data_1DP6
#
_model_server_result.job_id            JCCsQ-5dsswFiGRtROIr-Q 
_model_server_result.datetime_utc      '2024-11-04 23:22:17' 
_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          1dp6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":719}' 
#
_entry.id    1DP6 
#
_exptl.entry_id    1DP6 
_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    1 
_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         120 
_cell.entry_id            1DP6 
_cell.length_a            127.372 
_cell.length_b            127.372 
_cell.length_c            58.582 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DP6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 61 A HIS 200 1_555 C FE HEM . A HEM 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc2 B O1 OXY . A OXY 500 1_555 C FE HEM . A HEM 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.808 ? 
metalc ? metalc3 B O2 OXY . A OXY 500 1_555 C FE HEM . A HEM 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
#
_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 116 n n 
CHA C4D HEM doub 117 n n 
CHA HHA HEM sing 118 n n 
CHB C4A HEM sing 119 n n 
CHB C1B HEM doub 120 n n 
CHB HHB HEM sing 121 n n 
CHC C4B HEM sing 122 n n 
CHC C1C HEM doub 123 n n 
CHC HHC HEM sing 124 n n 
CHD C4C HEM doub 125 n n 
CHD C1D HEM sing 126 n n 
CHD HHD HEM sing 127 n n 
C1A C2A HEM doub 128 n y 
C1A NA HEM sing 129 n y 
C2A C3A HEM sing 130 n y 
C2A CAA HEM sing 131 n n 
C3A C4A HEM doub 132 n y 
C3A CMA HEM sing 133 n n 
C4A NA HEM sing 134 n y 
CMA HMA HEM sing 135 n n 
CMA HMAA HEM sing 136 n n 
CMA HMAB HEM sing 137 n n 
CAA CBA HEM sing 138 n n 
CAA HAA HEM sing 139 n n 
CAA HAAA HEM sing 140 n n 
CBA CGA HEM sing 141 n n 
CBA HBA HEM sing 142 n n 
CBA HBAA HEM sing 143 n n 
CGA O1A HEM doub 144 n n 
CGA O2A HEM sing 145 n n 
C1B C2B HEM sing 146 n n 
C1B NB HEM sing 147 n n 
C2B C3B HEM doub 148 n n 
C2B CMB HEM sing 149 n n 
C3B C4B HEM sing 150 n n 
C3B CAB HEM sing 151 n n 
C4B NB HEM doub 152 n n 
CMB HMB HEM sing 153 n n 
CMB HMBA HEM sing 154 n n 
CMB HMBB HEM sing 155 n n 
CAB CBB HEM doub 156 n n 
CAB HAB HEM sing 157 n n 
CBB HBB HEM sing 158 n n 
CBB HBBA HEM sing 159 n n 
C1C C2C HEM sing 160 n y 
C1C NC HEM sing 161 n y 
C2C C3C HEM doub 162 n y 
C2C CMC HEM sing 163 n n 
C3C C4C HEM sing 164 n y 
C3C CAC HEM sing 165 n n 
C4C NC HEM sing 166 n y 
CMC HMC HEM sing 167 n n 
CMC HMCA HEM sing 168 n n 
CMC HMCB HEM sing 169 n n 
CAC CBC HEM doub 170 n n 
CAC HAC HEM sing 171 n n 
CBC HBC HEM sing 172 n n 
CBC HBCA HEM sing 173 n n 
C1D C2D HEM sing 174 n n 
C1D ND HEM doub 175 n n 
C2D C3D HEM doub 176 n n 
C2D CMD HEM sing 177 n n 
C3D C4D HEM sing 178 n n 
C3D CAD HEM sing 179 n n 
C4D ND HEM sing 180 n n 
CMD HMD HEM sing 181 n n 
CMD HMDA HEM sing 182 n n 
CMD HMDB HEM sing 183 n n 
CAD CBD HEM sing 184 n n 
CAD HAD HEM sing 185 n n 
CAD HADA HEM sing 186 n n 
CBD CGD HEM sing 187 n n 
CBD HBD HEM sing 188 n n 
CBD HBDA HEM sing 189 n n 
CGD O1D HEM doub 190 n n 
CGD O2D HEM sing 191 n n 
O2A H2A HEM sing 192 n n 
O2D H2D HEM sing 193 n n 
FE NA HEM sing 194 n n 
FE NB HEM sing 195 n n 
FE NC HEM sing 196 n n 
FE ND HEM sing 197 n n 
#
_atom_sites.entry_id                     1DP6 
_atom_sites.fract_transf_matrix[1][1]    0.007851 
_atom_sites.fract_transf_matrix[1][2]    0.004532 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009065 
_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]    0.01707 
_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
B 2 OXY A 1 500 500 OXY OO . 
