data_5BV5
#
_model_server_result.job_id            2DbBIbaAa8Okp9l5QROb5w 
_model_server_result.datetime_utc      '2024-11-28 12:07:28' 
_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          5bv5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":500}' 
#
_entry.id    5BV5 
#
_exptl.entry_id    5BV5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_entity.src_method                  man 
_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          101.18 
_cell.angle_gamma         90 
_cell.entry_id            5BV5 
_cell.length_a            64.486 
_cell.length_b            137.871 
_cell.length_c            91.779 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5BV5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
PISA tetrameric 4 software_defined_assembly 5 
PISA tetrameric 4 software_defined_assembly 6 
PISA dimeric 2 software_defined_assembly 7 
PISA dimeric 2 software_defined_assembly 8 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,N 1 1 
B,G,H,I,O 2 1 
C,J,K,P 3 1 
D,L,M,Q 4 1 
B,C,G,H,I,J,K,O,P 5 1 
A,D,E,F,L,M,N,Q 5 2 
B,G,H,I,O 6 1 
D,L,M,Q 6 2 
A,E,F,N 6 4 
C,J,K,P 6 5 
A,E,F,N 7 1 
C,J,K,P 7 3 
B,G,H,I,O 8 1 
D,L,M,Q 8 2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 1_454 x-1,y,z-1 1 0 0 0 1 0 0 0 1 -46.690793 0 -90.0373 
3 'crystal symmetry operation' 1_656 x+1,y,z+1 1 0 0 0 1 0 0 0 1 46.690793 0 90.0373 
4 'crystal symmetry operation' 2_444 -x-1,y-1/2,-z-1 -1 0 0 0 1 0 0 0 -1 -46.690793 -68.9355 -90.0373 
5 'crystal symmetry operation' 2_343 -x-2,y-1/2,-z-2 -1 0 0 0 1 0 0 0 -1 -93.381587 -68.9355 -180.074601 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 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 NE2 HIS 317 A HIS 317 1_555 F FE HEM . A HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? 
metalc ? metalc2 F FE HEM . A HEM 602 1_555 N O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc3 B NE2 HIS 317 B HIS 317 1_555 H FE HEM . B HEM 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.873 ? 
metalc ? metalc4 H FE HEM . B HEM 602 1_555 I N3 PIM . B PIM 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? 
metalc ? metalc5 C NE2 HIS 317 D HIS 317 1_555 J FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? 
metalc ? metalc6 J FE HEM . D HEM 500 1_555 K N3 PIM . D PIM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
metalc ? metalc7 D NE2 HIS 317 C HIS 317 1_555 L FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? 
metalc ? metalc8 L FE HEM . C HEM 500 1_555 M N3 PIM . C PIM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? 
#
_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                     5BV5 
_atom_sites.fract_transf_matrix[1][1]    0.015507 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003064 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007253 
_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]    0.011106 
_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 PO4 A 1 601 2 PO4 PO4 . 
F 3 HEM A 1 602 500 HEM HEM . 
G 2 PO4 B 1 601 1 PO4 PO4 . 
H 3 HEM B 1 602 500 HEM HEM . 
I 4 PIM B 1 603 501 PIM PIM . 
J 3 HEM D 1 500 500 HEM HEM . 
K 4 PIM D 1 501 501 PIM PIM . 
L 3 HEM C 1 500 500 HEM HEM . 
M 4 PIM C 1 501 501 PIM PIM . 
N 5 HOH A 1 701 9 HOH HOH . 
N 5 HOH A 2 702 1 HOH HOH . 
O 5 HOH B 1 701 4 HOH HOH . 
O 5 HOH B 2 702 11 HOH HOH . 
O 5 HOH B 3 703 5 HOH HOH . 
P 5 HOH D 1 601 10 HOH HOH . 
P 5 HOH D 2 602 7 HOH HOH . 
P 5 HOH D 3 603 2 HOH HOH . 
Q 5 HOH C 1 601 3 HOH HOH . 
Q 5 HOH C 2 602 8 HOH HOH . 
