data_5BV5
#
_model_server_result.job_id            qXPalObRrooYIDT4qCTn-Q 
_model_server_result.datetime_utc      '2024-11-28 12:10:04' 
_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":"F","auth_seq_id":602}' 
#
_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 . . . F 3 -25.361 -19.712 -3.369 1 50.65 ? CHA HEM 602 A 1 
HETATM 2 C CHB HEM . . . F 3 -23.102 -22.782 -6.355 1 46.13 ? CHB HEM 602 A 1 
HETATM 3 C CHC HEM . . . F 3 -19.264 -19.795 -6.521 1 45.69 ? CHC HEM 602 A 1 
HETATM 4 C CHD HEM . . . F 3 -21.54 -16.729 -3.559 1 47.73 ? CHD HEM 602 A 1 
HETATM 5 C C1A HEM . . . F 3 -25.067 -20.791 -4.163 1 49.35 ? C1A HEM 602 A 1 
HETATM 6 C C2A HEM . . . F 3 -25.944 -21.868 -4.407 1 50.09 ? C2A HEM 602 A 1 
HETATM 7 C C3A HEM . . . F 3 -25.316 -22.73 -5.246 1 48.53 ? C3A HEM 602 A 1 
HETATM 8 C C4A HEM . . . F 3 -24.041 -22.192 -5.525 1 47.62 ? C4A HEM 602 A 1 
HETATM 9 C CMA HEM . . . F 3 -25.895 -24.02 -5.776 1 47.97 ? CMA HEM 602 A 1 
HETATM 10 C CAA HEM . . . F 3 -27.339 -22.026 -3.856 1 51.2 ? CAA HEM 602 A 1 
HETATM 11 C CBA HEM . . . F 3 -28.292 -21.181 -4.708 1 52.12 ? CBA HEM 602 A 1 
HETATM 12 C CGA HEM . . . F 3 -29.721 -21.618 -4.515 1 53.71 ? CGA HEM 602 A 1 
HETATM 13 O O1A HEM . . . F 3 -30.045 -22.331 -3.538 1 55.76 ? O1A HEM 602 A 1 
HETATM 14 O O2A HEM . . . F 3 -30.59 -21.258 -5.342 1 54.66 ? O2A HEM 602 A 1 
HETATM 15 C C1B HEM . . . F 3 -21.856 -22.215 -6.66 1 44.77 ? C1B HEM 602 A 1 
HETATM 16 C C2B HEM . . . F 3 -20.902 -22.852 -7.505 1 44.14 ? C2B HEM 602 A 1 
HETATM 17 C C3B HEM . . . F 3 -19.806 -22.033 -7.571 1 43.42 ? C3B HEM 602 A 1 
HETATM 18 C C4B HEM . . . F 3 -20.142 -20.861 -6.724 1 44.68 ? C4B HEM 602 A 1 
HETATM 19 C CMB HEM . . . F 3 -21.088 -24.183 -8.191 1 44.01 ? CMB HEM 602 A 1 
HETATM 20 C CAB HEM . . . F 3 -18.529 -22.187 -8.309 1 42.77 ? CAB HEM 602 A 1 
HETATM 21 C CBB HEM . . . F 3 -18.244 -23.197 -9.128 1 42.77 ? CBB HEM 602 A 1 
HETATM 22 C C1C HEM . . . F 3 -19.542 -18.686 -5.726 1 45.7 ? C1C HEM 602 A 1 
HETATM 23 C C2C HEM . . . F 3 -18.716 -17.556 -5.602 1 45.28 ? C2C HEM 602 A 1 
HETATM 24 C C3C HEM . . . F 3 -19.363 -16.666 -4.75 1 46.11 ? C3C HEM 602 A 1 
HETATM 25 C C4C HEM . . . F 3 -20.592 -17.284 -4.374 1 46.68 ? C4C HEM 602 A 1 
HETATM 26 C CMC HEM . . . F 3 -17.377 -17.381 -6.279 1 45.29 ? CMC HEM 602 A 1 
HETATM 27 C CAC HEM . . . F 3 -18.937 -15.325 -4.283 1 46.23 ? CAC HEM 602 A 1 
HETATM 28 C CBC HEM . . . F 3 -17.812 -14.715 -4.65 1 46.64 ? CBC HEM 602 A 1 
HETATM 29 C C1D HEM . . . F 3 -22.761 -17.353 -3.313 1 49.74 ? C1D HEM 602 A 1 
HETATM 30 C C2D HEM . . . F 3 -23.726 -16.705 -2.418 1 53.07 ? C2D HEM 602 A 1 
HETATM 31 C C3D HEM . . . F 3 -24.789 -17.523 -2.357 1 54.96 ? C3D HEM 602 A 1 
HETATM 32 C C4D HEM . . . F 3 -24.458 -18.668 -3.221 1 51.88 ? C4D HEM 602 A 1 
HETATM 33 C CMD HEM . . . F 3 -23.556 -15.384 -1.704 1 53.92 ? CMD HEM 602 A 1 
HETATM 34 C CAD HEM . . . F 3 -26.05 -17.283 -1.558 1 59.05 ? CAD HEM 602 A 1 
HETATM 35 C CBD HEM . . . F 3 -26.848 -16.102 -2.132 1 62.82 ? CBD HEM 602 A 1 
HETATM 36 C CGD HEM . . . F 3 -27.134 -16.267 -3.607 1 67.56 ? CGD HEM 602 A 1 
HETATM 37 O O1D HEM . . . F 3 -27.555 -17.36 -4.052 1 69.83 ? O1D HEM 602 A 1 
HETATM 38 O O2D HEM . . . F 3 -26.96 -15.304 -4.392 1 70.16 ? O2D HEM 602 A 1 
HETATM 39 N NA HEM . . . F 3 -23.891 -21.016 -4.827 1 47.42 ? NA HEM 602 A 1 
HETATM 40 N NB HEM . . . F 3 -21.366 -21.053 -6.222 1 44.99 ? NB HEM 602 A 1 
HETATM 41 N NC HEM . . . F 3 -20.671 -18.515 -4.964 1 45.71 ? NC HEM 602 A 1 
HETATM 42 N ND HEM . . . F 3 -23.231 -18.528 -3.768 1 49.88 ? ND HEM 602 A 1 
HETATM 43 FE FE HEM . . . F 3 -22.388 -19.717 -4.965 1 47.03 ? FE HEM 602 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           239 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#