C 3 HEM A 1 719 719 HEM HEM . 
D 4 HOH A 1 720 1 HOH TIP . 
D 4 HOH A 2 721 2 HOH TIP . 
D 4 HOH A 3 722 3 HOH TIP . 
D 4 HOH A 4 723 4 HOH TIP . 
D 4 HOH A 5 724 5 HOH TIP . 
D 4 HOH A 6 725 6 HOH TIP . 
D 4 HOH A 7 726 7 HOH TIP . 
D 4 HOH A 8 727 8 HOH TIP . 
D 4 HOH A 9 728 9 HOH TIP . 
D 4 HOH A 10 729 10 HOH TIP . 
D 4 HOH A 11 730 11 HOH TIP . 
D 4 HOH A 12 731 12 HOH TIP . 
D 4 HOH A 13 732 13 HOH TIP . 
D 4 HOH A 14 733 15 HOH TIP . 
D 4 HOH A 15 734 16 HOH TIP . 
D 4 HOH A 16 735 17 HOH TIP . 
D 4 HOH A 17 736 18 HOH TIP . 
D 4 HOH A 18 737 19 HOH TIP . 
D 4 HOH A 19 738 20 HOH TIP . 
D 4 HOH A 20 739 21 HOH TIP . 
D 4 HOH A 21 740 22 HOH TIP . 
D 4 HOH A 22 741 23 HOH TIP . 
D 4 HOH A 23 742 25 HOH TIP . 
D 4 HOH A 24 743 26 HOH TIP . 
D 4 HOH A 25 744 27 HOH TIP . 
D 4 HOH A 26 745 28 HOH TIP . 
D 4 HOH A 27 746 29 HOH TIP . 
D 4 HOH A 28 747 31 HOH TIP . 
D 4 HOH A 29 748 32 HOH TIP . 
D 4 HOH A 30 749 33 HOH TIP . 
D 4 HOH A 31 750 34 HOH TIP . 
D 4 HOH A 32 751 38 HOH TIP . 
D 4 HOH A 33 752 39 HOH TIP . 
D 4 HOH A 34 753 41 HOH TIP . 
D 4 HOH A 35 754 45 HOH TIP . 
D 4 HOH A 36 755 46 HOH TIP . 
D 4 HOH A 37 756 52 HOH TIP . 
D 4 HOH A 38 757 56 HOH TIP . 
D 4 HOH A 39 758 58 HOH TIP . 
D 4 HOH A 40 759 60 HOH TIP . 
D 4 HOH A 41 760 61 HOH TIP . 
D 4 HOH A 42 761 62 HOH TIP . 
D 4 HOH A 43 762 64 HOH TIP . 
D 4 HOH A 44 763 65 HOH TIP . 
D 4 HOH A 45 764 66 HOH TIP . 
D 4 HOH A 46 765 67 HOH TIP . 
D 4 HOH A 47 766 68 HOH TIP . 
D 4 HOH A 48 767 70 HOH TIP . 
D 4 HOH A 49 768 71 HOH TIP . 
D 4 HOH A 50 769 72 HOH TIP . 
D 4 HOH A 51 770 74 HOH TIP . 
D 4 HOH A 52 771 75 HOH TIP . 
D 4 HOH A 53 772 116 HOH TIP . 
D 4 HOH A 54 773 117 HOH TIP . 
D 4 HOH A 55 774 118 HOH TIP . 
D 4 HOH A 56 775 123 HOH TIP . 
D 4 HOH A 57 776 124 HOH TIP . 
D 4 HOH A 58 777 125 HOH TIP . 