Q 5 HOH C 3 603 6 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 -7.38 -59.672 0.739 1 51.12 ? CHA HEM 500 C 1 
HETATM 2 C CHB HEM . . . L 3 -12.026 -58.414 0.309 1 47.97 ? CHB HEM 500 C 1 
HETATM 3 C CHC HEM . . . L 3 -12.73 -59.436 5.024 1 48.26 ? CHC HEM 500 C 1 
HETATM 4 C CHD HEM . . . L 3 -8.032 -60.481 5.479 1 50.78 ? CHD HEM 500 C 1 
HETATM 5 C C1A HEM . . . L 3 -8.591 -59.271 0.227 1 50.6 ? C1A HEM 500 C 1 
HETATM 6 C C2A HEM . . . L 3 -8.796 -58.919 -1.123 1 50.26 ? C2A HEM 500 C 1 
HETATM 7 C C3A HEM . . . L 3 -10.1 -58.564 -1.251 1 49.47 ? C3A HEM 500 C 1 
HETATM 8 C C4A HEM . . . L 3 -10.704 -58.687 0.021 1 49.21 ? C4A HEM 500 C 1 
HETATM 9 C CMA HEM . . . L 3 -10.776 -58.125 -2.526 1 49.44 ? CMA HEM 500 C 1 
HETATM 10 C CAA HEM . . . L 3 -7.757 -58.957 -2.219 1 50.8 ? CAA HEM 500 C 1 
HETATM 11 C CBA HEM . . . L 3 -7.538 -60.41 -2.654 1 52.29 ? CBA HEM 500 C 1 
HETATM 12 C CGA HEM . . . L 3 -6.843 -60.473 -3.993 1 52.46 ? CGA HEM 500 C 1 
HETATM 13 O O1A HEM . . . L 3 -5.85 -59.745 -4.222 1 52.54 ? O1A HEM 500 C 1 
HETATM 14 O O2A HEM . . . L 3 -7.25 -61.26 -4.879 1 51.69 ? O2A HEM 500 C 1 
HETATM 15 C C1B HEM . . . L 3 -12.593 -58.606 1.577 1 47.22 ? C1B HEM 500 C 1 
HETATM 16 C C2B HEM . . . L 3 -13.981 -58.395 1.818 1 46.37 ? C2B HEM 500 C 1 
HETATM 17 C C3B HEM . . . L 3 -14.21 -58.676 3.138 1 46.35 ? C3B HEM 500 C 1 
HETATM 18 C C4B HEM . . . L 3 -12.889 -59.074 3.687 1 47.41 ? C4B HEM 500 C 1 
HETATM 19 C CMB HEM . . . L 3 -14.997 -57.938 0.801 1 46.85 ? CMB HEM 500 C 1 
HETATM 20 C CAB HEM . . . L 3 -15.464 -58.63 3.928 1 45.61 ? CAB HEM 500 C 1 
HETATM 21 C CBB HEM . . . L 3 -16.661 -58.304 3.442 1 45.62 ? CBB HEM 500 C 1 
HETATM 22 C C1C HEM . . . L 3 -11.519 -59.819 5.582 1 49.37 ? C1C HEM 500 C 1 
HETATM 23 C C2C HEM . . . L 3 -11.313 -60.24 6.909 1 49.36 ? C2C HEM 500 C 1 
HETATM 24 C C3C HEM . . . L 3 -9.96 -60.537 7.042 1 49.99 ? C3C HEM 500 C 1 
HETATM 25 C C4C HEM . . . L 3 -9.362 -60.292 5.77 1 50.2 ? C4C HEM 500 C 1 
HETATM 26 C CMC HEM . . . L 3 -12.388 -60.332 7.967 1 49.59 ? CMC HEM 500 C 1 
HETATM 27 C CAC HEM . . . L 3 -9.211 -61.032 8.223 1 51.38 ? CAC HEM 500 C 1 
HETATM 28 C CBC HEM . . . L 3 -9.76 -61.332 9.399 1 52.36 ? CBC HEM 500 C 1 
HETATM 29 C C1D HEM . . . L 3 -7.509 -60.34 4.192 1 51.34 ? C1D HEM 500 C 1 
HETATM 30 C C2D HEM . . . L 3 -6.096 -60.641 3.917 1 52.86 ? C2D HEM 500 C 1 
HETATM 31 C C3D HEM . . . L 3 -5.915 -60.416 2.603 1 54.24 ? C3D HEM 500 C 1 
HETATM 32 C C4D HEM . . . L 3 -7.22 -59.986 2.083 1 51.73 ? C4D HEM 500 C 1 
HETATM 33 C CMD HEM . . . L 3 -5.042 -61.102 4.892 1 53.38 ? CMD HEM 500 C 1 
HETATM 34 C CAD HEM . . . L 3 -4.632 -60.571 1.823 1 57.04 ? CAD HEM 500 C 1 
HETATM 35 C CBD HEM . . . L 3 -4.823 -61.578 0.684 1 60.94 ? CBD HEM 500 C 1 
HETATM 36 C CGD HEM . . . L 3 -3.855 -62.723 0.808 1 64.09 ? CGD HEM 500 C 1 
HETATM 37 O O1D HEM . . . L 3 -3.098 -63.005 -0.149 1 66.15 ? O1D HEM 500 C 1 
HETATM 38 O O2D HEM . . . L 3 -3.806 -63.393 1.864 1 67.74 ? O2D HEM 500 C 1 
HETATM 39 N NA HEM . . . L 3 -9.762 -59.095 0.929 1 49.78 ? NA HEM 500 C 1 
HETATM 40 N NB HEM . . . L 3 -11.984 -59.021 2.698 1 47.39 ? NB HEM 500 C 1 
HETATM 41 N NC HEM . . . L 3 -10.33 -59.846 4.906 1 49.55 ? NC HEM 500 C 1 
HETATM 42 N ND HEM . . . L 3 -8.136 -59.967 3.065 1 50.42 ? ND HEM 500 C 1 
HETATM 43 FE FE HEM . . . L 3 -9.932 -59.465 2.882 1 49.6 ? FE HEM 500 C 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#