data_3L4D
#
_model_server_result.job_id            mmRZyeBJLUEZndt9cJPWTA 
_model_server_result.datetime_utc      '2024-10-19 11:34:10' 
_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          3l4d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":481}' 
#
_entry.id    3L4D 
#
_exptl.entry_id    3L4D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          2 
_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          104.82 
_cell.angle_gamma         90 
_cell.entry_id            3L4D 
_cell.length_a            84.891 
_cell.length_b            118.509 
_cell.length_c            100.96 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3L4D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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 
_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
? 2 E N N 
? 2 G N N 
? 2 I N N 
? 2 L 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 SG CYS 395 A CYS 422 1_555 E FE HEM . A HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc2 E FE HEM . A HEM 481 1_555 F N5 TPF . A TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? 
metalc ? metalc3 B SG CYS 395 B CYS 422 1_555 G FE HEM . B HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc4 G FE HEM . B HEM 481 1_555 H N5 TPF . B TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? 
metalc ? metalc5 C SG CYS 395 C CYS 422 1_555 I FE HEM . C HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc6 I FE HEM . C HEM 481 1_555 J N5 TPF . C TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? 
metalc ? metalc7 D SG CYS 395 D CYS 422 1_555 L FE HEM . D HEM 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc8 L FE HEM . D HEM 481 1_555 M N5 TPF . D TPF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? 
#
_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 129 n n 
CHA C4D HEM doub 130 n n 
CHA HHA HEM sing 131 n n 
CHB C4A HEM sing 132 n n 
CHB C1B HEM doub 133 n n 
CHB HHB HEM sing 134 n n 
CHC C4B HEM sing 135 n n 
CHC C1C HEM doub 136 n n 
CHC HHC HEM sing 137 n n 
CHD C4C HEM doub 138 n n 
CHD C1D HEM sing 139 n n 
CHD HHD HEM sing 140 n n 
C1A C2A HEM doub 141 n y 
C1A NA HEM sing 142 n y 
C2A C3A HEM sing 143 n y 
C2A CAA HEM sing 144 n n 
C3A C4A HEM doub 145 n y 
C3A CMA HEM sing 146 n n 
C4A NA HEM sing 147 n y 
CMA HMA HEM sing 148 n n 
CMA HMAA HEM sing 149 n n 
CMA HMAB HEM sing 150 n n 
CAA CBA HEM sing 151 n n 
CAA HAA HEM sing 152 n n 
CAA HAAA HEM sing 153 n n 
CBA CGA HEM sing 154 n n 
CBA HBA HEM sing 155 n n 
CBA HBAA HEM sing 156 n n 
CGA O1A HEM doub 157 n n 
CGA O2A HEM sing 158 n n 
C1B C2B HEM sing 159 n n 
C1B NB HEM sing 160 n n 
C2B C3B HEM doub 161 n n 
C2B CMB HEM sing 162 n n 
C3B C4B HEM sing 163 n n 
C3B CAB HEM sing 164 n n 
C4B NB HEM doub 165 n n 
CMB HMB HEM sing 166 n n 
CMB HMBA HEM sing 167 n n 
CMB HMBB HEM sing 168 n n 
CAB CBB HEM doub 169 n n 
CAB HAB HEM sing 170 n n 
CBB HBB HEM sing 171 n n 
CBB HBBA HEM sing 172 n n 
C1C C2C HEM sing 173 n y 
C1C NC HEM sing 174 n y 
C2C C3C HEM doub 175 n y 
C2C CMC HEM sing 176 n n 
C3C C4C HEM sing 177 n y 
C3C CAC HEM sing 178 n n 
C4C NC HEM sing 179 n y 
CMC HMC HEM sing 180 n n 
CMC HMCA HEM sing 181 n n 
CMC HMCB HEM sing 182 n n 
CAC CBC HEM doub 183 n n 
CAC HAC HEM sing 184 n n 
CBC HBC HEM sing 185 n n 
CBC HBCA HEM sing 186 n n 
C1D C2D HEM sing 187 n n 
C1D ND HEM doub 188 n n 
C2D C3D HEM doub 189 n n 
C2D CMD HEM sing 190 n n 
C3D C4D HEM sing 191 n n 
C3D CAD HEM sing 192 n n 
C4D ND HEM sing 193 n n 
CMD HMD HEM sing 194 n n 
CMD HMDA HEM sing 195 n n 
CMD HMDB HEM sing 196 n n 
CAD CBD HEM sing 197 n n 
CAD HAD HEM sing 198 n n 
CAD HADA HEM sing 199 n n 
CBD CGD HEM sing 200 n n 
CBD HBD HEM sing 201 n n 
CBD HBDA HEM sing 202 n n 
CGD O1D HEM doub 203 n n 
CGD O2D HEM sing 204 n n 
O2A H2A HEM sing 205 n n 
O2D H2D HEM sing 206 n n 
FE NA HEM sing 207 n n 
FE NB HEM sing 208 n n 
FE NC HEM sing 209 n n 
FE ND HEM sing 210 n n 
#
_atom_sites.entry_id                     3L4D 
_atom_sites.fract_transf_matrix[1][1]    0.01178 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003117 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008438 
_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]    0.010246 
_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 HEM A 1 481 481 HEM HEM . 
F 3 TPF A 1 490 490 TPF TPF . 
G 2 HEM B 1 481 481 HEM HEM . 
H 3 TPF B 1 490 490 TPF TPF . 
I 2 HEM C 1 481 481 HEM HEM . 
J 3 TPF C 1 490 490 TPF TPF . 
K 4 N8E C 1 1 1 N8E N8E . 
L 2 HEM D 1 481 481 HEM HEM . 
M 3 TPF D 1 490 490 TPF TPF . 
N 5 HOH A 1 3 3 HOH HOH . 
N 5 HOH A 2 4 4 HOH HOH . 
N 5 HOH A 3 8 8 HOH HOH . 
N 5 HOH A 4 15 15 HOH HOH . 
N 5 HOH A 5 18 18 HOH HOH . 
N 5 HOH A 6 20 20 HOH HOH . 
N 5 HOH A 7 21 21 HOH HOH . 
N 5 HOH A 8 22 22 HOH HOH . 
N 5 HOH A 9 482 482 HOH HOH . 
N 5 HOH A 10 483 483 HOH HOH . 
N 5 HOH A 11 484 484 HOH HOH . 
N 5 HOH A 12 485 485 HOH HOH . 
N 5 HOH A 13 486 486 HOH HOH . 
N 5 HOH A 14 487 487 HOH HOH . 
N 5 HOH A 15 488 488 HOH HOH . 
N 5 HOH A 16 489 489 HOH HOH . 
O 5 HOH B 1 1 1 HOH HOH . 
O 5 HOH B 2 5 5 HOH HOH . 
O 5 HOH B 3 6 6 HOH HOH . 
O 5 HOH B 4 9 9 HOH HOH . 
O 5 HOH B 5 11 11 HOH HOH . 
O 5 HOH B 6 19 19 HOH HOH . 
O 5 HOH B 7 482 482 HOH HOH . 
O 5 HOH B 8 483 483 HOH HOH . 
O 5 HOH B 9 484 484 HOH HOH . 
O 5 HOH B 10 485 485 HOH HOH . 
O 5 HOH B 11 486 486 HOH HOH . 
P 5 HOH C 1 2 2 HOH HOH . 
P 5 HOH C 2 7 7 HOH HOH . 
P 5 HOH C 3 12 12 HOH HOH . 
P 5 HOH C 4 16 16 HOH HOH . 
P 5 HOH C 5 17 17 HOH HOH . 
P 5 HOH C 6 26 26 HOH HOH . 
P 5 HOH C 7 27 27 HOH HOH . 
P 5 HOH C 8 482 482 HOH HOH . 
P 5 HOH C 9 483 483 HOH HOH . 
P 5 HOH C 10 484 484 HOH HOH . 
P 5 HOH C 11 485 485 HOH HOH . 
P 5 HOH C 12 486 486 HOH HOH . 
P 5 HOH C 13 487 487 HOH HOH . 
P 5 HOH C 14 488 488 HOH HOH . 
P 5 HOH C 15 489 489 HOH HOH . 
P 5 HOH C 16 491 491 HOH HOH . 
Q 5 HOH D 1 10 10 HOH HOH . 
Q 5 HOH D 2 13 13 HOH HOH . 
Q 5 HOH D 3 14 14 HOH HOH . 
Q 5 HOH D 4 23 23 HOH HOH . 
Q 5 HOH D 5 24 24 HOH HOH . 
Q 5 HOH D 6 25 25 HOH HOH . 
Q 5 HOH D 7 482 482 HOH HOH . 
Q 5 HOH D 8 483 483 HOH HOH . 
Q 5 HOH D 9 484 484 HOH HOH . 
Q 5 HOH D 10 485 485 HOH HOH . 
Q 5 HOH D 11 486 486 HOH HOH . 
Q 5 HOH D 12 487 487 HOH HOH . 
Q 5 HOH D 13 488 488 HOH HOH . 
Q 5 HOH D 14 489 489 HOH HOH . 
Q 5 HOH D 15 491 491 HOH HOH . 
Q 5 HOH D 16 492 492 HOH HOH . 
Q 5 HOH D 17 493 493 HOH HOH . 
Q 5 HOH D 18 494 494 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 2 8.504 -44.161 -34.019 1 64.11 ? CHA HEM 481 D 1 
HETATM 2 C CHB HEM . . . L 2 10.612 -47.835 -36.378 1 58.14 ? CHB HEM 481 D 1 
HETATM 3 C CHC HEM . . . L 2 8.742 -46.096 -40.504 1 57.63 ? CHC HEM 481 D 1 
HETATM 4 C CHD HEM . . . L 2 7.691 -41.918 -38.29 1 58.01 ? CHD HEM 481 D 1 
HETATM 5 C C1A HEM . . . L 2 9.195 -45.322 -34.278 1 61.77 ? C1A HEM 481 D 1 
HETATM 6 C C2A HEM . . . L 2 9.784 -46.205 -33.291 1 61.63 ? C2A HEM 481 D 1 
HETATM 7 C C3A HEM . . . L 2 10.366 -47.217 -33.938 1 61 ? C3A HEM 481 D 1 
HETATM 8 C C4A HEM . . . L 2 10.167 -47.018 -35.361 1 60.84 ? C4A HEM 481 D 1 
HETATM 9 C CMA HEM . . . L 2 11.12 -48.393 -33.281 1 60.36 ? CMA HEM 481 D 1 
HETATM 10 C CAA HEM . . . L 2 9.754 -46.006 -31.759 1 58.55 ? CAA HEM 481 D 1 
HETATM 11 C CBA HEM . . . L 2 10.938 -45.126 -31.371 1 59.55 ? CBA HEM 481 D 1 
HETATM 12 C CGA HEM . . . L 2 11.088 -45.053 -29.874 1 62.21 ? CGA HEM 481 D 1 
HETATM 13 O O1A HEM . . . L 2 10.658 -46.005 -29.173 1 60.69 ? O1A HEM 481 D 1 
HETATM 14 O O2A HEM . . . L 2 11.645 -44.037 -29.381 1 64.75 ? O2A HEM 481 D 1 
HETATM 15 C C1B HEM . . . L 2 10.242 -47.721 -37.7 1 59.2 ? C1B HEM 481 D 1 
HETATM 16 C C2B HEM . . . L 2 10.481 -48.69 -38.754 1 59.73 ? C2B HEM 481 D 1 
HETATM 17 C C3B HEM . . . L 2 9.964 -48.206 -39.885 1 56.65 ? C3B HEM 481 D 1 
HETATM 18 C C4B HEM . . . L 2 9.377 -46.915 -39.597 1 56.49 ? C4B HEM 481 D 1 
HETATM 19 C CMB HEM . . . L 2 11.206 -50.047 -38.601 1 58.2 ? CMB HEM 481 D 1 
HETATM 20 C CAB HEM . . . L 2 9.988 -48.897 -41.264 1 52.26 ? CAB HEM 481 D 1 
HETATM 21 C CBB HEM . . . L 2 9.163 -49.916 -41.516 1 52.26 ? CBB HEM 481 D 1 
HETATM 22 C C1C HEM . . . L 2 8.293 -44.815 -40.269 1 56.32 ? C1C HEM 481 D 1 
HETATM 23 C C2C HEM . . . L 2 7.673 -43.937 -41.24 1 54.5 ? C2C HEM 481 D 1 
HETATM 24 C C3C HEM . . . L 2 7.383 -42.785 -40.632 1 54.26 ? C3C HEM 481 D 1 
HETATM 25 C C4C HEM . . . L 2 7.807 -42.891 -39.253 1 53.6 ? C4C HEM 481 D 1 
HETATM 26 C CMC HEM . . . L 2 7.399 -44.278 -42.72 1 51.41 ? CMC HEM 481 D 1 
HETATM 27 C CAC HEM . . . L 2 6.714 -41.553 -41.279 1 54.08 ? CAC HEM 481 D 1 
HETATM 28 C CBC HEM . . . L 2 6.626 -41.464 -42.611 1 55.68 ? CBC HEM 481 D 1 
HETATM 29 C C1D HEM . . . L 2 7.762 -42.129 -36.934 1 60.1 ? C1D HEM 481 D 1 
HETATM 30 C C2D HEM . . . L 2 7.39 -41.169 -35.921 1 61.92 ? C2D HEM 481 D 1 
HETATM 31 C C3D HEM . . . L 2 7.645 -41.876 -34.584 1 64.82 ? C3D HEM 481 D 1 
HETATM 32 C C4D HEM . . . L 2 8.146 -43.189 -34.928 1 63.65 ? C4D HEM 481 D 1 
HETATM 33 C CMD HEM . . . L 2 6.851 -39.74 -36.143 1 63.09 ? CMD HEM 481 D 1 
HETATM 34 C CAD HEM . . . L 2 7.423 -41.305 -33.166 1 64.55 ? CAD HEM 481 D 1 
HETATM 35 C CBD HEM . . . L 2 5.999 -41.573 -32.692 1 62.05 ? CBD HEM 481 D 1 
HETATM 36 C CGD HEM . . . L 2 5.826 -40.93 -31.341 1 60.91 ? CGD HEM 481 D 1 
HETATM 37 O O1D HEM . . . L 2 6.815 -40.333 -30.839 1 60.19 ? O1D HEM 481 D 1 
HETATM 38 O O2D HEM . . . L 2 4.709 -41.013 -30.767 1 57.72 ? O2D HEM 481 D 1 
HETATM 39 N NA HEM . . . L 2 9.449 -45.848 -35.528 1 60.73 ? NA HEM 481 D 1 
HETATM 40 N NB HEM . . . L 2 9.568 -46.649 -38.256 1 57.1 ? NB HEM 481 D 1 
HETATM 41 N NC HEM . . . L 2 8.36 -44.14 -39.066 1 54.51 ? NC HEM 481 D 1 
HETATM 42 N ND HEM . . . L 2 8.202 -43.296 -36.315 1 61.21 ? ND HEM 481 D 1 
HETATM 43 FE FE HEM . . . L 2 8.936 -44.97 -37.299 1 58.76 ? FE HEM 481 D 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#