D 4 HOH A 59 778 127 HOH TIP . 
D 4 HOH A 60 779 132 HOH TIP . 
D 4 HOH A 61 780 134 HOH TIP . 
D 4 HOH A 62 781 137 HOH TIP . 
D 4 HOH A 63 782 138 HOH TIP . 
D 4 HOH A 64 783 144 HOH TIP . 
D 4 HOH A 65 784 145 HOH TIP . 
D 4 HOH A 66 785 150 HOH TIP . 
D 4 HOH A 67 786 156 HOH TIP . 
D 4 HOH A 68 787 158 HOH TIP . 
D 4 HOH A 69 788 168 HOH TIP . 
D 4 HOH A 70 789 171 HOH TIP . 
D 4 HOH A 71 790 181 HOH TIP . 
D 4 HOH A 72 791 182 HOH TIP . 
D 4 HOH A 73 792 186 HOH TIP . 
D 4 HOH A 74 793 193 HOH TIP . 
D 4 HOH A 75 794 198 HOH TIP . 
D 4 HOH A 76 795 199 HOH TIP . 
D 4 HOH A 77 796 200 HOH TIP . 
D 4 HOH A 78 797 202 HOH TIP . 
D 4 HOH A 79 798 204 HOH TIP . 
D 4 HOH A 80 799 213 HOH TIP . 
D 4 HOH A 81 800 221 HOH TIP . 
D 4 HOH A 82 801 235 HOH TIP . 
D 4 HOH A 83 802 250 HOH TIP . 
D 4 HOH A 84 803 254 HOH TIP . 
D 4 HOH A 85 804 255 HOH TIP . 
D 4 HOH A 86 805 259 HOH TIP . 
D 4 HOH A 87 806 260 HOH TIP . 
D 4 HOH A 88 807 271 HOH TIP . 
D 4 HOH A 89 808 272 HOH TIP . 
D 4 HOH A 90 809 278 HOH TIP . 
D 4 HOH A 91 810 280 HOH TIP . 
D 4 HOH A 92 811 281 HOH TIP . 
D 4 HOH A 93 812 290 HOH TIP . 
D 4 HOH A 94 813 292 HOH TIP . 
D 4 HOH A 95 814 294 HOH TIP . 
D 4 HOH A 96 815 298 HOH TIP . 
D 4 HOH A 97 816 299 HOH TIP . 
D 4 HOH A 98 817 300 HOH TIP . 
#
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 . . . C 3 44.95 54.842 32.887 1 14.41 ? CHA HEM 719 A 1 
HETATM 2 C CHB HEM . . . C 3 49.295 54.643 30.988 1 10.25 ? CHB HEM 719 A 1 
HETATM 3 C CHC HEM . . . C 3 51.24 56.55 34.92 1 6.1 ? CHC HEM 719 A 1 
HETATM 4 C CHD HEM . . . C 3 46.796 57.268 36.551 1 5.17 ? CHD HEM 719 A 1 
HETATM 5 C C1A HEM . . . C 3 45.958 54.578 32.015 1 16.07 ? C1A HEM 719 A 1 
HETATM 6 C C2A HEM . . . C 3 45.848 53.851 30.766 1 15.74 ? C2A HEM 719 A 1 
HETATM 7 C C3A HEM . . . C 3 47.065 53.785 30.259 1 16.61 ? C3A HEM 719 A 1 
HETATM 8 C C4A HEM . . . C 3 47.974 54.486 31.145 1 12.64 ? C4A HEM 719 A 1 
HETATM 9 C CMA HEM . . . C 3 47.516 53.071 28.972 1 21.65 ? CMA HEM 719 A 1 
HETATM 10 C CAA HEM . . . C 3 44.557 53.094 30.309 1 18.56 ? CAA HEM 719 A 1 
HETATM 11 C CBA HEM . . . C 3 44.644 51.599 30.631 1 17.55 ? CBA HEM 719 A 1 
HETATM 12 C CGA HEM . . . C 3 43.486 50.758 30.114 1 19 ? CGA HEM 719 A 1 
HETATM 13 O O1A HEM . . . C 3 43.611 49.516 30.101 1 20.97 ? O1A HEM 719 A 1 
HETATM 14 O O2A HEM . . . C 3 42.474 51.424 29.695 1 18.99 ? O2A HEM 719 A 1 
HETATM 15 C C1B HEM . . . C 3 50.187 55.152 31.863 1 9.48 ? C1B HEM 719 A 1 
HETATM 16 C C2B HEM . . . C 3 51.561 55.193 31.634 1 5.24 ? C2B HEM 719 A 1 
HETATM 17 C C3B HEM . . . C 3 52.137 55.749 32.728 1 4.35 ? C3B HEM 719 A 1 
HETATM 18 C C4B HEM . . . C 3 51.088 56.116 33.633 1 6.61 ? C4B HEM 719 A 1 
HETATM 19 C CMB HEM . . . C 3 52.278 54.558 30.421 1 13.39 ? CMB HEM 719 A 1 
HETATM 20 C CAB HEM . . . C 3 53.651 55.893 32.984 1 2.65 ? CAB HEM 719 A 1 
HETATM 21 C CBB HEM . . . C 3 54.15 57.188 33.678 1 9.36 ? CBB HEM 719 A 1 
HETATM 22 C C1C HEM . . . C 3 50.167 56.875 35.706 1 4.98 ? C1C HEM 719 A 1 
HETATM 23 C C2C HEM . . . C 3 50.307 57.374 37.017 1 6.06 ? C2C HEM 719 A 1 
HETATM 24 C C3C HEM . . . C 3 49.041 57.562 37.511 1 3.1 ? C3C HEM 719 A 1 
HETATM 25 C C4C HEM . . . C 3 48.157 57.209 36.485 1 4.51 ? C4C HEM 719 A 1 
HETATM 26 C CMC HEM . . . C 3 51.703 57.605 37.635 1 4.39 ? CMC HEM 719 A 1 
HETATM 27 C CAC HEM . . . C 3 48.493 57.847 38.935 1 2 ? CAC HEM 719 A 1 
HETATM 28 C CBC HEM . . . C 3 49.387 58.552 39.891 1 2 ? CBC HEM 719 A 1 
HETATM 29 C C1D HEM . . . C 3 45.908 56.722 35.709 1 11.51 ? C1D HEM 719 A 1 
HETATM 30 C C2D HEM . . . C 3 44.481 56.662 35.899 1 12.26 ? C2D HEM 719 A 1 
HETATM 31 C C3D HEM . . . C 3 43.978 56.004 34.843 1 13.72 ? C3D HEM 719 A 1 
HETATM 32 C C4D HEM . . . C 3 45.072 55.639 34 1 16.04 ? C4D HEM 719 A 1 
HETATM 33 C CMD HEM . . . C 3 43.741 57.303 37.095 1 10.12 ? CMD HEM 719 A 1 
HETATM 34 C CAD HEM . . . C 3 42.585 55.486 34.58 1 17.03 ? CAD HEM 719 A 1 
HETATM 35 C CBD HEM . . . C 3 42.495 54.016 35.013 1 19.83 ? CBD HEM 719 A 1 
HETATM 36 C CGD HEM . . . C 3 41.45 53.194 34.482 1 23.55 ? CGD HEM 719 A 1 
HETATM 37 O O1D HEM . . . C 3 41.006 52.215 35.137 1 22.04 ? O1D HEM 719 A 1 
HETATM 38 O O2D HEM . . . C 3 41.078 53.503 33.313 1 23.1 ? O2D HEM 719 A 1 
HETATM 39 N NA HEM . . . C 3 47.274 54.938 32.21 1 13.07 ? NA HEM 719 A 1 
HETATM 40 N NB HEM . . . C 3 49.888 55.722 33.099 1 7.62 ? NB HEM 719 A 1 
HETATM 41 N NC HEM . . . C 3 48.837 56.762 35.392 1 8.08 ? NC HEM 719 A 1 
HETATM 42 N ND HEM . . . C 3 46.265 56.081 34.524 1 11.86 ? ND HEM 719 A 1 
HETATM 43 FE FE HEM . . . C 3 48.018 55.919 33.778 1 14.76 ? FE HEM 719 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#