data_3PGH # _model_server_result.job_id gX24egccarSl8BtKHc8OKg _model_server_result.datetime_utc '2024-11-14 08:52:34' _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 3pgh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":682}' # _entry.id 3PGH # _exptl.entry_id 3PGH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 3 _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 3PGH _cell.length_a 179.5 _cell.length_b 133.8 _cell.length_c 117.1 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PGH _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,N 1 1 C,D,O,P,Q,R,S,T,U,V,W,X 2 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 ? 3 H N N ? 3 M N N ? 3 R N N ? 3 W 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 A SG CYS 4 A CYS 36 1_555 A SG CYS 15 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 5 A CYS 37 1_555 A SG CYS 128 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 9 A CYS 41 1_555 A SG CYS 25 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf4 A SG CYS 27 A CYS 59 1_555 A SG CYS 37 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 A SG CYS 538 A CYS 569 1_555 A SG CYS 544 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf6 B SG CYS 4 B CYS 36 1_555 B SG CYS 15 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf7 B SG CYS 5 B CYS 37 1_555 B SG CYS 128 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf8 B SG CYS 9 B CYS 41 1_555 B SG CYS 25 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf9 B SG CYS 27 B CYS 59 1_555 B SG CYS 37 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf10 B SG CYS 538 B CYS 569 1_555 B SG CYS 544 B CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf11 C SG CYS 4 C CYS 36 1_555 C SG CYS 15 C CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf12 C SG CYS 5 C CYS 37 1_555 C SG CYS 128 C CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf13 C SG CYS 9 C CYS 41 1_555 C SG CYS 25 C CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf14 C SG CYS 27 C CYS 59 1_555 C SG CYS 37 C CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 C SG CYS 538 C CYS 569 1_555 C SG CYS 544 C CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf16 D SG CYS 4 D CYS 36 1_555 D SG CYS 15 D CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf17 D SG CYS 5 D CYS 37 1_555 D SG CYS 128 D CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf18 D SG CYS 9 D CYS 41 1_555 D SG CYS 25 D CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf19 D SG CYS 27 D CYS 59 1_555 D SG CYS 37 D CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf20 D SG CYS 538 D CYS 569 1_555 D SG CYS 544 D CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A ND2 ASN 36 A ASN 68 1_555 E C1 NAG . A NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 113 A ASN 144 1_555 F C1 NAG . A NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale3 A ND2 ASN 379 A ASN 410 1_555 G C1 NAG . A NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale4 B ND2 ASN 36 B ASN 68 1_555 J C1 NAG . B NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale5 B ND2 ASN 113 B ASN 144 1_555 K C1 NAG . B NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 379 B ASN 410 1_555 L C1 NAG . B NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 C ND2 ASN 36 C ASN 68 1_555 O C1 NAG . C NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C ND2 ASN 113 C ASN 144 1_555 P C1 NAG . C NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale9 C ND2 ASN 379 C ASN 410 1_555 Q C1 NAG . C NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 D ND2 ASN 36 D ASN 68 1_555 T C1 NAG . D NAG 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale11 D ND2 ASN 113 D ASN 144 1_555 U C1 NAG . D NAG 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 D ND2 ASN 379 D ASN 410 1_555 V C1 NAG . D NAG 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? metalc ? metalc1 A NE2 HIS 357 A HIS 388 1_555 H FE HEM . A HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc2 B NE2 HIS 357 B HIS 388 1_555 M FE HEM . B HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 C NE2 HIS 357 C HIS 388 1_555 R FE HEM . C HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc4 D NE2 HIS 357 D HIS 388 1_555 W FE HEM . D HEM 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _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 # _atom_sites.entry_id 3PGH _atom_sites.fract_transf_matrix[1][1] 0.005571 _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] 0.007474 _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] 0.00854 _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 NAG A 1 661 661 NAG NAG . F 2 NAG A 1 671 671 NAG NAG . G 2 NAG A 1 681 681 NAG NAG . H 3 HEM A 1 682 601 HEM HEM . I 4 FLP A 1 701 701 FLP FLP . J 2 NAG B 1 661 661 NAG NAG . K 2 NAG B 1 671 671 NAG NAG . L 2 NAG B 1 681 681 NAG NAG . M 3 HEM B 1 682 601 HEM HEM . N 4 FLP B 1 701 701 FLP FLP . O 2 NAG C 1 661 661 NAG NAG . P 2 NAG C 1 671 671 NAG NAG . Q 2 NAG C 1 681 681 NAG NAG . R 3 HEM C 1 682 601 HEM HEM . S 4 FLP C 1 701 701 FLP FLP . T 2 NAG D 1 661 661 NAG NAG . U 2 NAG D 1 671 671 NAG NAG . V 2 NAG D 1 681 681 NAG NAG . W 3 HEM D 1 682 601 HEM HEM . X 4 FLP D 1 701 701 FLP FLP . # 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 3 23.631 34.394 -0.678 1 10.09 ? CHA HEM 682 A 1 HETATM 2 C CHB HEM . . . H 3 20.304 37.84 -0.3 1 14.05 ? CHB HEM 682 A 1 HETATM 3 C CHC HEM . . . H 3 19.821 36.826 4.322 1 9.22 ? CHC HEM 682 A 1 HETATM 4 C CHD HEM . . . H 3 22.772 33.106 3.845 1 12.28 ? CHD HEM 682 A 1 HETATM 5 C C1A HEM . . . H 3 22.739 35.384 -1.004 1 13.16 ? C1A HEM 682 A 1 HETATM 6 C C2A HEM . . . H 3 22.647 36.006 -2.318 1 18.65 ? C2A HEM 682 A 1 HETATM 7 C C3A HEM . . . H 3 21.693 36.976 -2.211 1 18.53 ? C3A HEM 682 A 1 HETATM 8 C C4A HEM . . . H 3 21.214 36.925 -0.834 1 16.39 ? C4A HEM 682 A 1 HETATM 9 C CMA HEM . . . H 3 21.219 37.968 -3.282 1 8.76 ? CMA HEM 682 A 1 HETATM 10 C CAA HEM . . . H 3 23.46 35.66 -3.564 1 21.67 ? CAA HEM 682 A 1 HETATM 11 C CBA HEM . . . H 3 22.676 34.813 -4.575 1 32.69 ? CBA HEM 682 A 1 HETATM 12 C CGA HEM . . . H 3 23.529 34.309 -5.755 1 34.61 ? CGA HEM 682 A 1 HETATM 13 O O1A HEM . . . H 3 24.097 33.202 -5.644 1 39.74 ? O1A HEM 682 A 1 HETATM 14 O O2A HEM . . . H 3 23.629 35.012 -6.787 1 31.22 ? O2A HEM 682 A 1 HETATM 15 C C1B HEM . . . H 3 19.91 37.889 1.006 1 4.43 ? C1B HEM 682 A 1 HETATM 16 C C2B HEM . . . H 3 19.152 38.95 1.585 1 6.84 ? C2B HEM 682 A 1 HETATM 17 C C3B HEM . . . H 3 19.131 38.722 2.915 1 8.58 ? C3B HEM 682 A 1 HETATM 18 C C4B HEM . . . H 3 19.789 37.48 3.115 1 10.51 ? C4B HEM 682 A 1 HETATM 19 C CMB HEM . . . H 3 18.46 40.079 0.836 1 12.94 ? CMB HEM 682 A 1 HETATM 20 C CAB HEM . . . H 3 18.766 39.57 3.944 1 9.6 ? CAB HEM 682 A 1 HETATM 21 C CBB HEM . . . H 3 17.564 40.345 3.932 1 9.34 ? CBB HEM 682 A 1 HETATM 22 C C1C HEM . . . H 3 20.476 35.644 4.547 1 10.14 ? C1C HEM 682 A 1 HETATM 23 C C2C HEM . . . H 3 20.516 34.998 5.831 1 9.82 ? C2C HEM 682 A 1 HETATM 24 C C3C HEM . . . H 3 21.319 33.941 5.706 1 6.95 ? C3C HEM 682 A 1 HETATM 25 C C4C HEM . . . H 3 21.797 33.953 4.339 1 9.93 ? C4C HEM 682 A 1 HETATM 26 C CMC HEM . . . H 3 19.845 35.493 7.096 1 7.39 ? CMC HEM 682 A 1 HETATM 27 C CAC HEM . . . H 3 21.566 33.025 6.702 1 11.84 ? CAC HEM 682 A 1 HETATM 28 C CBC HEM . . . H 3 22.81 32.326 6.868 1 16.29 ? CBC HEM 682 A 1 HETATM 29 C C1D HEM . . . H 3 23.301 33.167 2.577 1 12.78 ? C1D HEM 682 A 1 HETATM 30 C C2D HEM . . . H 3 24.394 32.372 2.14 1 11.9 ? C2D HEM 682 A 1 HETATM 31 C C3D HEM . . . H 3 24.689 32.787 0.891 1 10.65 ? C3D HEM 682 A 1 HETATM 32 C C4D HEM . . . H 3 23.731 33.795 0.547 1 9.89 ? C4D HEM 682 A 1 HETATM 33 C CMD HEM . . . H 3 25.123 31.322 2.964 1 15.15 ? CMD HEM 682 A 1 HETATM 34 C CAD HEM . . . H 3 25.92 32.421 0.082 1 11.48 ? CAD HEM 682 A 1 HETATM 35 C CBD HEM . . . H 3 27.072 33.372 0.263 1 6.61 ? CBD HEM 682 A 1 HETATM 36 C CGD HEM . . . H 3 28.032 33.322 -0.881 1 8.25 ? CGD HEM 682 A 1 HETATM 37 O O1D HEM . . . H 3 28.291 32.235 -1.403 1 8.3 ? O1D HEM 682 A 1 HETATM 38 O O2D HEM . . . H 3 28.522 34.375 -1.287 1 9.56 ? O2D HEM 682 A 1 HETATM 39 N NA HEM . . . H 3 21.851 35.946 -0.114 1 7.2 ? NA HEM 682 A 1 HETATM 40 N NB HEM . . . H 3 20.322 36.997 1.946 1 10.72 ? NB HEM 682 A 1 HETATM 41 N NC HEM . . . H 3 21.25 34.994 3.62 1 7.37 ? NC HEM 682 A 1 HETATM 42 N ND HEM . . . H 3 22.905 34.061 1.599 1 15.39 ? ND HEM 682 A 1 HETATM 43 FE FE HEM . . . H 3 21.573 35.507 1.75 1 20.01 ? FE HEM 682 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #