data_3D17
#
_model_server_result.job_id            S14wfFNg2IZ2_hHYzqwSjA 
_model_server_result.datetime_utc      '2024-11-22 13:08:44' 
_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          3d17 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":143}' 
#
_entry.id    3D17 
#
_exptl.entry_id    3D17 
_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            3D17 
_cell.length_a            87.282 
_cell.length_b            87.282 
_cell.length_c            174.466 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D17 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 3 E N N 
? 3 J N N 
? 3 L N N 
? 3 N 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 NE2 HIS 87 A HIS 87 1_555 E FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc2 G C CMO . A CMO 142 1_555 E FE HEM . A HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? 
metalc ? metalc3 B NE2 HIS 92 B HIS 92 1_555 J FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc4 K C CMO . B CMO 147 1_555 J FE HEM . B HEM 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? 
metalc ? metalc5 C NE2 HIS 87 C HIS 87 1_555 L FE HEM . C HEM 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc6 D NE2 HIS 92 D HIS 92 1_555 N FE HEM . D HEM 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc7 N FE HEM . D HEM 148 1_555 O C CMO . D CMO 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? 
#
_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 130 n n 
CHA C4D HEM doub 131 n n 
CHA HHA HEM sing 132 n n 
CHB C4A HEM sing 133 n n 
CHB C1B HEM doub 134 n n 
CHB HHB HEM sing 135 n n 
CHC C4B HEM sing 136 n n 
CHC C1C HEM doub 137 n n 
CHC HHC HEM sing 138 n n 
CHD C4C HEM doub 139 n n 
CHD C1D HEM sing 140 n n 
CHD HHD HEM sing 141 n n 
C1A C2A HEM doub 142 n y 
C1A NA HEM sing 143 n y 
C2A C3A HEM sing 144 n y 
C2A CAA HEM sing 145 n n 
C3A C4A HEM doub 146 n y 
C3A CMA HEM sing 147 n n 
C4A NA HEM sing 148 n y 
CMA HMA HEM sing 149 n n 
CMA HMAA HEM sing 150 n n 
CMA HMAB HEM sing 151 n n 
CAA CBA HEM sing 152 n n 
CAA HAA HEM sing 153 n n 
CAA HAAA HEM sing 154 n n 
CBA CGA HEM sing 155 n n 
CBA HBA HEM sing 156 n n 
CBA HBAA HEM sing 157 n n 
CGA O1A HEM doub 158 n n 
CGA O2A HEM sing 159 n n 
C1B C2B HEM sing 160 n n 
C1B NB HEM sing 161 n n 
C2B C3B HEM doub 162 n n 
C2B CMB HEM sing 163 n n 
C3B C4B HEM sing 164 n n 
C3B CAB HEM sing 165 n n 
C4B NB HEM doub 166 n n 
CMB HMB HEM sing 167 n n 
CMB HMBA HEM sing 168 n n 
CMB HMBB HEM sing 169 n n 
CAB CBB HEM doub 170 n n 
CAB HAB HEM sing 171 n n 
CBB HBB HEM sing 172 n n 
CBB HBBA HEM sing 173 n n 
C1C C2C HEM sing 174 n y 
C1C NC HEM sing 175 n y 
C2C C3C HEM doub 176 n y 
C2C CMC HEM sing 177 n n 
C3C C4C HEM sing 178 n y 
C3C CAC HEM sing 179 n n 
C4C NC HEM sing 180 n y 
CMC HMC HEM sing 181 n n 
CMC HMCA HEM sing 182 n n 
CMC HMCB HEM sing 183 n n 
CAC CBC HEM doub 184 n n 
CAC HAC HEM sing 185 n n 
CBC HBC HEM sing 186 n n 
CBC HBCA HEM sing 187 n n 
C1D C2D HEM sing 188 n n 
C1D ND HEM doub 189 n n 
C2D C3D HEM doub 190 n n 
C2D CMD HEM sing 191 n n 
C3D C4D HEM sing 192 n n 
C3D CAD HEM sing 193 n n 
C4D ND HEM sing 194 n n 
CMD HMD HEM sing 195 n n 
CMD HMDA HEM sing 196 n n 
CMD HMDB HEM sing 197 n n 
CAD CBD HEM sing 198 n n 
CAD HAD HEM sing 199 n n 
CAD HADA HEM sing 200 n n 
CBD CGD HEM sing 201 n n 
CBD HBD HEM sing 202 n n 
CBD HBDA HEM sing 203 n n 
CGD O1D HEM doub 204 n n 
CGD O2D HEM sing 205 n n 
O2A H2A HEM sing 206 n n 
O2D H2D HEM sing 207 n n 
FE NA HEM sing 208 n n 
FE NB HEM sing 209 n n 
FE NC HEM sing 210 n n 
FE ND HEM sing 211 n n 
#
_atom_sites.entry_id                     3D17 
_atom_sites.fract_transf_matrix[1][1]    0.011457 
_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]    0.011457 
_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]    0.005732 
_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 3 HEM A 1 143 143 HEM HEM . 
F 4 MBN A 1 144 1 MBN MBN . 
G 5 CMO A 1 142 142 CMO CO . 
H 6 PO4 B 1 148 1 PO4 PO4 . 
I 6 PO4 B 1 149 5 PO4 PO4 . 
J 3 HEM B 1 150 148 HEM HEM . 
K 5 CMO B 1 147 147 CMO CO . 
L 3 HEM C 1 143 143 HEM HEM . 
M 6 PO4 D 1 147 3 PO4 PO4 . 
N 3 HEM D 1 148 148 HEM HEM . 
O 5 CMO D 1 149 147 CMO CO . 
P 7 HOH A 1 145 1 HOH HOH . 
P 7 HOH A 2 146 2 HOH HOH . 
P 7 HOH A 3 147 3 HOH HOH . 
P 7 HOH A 4 148 4 HOH HOH . 
P 7 HOH A 5 149 10 HOH HOH . 
P 7 HOH A 6 150 11 HOH HOH . 
P 7 HOH A 7 151 17 HOH HOH . 
P 7 HOH A 8 152 18 HOH HOH . 
P 7 HOH A 9 153 19 HOH HOH . 
P 7 HOH A 10 154 20 HOH HOH . 
P 7 HOH A 11 155 21 HOH HOH . 
P 7 HOH A 12 156 22 HOH HOH . 
P 7 HOH A 13 157 25 HOH HOH . 
P 7 HOH A 14 158 26 HOH HOH . 
P 7 HOH A 15 159 37 HOH HOH . 
P 7 HOH A 16 160 38 HOH HOH . 
P 7 HOH A 17 161 39 HOH HOH . 
P 7 HOH A 18 162 41 HOH HOH . 
P 7 HOH A 19 163 42 HOH HOH . 
P 7 HOH A 20 164 43 HOH HOH . 
P 7 HOH A 21 165 44 HOH HOH . 
P 7 HOH A 22 166 45 HOH HOH . 
P 7 HOH A 23 167 58 HOH HOH . 
P 7 HOH A 24 168 63 HOH HOH . 
P 7 HOH A 25 169 66 HOH HOH . 
P 7 HOH A 26 170 67 HOH HOH . 
P 7 HOH A 27 171 72 HOH HOH . 
P 7 HOH A 28 172 73 HOH HOH . 
P 7 HOH A 29 173 84 HOH HOH . 
Q 7 HOH B 1 151 8 HOH HOH . 
Q 7 HOH B 2 152 9 HOH HOH . 
Q 7 HOH B 3 153 16 HOH HOH . 
Q 7 HOH B 4 154 24 HOH HOH . 
Q 7 HOH B 5 155 27 HOH HOH . 
Q 7 HOH B 6 156 28 HOH HOH . 
Q 7 HOH B 7 157 29 HOH HOH . 
Q 7 HOH B 8 158 30 HOH HOH . 
Q 7 HOH B 9 159 46 HOH HOH . 
Q 7 HOH B 10 160 48 HOH HOH . 
Q 7 HOH B 11 161 49 HOH HOH . 
Q 7 HOH B 12 162 50 HOH HOH . 
Q 7 HOH B 13 163 51 HOH HOH . 
Q 7 HOH B 14 164 56 HOH HOH . 
Q 7 HOH B 15 165 57 HOH HOH . 
Q 7 HOH B 16 166 64 HOH HOH . 
Q 7 HOH B 17 167 78 HOH HOH . 
Q 7 HOH B 18 168 79 HOH HOH . 
Q 7 HOH B 19 169 83 HOH HOH . 
Q 7 HOH B 20 170 87 HOH HOH . 
Q 7 HOH B 21 171 88 HOH HOH . 
R 7 HOH C 1 144 5 HOH HOH . 
R 7 HOH C 2 145 12 HOH HOH . 
R 7 HOH C 3 146 23 HOH HOH . 
R 7 HOH C 4 147 31 HOH HOH . 
R 7 HOH C 5 148 32 HOH HOH . 
R 7 HOH C 6 149 33 HOH HOH . 
R 7 HOH C 7 150 52 HOH HOH . 
R 7 HOH C 8 151 53 HOH HOH . 
R 7 HOH C 9 152 68 HOH HOH . 
R 7 HOH C 10 153 69 HOH HOH . 
R 7 HOH C 11 154 74 HOH HOH . 
R 7 HOH C 12 155 75 HOH HOH . 
R 7 HOH C 13 156 76 HOH HOH . 
R 7 HOH C 14 157 77 HOH HOH . 
R 7 HOH C 15 158 85 HOH HOH . 
R 7 HOH C 16 159 86 HOH HOH . 
S 7 HOH D 1 150 6 HOH HOH . 
S 7 HOH D 2 151 7 HOH HOH . 
S 7 HOH D 3 152 13 HOH HOH . 
S 7 HOH D 4 153 14 HOH HOH . 
S 7 HOH D 5 154 15 HOH HOH . 
S 7 HOH D 6 155 34 HOH HOH . 
S 7 HOH D 7 156 35 HOH HOH . 
S 7 HOH D 8 157 36 HOH HOH . 
S 7 HOH D 9 158 40 HOH HOH . 
S 7 HOH D 10 159 47 HOH HOH . 
S 7 HOH D 11 160 54 HOH HOH . 
S 7 HOH D 12 161 55 HOH HOH . 
S 7 HOH D 13 162 59 HOH HOH . 
S 7 HOH D 14 163 60 HOH HOH . 
S 7 HOH D 15 164 61 HOH HOH . 
S 7 HOH D 16 165 62 HOH HOH . 
S 7 HOH D 17 166 65 HOH HOH . 
S 7 HOH D 18 167 70 HOH HOH . 
S 7 HOH D 19 168 71 HOH HOH . 
S 7 HOH D 20 169 80 HOH HOH . 
S 7 HOH D 21 170 81 HOH HOH . 
S 7 HOH D 22 171 82 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 . . . L 3 -15.697 61.586 8.639 1 44.93 ? CHA HEM 143 C 1 
HETATM 2 C CHB HEM . . . L 3 -15.444 59.481 13.091 1 52.88 ? CHB HEM 143 C 1 
HETATM 3 C CHC HEM . . . L 3 -12.696 63.15 14.724 1 33.82 ? CHC HEM 143 C 1 
HETATM 4 C CHD HEM . . . L 3 -12.935 65.311 10.342 1 28.68 ? CHD HEM 143 C 1 
HETATM 5 C C1A HEM . . . L 3 -15.956 60.734 9.748 1 47.94 ? C1A HEM 143 C 1 
HETATM 6 C C2A HEM . . . L 3 -16.743 59.516 9.723 1 47.46 ? C2A HEM 143 C 1 
HETATM 7 C C3A HEM . . . L 3 -16.619 58.89 10.942 1 50.83 ? C3A HEM 143 C 1 
HETATM 8 C C4A HEM . . . L 3 -15.837 59.784 11.769 1 52.1 ? C4A HEM 143 C 1 
HETATM 9 C CMA HEM . . . L 3 -17.105 57.508 11.398 1 42.87 ? CMA HEM 143 C 1 
HETATM 10 C CAA HEM . . . L 3 -17.647 59.095 8.599 1 50.52 ? CAA HEM 143 C 1 
HETATM 11 C CBA HEM . . . L 3 -17.14 57.886 7.838 1 57.58 ? CBA HEM 143 C 1 
HETATM 12 C CGA HEM . . . L 3 -17.991 57.584 6.621 1 60.97 ? CGA HEM 143 C 1 
HETATM 13 O O1A HEM . . . L 3 -18.242 58.523 5.829 1 60.68 ? O1A HEM 143 C 1 
HETATM 14 O O2A HEM . . . L 3 -18.401 56.415 6.456 1 60.86 ? O2A HEM 143 C 1 
HETATM 15 C C1B HEM . . . L 3 -14.669 60.309 13.915 1 49.76 ? C1B HEM 143 C 1 
HETATM 16 C C2B HEM . . . L 3 -14.343 60.014 15.303 1 45.94 ? C2B HEM 143 C 1 
HETATM 17 C C3B HEM . . . L 3 -13.664 61.074 15.792 1 45.82 ? C3B HEM 143 C 1 
HETATM 18 C C4B HEM . . . L 3 -13.535 62.036 14.698 1 43.9 ? C4B HEM 143 C 1 
HETATM 19 C CMB HEM . . . L 3 -14.728 58.781 16.105 1 33.6 ? CMB HEM 143 C 1 
HETATM 20 C CAB HEM . . . L 3 -13.187 61.161 17.096 1 50.07 ? CAB HEM 143 C 1 
HETATM 21 C CBB HEM . . . L 3 -13.64 62.158 18.038 1 37.64 ? CBB HEM 143 C 1 
HETATM 22 C C1C HEM . . . L 3 -12.399 63.945 13.616 1 28.83 ? C1C HEM 143 C 1 
HETATM 23 C C2C HEM . . . L 3 -11.688 65.135 13.758 1 24.99 ? C2C HEM 143 C 1 
HETATM 24 C C3C HEM . . . L 3 -11.766 65.803 12.586 1 29.5 ? C3C HEM 143 C 1 
HETATM 25 C C4C HEM . . . L 3 -12.543 64.969 11.65 1 23.96 ? C4C HEM 143 C 1 
HETATM 26 C CMC HEM . . . L 3 -11.088 65.646 15.051 1 38.01 ? CMC HEM 143 C 1 
HETATM 27 C CAC HEM . . . L 3 -11.208 67.082 12.417 1 26.44 ? CAC HEM 143 C 1 
HETATM 28 C CBC HEM . . . L 3 -11.903 68.294 12.074 1 16.5 ? CBC HEM 143 C 1 
HETATM 29 C C1D HEM . . . L 3 -13.783 64.553 9.503 1 43.96 ? C1D HEM 143 C 1 
HETATM 30 C C2D HEM . . . L 3 -14.074 64.795 8.033 1 45.57 ? C2D HEM 143 C 1 
HETATM 31 C C3D HEM . . . L 3 -14.824 63.77 7.592 1 46.46 ? C3D HEM 143 C 1 
HETATM 32 C C4D HEM . . . L 3 -14.999 62.826 8.713 1 49.58 ? C4D HEM 143 C 1 
HETATM 33 C CMD HEM . . . L 3 -13.596 65.854 7.043 1 34.31 ? CMD HEM 143 C 1 
HETATM 34 C CAD HEM . . . L 3 -15.346 63.659 6.172 1 54.91 ? CAD HEM 143 C 1 
HETATM 35 C CBD HEM . . . L 3 -16.812 64.037 6.089 1 71.22 ? CBD HEM 143 C 1 
HETATM 36 C CGD HEM . . . L 3 -17.486 63.481 4.85 1 77.1 ? CGD HEM 143 C 1 
HETATM 37 O O1D HEM . . . L 3 -17.21 63.993 3.745 1 78.12 ? O1D HEM 143 C 1 
HETATM 38 O O2D HEM . . . L 3 -18.285 62.524 4.982 1 80.25 ? O2D HEM 143 C 1 
HETATM 39 N NA HEM . . . L 3 -15.437 60.918 11.041 1 45.65 ? NA HEM 143 C 1 
HETATM 40 N NB HEM . . . L 3 -14.172 61.558 13.54 1 45.52 ? NB HEM 143 C 1 
HETATM 41 N NC HEM . . . L 3 -12.956 63.835 12.325 1 35.22 ? NC HEM 143 C 1 
HETATM 42 N ND HEM . . . L 3 -14.369 63.336 9.892 1 46.36 ? ND HEM 143 C 1 
HETATM 43 FE FE HEM . . . L 3 -14.272 62.426 11.692 1 42.19 ? FE HEM 143 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#