sing 630 n n CAB CBB HEM doub 631 n n CAB HAB HEM sing 632 n n CBB HBB HEM sing 633 n n CBB HBBA HEM sing 634 n n C1C C2C HEM sing 635 n y C1C NC HEM sing 636 n y C2C C3C HEM doub 637 n y C2C CMC HEM sing 638 n n C3C C4C HEM sing 639 n y C3C CAC HEM sing 640 n n C4C NC HEM sing 641 n y CMC HMC HEM sing 642 n n CMC HMCA HEM sing 643 n n CMC HMCB HEM sing 644 n n CAC CBC HEM doub 645 n n CAC HAC HEM sing 646 n n CBC HBC HEM sing 647 n n CBC HBCA HEM sing 648 n n C1D C2D HEM sing 649 n n C1D ND HEM doub 650 n n C2D C3D HEM doub 651 n n C2D CMD HEM sing 652 n n C3D C4D HEM sing 653 n n C3D CAD HEM sing 654 n n C4D ND HEM sing 655 n n CMD HMD HEM sing 656 n n CMD HMDA HEM sing 657 n n CMD HMDB HEM sing 658 n n CAD CBD HEM sing 659 n n CAD HAD HEM sing 660 n n CAD HADA HEM sing 661 n n CBD CGD HEM sing 662 n n CBD HBD HEM sing 663 n n CBD HBDA HEM sing 664 n n CGD O1D HEM doub 665 n n CGD O2D HEM sing 666 n n O2A H2A HEM sing 667 n n O2D H2D HEM sing 668 n n FE NA HEM sing 669 n n FE NB HEM sing 670 n n FE NC HEM sing 671 n n FE ND HEM sing 672 n n # _atom_sites.entry_id 3H1L _atom_sites.fract_transf_matrix[1][1] 0.005743 _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] 0.005484 _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] 0.004139 _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 UNL A 1 3016 3016 UNL UNL . W 13 HEM C 1 501 501 HEM HEM . X 13 HEM C 1 502 502 HEM HEM . Y 14 3H1 C 1 2001 2001 3H1 ACL . Z 14 3H1 C 1 2002 2002 3H1 ACL . AA 15 CDL C 1 2003 2003 CDL CDL . BA 11 PEE C 1 2007 2007 PEE PEE . CA 12 UNL C 1 2010 2010 UNL UNL . DA 12 UNL C 1 2104 2104 UNL UNL . EA 12 UNL C 1 3015 3015 UNL UNL . FA 12 UNL C 1 3106 3106 UNL UNL . GA 16 GOL C 1 2011 2011 GOL GOL . HA 17 HEC D 1 501 501 HEC HEC . IA 18 BOG D 1 2009 2009 BOG BOG . JA 19 FES E 1 501 501 FES FES . KA 11 PEE E 1 2005 2005 PEE PEE . LA 12 UNL E 1 2105 2105 UNL UNL . MA 15 CDL G 1 2004 2004 CDL CDL . NA 13 HEM P 1 501 501 HEM HEM . OA 13 HEM P 1 502 502 HEM HEM . PA 12 UNL P 1 2015 2015 UNL UNL . QA 12 UNL P 1 2106 2106 UNL UNL . RA 14 3H1 P 1 3001 3001 3H1 ACL . SA 14 3H1 P 1 3002 3002 3H1 ACL . TA 15 CDL P 1 3003 3003 CDL CDL . UA 11 PEE P 1 3007 3007 PEE PEE . VA 11 PEE P 1 3008 3008 PEE PEE . WA 12 UNL P 1 3010 3010 UNL UNL . XA 12 UNL P 1 3103 3103 UNL UNL . YA 12 UNL P 1 3104 3104 UNL UNL . ZA 16 GOL P 1 3011 3011 GOL GOL . AB 17 HEC Q 1 501 501 HEC HEC . BB 19 FES R 1 501 501 FES FES . CB 12 UNL R 1 2103 2103 UNL UNL . DB 11 PEE R 1 3005 3005 PEE PEE . EB 18 BOG R 1 3009 3009 BOG BOG . FB 15 CDL T 1 3004 3004 CDL CDL . GB 20 HOH B 1 1234 1234 HOH HOH . HB 20 HOH C 1 381 2 HOH HOH . HB 20 HOH C 2 382 108 HOH HOH . HB 20 HOH C 3 383 119 HOH HOH . HB 20 HOH C 4 384 168 HOH HOH . HB 20 HOH C 5 385 222 HOH HOH . HB 20 HOH C 6 1008 1008 HOH HOH . IB 20 HOH P 1 381 1 HOH HOH . IB 20 HOH P 2 382 28 HOH HOH . IB 20 HOH P 3 383 35 HOH HOH . IB 20 HOH P 4 384 109 HOH HOH . IB 20 HOH P 5 385 214 HOH HOH . IB 20 HOH P 6 959 959 HOH HOH . JB 20 HOH U 1 1233 1233 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 13 23.133 111.236 75.477 1 40.43 ? CHA HEM 502 C 1 HETATM 2 C CHB HEM . . . X 13 24.607 115.713 75.906 1 42.92 ? CHB HEM 502 C 1 HETATM 3 C CHC HEM . . . X 13 20.385 116.865 77.858 1 41.12 ? CHC HEM 502 C 1 HETATM 4 C CHD HEM . . . X 13 19.128 112.343 77.788 1 39.43 ? CHD HEM 502 C 1 HETATM 5 C C1A HEM . . . X 13 23.837 112.378 75.347 1 41.38 ? C1A HEM 502 C 1 HETATM 6 C C2A HEM . . . X 13 25 112.527 74.543 1 41.96 ? C2A HEM 502 C 1 HETATM 7 C C3A HEM . . . X 13 25.458 113.736 74.708 1 42.02 ? C3A HEM 502 C 1 HETATM 8 C C4A HEM . . . X 13 24.55 114.371 75.616 1 42.93 ? C4A HEM 502 C 1 HETATM 9 C CMA HEM . . . X 13 26.617 114.359 73.955 1 42.97 ? CMA HEM 502 C 1 HETATM 10 C CAA HEM . . . X 13 25.671 111.492 73.691 1 43.36 ? CAA HEM 502 C 1 HETATM 11 C CBA HEM . . . X 13 25.247 111.432 72.238 1 45.45 ? CBA HEM 502 C 1 HETATM 12 C CGA HEM . . . X 13 23.764 111.169 72.065 1 45.33 ? CGA HEM 502 C 1 HETATM 13 O O1A HEM . . . X 13 23.009 112.136 71.813 1 46.83 ? O1A HEM 502 C 1 HETATM 14 O O2A HEM . . . X 13 23.36 109.996 72.195 1 42.11 ? O2A HEM 502 C 1 HETATM 15 C C1B HEM . . . X 13 23.596 116.43 76.462 1 42.59 ? C1B HEM 502 C 1 HETATM 16 C C2B HEM . . . X 13 23.638 117.911 76.63 1 42.12 ? C2B HEM 502 C 1 HETATM 17 C C3B HEM . . . X 13 22.47 118.17 77.329 1 43.27 ? C3B HEM 502 C 1 HETATM 18 C C4B HEM . . . X 13 21.67 116.917 77.357 1 43.2 ? C4B HEM 502 C 1 HETATM 19 C CMB HEM . . . X 13 24.695 118.898 76.183 1 37.22 ? CMB HEM 502 C 1 HETATM 20 C CAB HEM . . . X 13 22.058 119.304 77.975 1 41 ? CAB HEM 502 C 1 HETATM 21 C CBB HEM . . . X 13 23.033 120.186 78.572 1 43.73 ? CBB HEM 502 C 1 HETATM 22 C C1C HEM . . . X 13 19.692 115.75 78.052 1 39.53 ? C1C HEM 502 C 1 HETATM 23 C C2C HEM . . . X 13 18.352 115.742 78.474 1 38.83 ? C2C HEM 502 C 1 HETATM 24 C C3C HEM . . . X 13 18.023 114.467 78.616 1 39.38 ? C3C HEM 502 C 1 HETATM 25 C C4C HEM . . . X 13 19.113 113.704 78.016 1 39.93 ? C4C HEM 502 C 1 HETATM 26 C CMC HEM . . . X 13 17.478 116.938 78.749 1 38.04 ? CMC HEM 502 C 1 HETATM 27 C CAC HEM . . . X 13 16.889 113.941 79.238 1 40.21 ? CAC HEM 502 C 1 HETATM 28 C CBC HEM . . . X 13 15.449 114.46 79.121 1 39.08 ? CBC HEM 502 C 1 HETATM 29 C C1D HEM . . . X 13 20.184 111.637 77.305 1 40.52 ? C1D HEM 502 C 1 HETATM 30 C C2D HEM . . . X 13 20.236 110.199 77.257 1 42.21 ? C2D HEM 502 C 1 HETATM 31 C C3D HEM . . . X 13 21.358 109.838 76.574 1 42.02 ? C3D HEM 502 C 1 HETATM 32 C C4D HEM . . . X 13 21.984 111.133 76.222 1 40.73 ? C4D HEM 502 C 1 HETATM 33 C CMD HEM . . . X 13 19.129 109.242 77.708 1 44.25 ? CMD HEM 502 C 1 HETATM 34 C CAD HEM . . . X 13 21.651 108.445 76.056 1 41.63 ? CAD HEM 502 C 1 HETATM 35 C CBD HEM . . . X 13 21.221 108.468 74.605 1 47.52 ? CBD HEM 502 C 1 HETATM 36 C CGD HEM . . . X 13 21.198 107.096 73.964 1 52.07 ? CGD HEM 502 C 1 HETATM 37 O O1D HEM . . . X 13 20.342 106.272 74.331 1 56.25 ? O1D HEM 502 C 1 HETATM 38 O O2D HEM . . . X 13 22.037 106.826 73.081 1 56.34 ? O2D HEM 502 C 1 HETATM 39 N NA HEM . . . X 13 23.489 113.553 75.934 1 42.58 ? NA HEM 502 C 1 HETATM 40 N NB HEM . . . X 13 22.398 115.845 76.897 1 42 ? NB HEM 502 C 1 HETATM 41 N NC HEM . . . X 13 20.164 114.52 77.725 1 40.78 ? NC HEM 502 C 1 HETATM 42 N ND HEM . . . X 13 21.326 112.196 76.808 1 40.47 ? ND HEM 502 C 1 HETATM 43 FE FE HEM . . . X 13 21.846 114.034 76.848 1 44.26 ? FE HEM 502 C 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #