data_4ZVB
#
_model_server_result.job_id            5CSX7zC3GD8fa4pgatiuwA 
_model_server_result.datetime_utc      '2024-11-14 20:12:34' 
_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          4zvb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":201}' 
#
_entry.id    4ZVB 
#
_exptl.entry_id    4ZVB 
_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         79.52 
_cell.angle_beta          75.69 
_cell.angle_gamma         75.29 
_cell.entry_id            4ZVB 
_cell.length_a            47.96 
_cell.length_b            58.27 
_cell.length_c            59.4 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4ZVB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,I,J 1 1 
C,D,G,H,K,L 2 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 F N N 
? 2 G N N 
? 2 H 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 98 A HIS 98 1_555 E FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc2 B NE2 HIS 98 B HIS 98 1_555 F FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc3 C NE2 HIS 98 C HIS 98 1_555 G FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc4 D NE2 HIS 98 D HIS 98 1_555 H FE HEM . D HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
#
_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                     4ZVB 
_atom_sites.fract_transf_matrix[1][1]    0.020851 
_atom_sites.fract_transf_matrix[1][2]    -0.005473 
_atom_sites.fract_transf_matrix[1][3]    -0.00466 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017743 
_atom_sites.fract_transf_matrix[2][3]    -0.002274 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.017516 
_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 1 201 1 HEM HEM . 
F 2 HEM B 1 201 1 HEM HEM . 
G 2 HEM C 1 201 1 HEM HEM . 
H 2 HEM D 1 201 1 HEM HEM . 
I 3 HOH A 1 301 2 HOH HOH . 
I 3 HOH A 2 302 34 HOH HOH . 
I 3 HOH A 3 303 38 HOH HOH . 
I 3 HOH A 4 304 17 HOH HOH . 
I 3 HOH A 5 305 19 HOH HOH . 
I 3 HOH A 6 306 30 HOH HOH . 
I 3 HOH A 7 307 40 HOH HOH . 
I 3 HOH A 8 308 5 HOH HOH . 
I 3 HOH A 9 309 70 HOH HOH . 
I 3 HOH A 10 310 42 HOH HOH . 
I 3 HOH A 11 311 15 HOH HOH . 
I 3 HOH A 12 312 16 HOH HOH . 
I 3 HOH A 13 313 75 HOH HOH . 
I 3 HOH A 14 314 13 HOH HOH . 
I 3 HOH A 15 315 55 HOH HOH . 
I 3 HOH A 16 316 62 HOH HOH . 
I 3 HOH A 17 317 81 HOH HOH . 
I 3 HOH A 18 318 92 HOH HOH . 
J 3 HOH B 1 301 35 HOH HOH . 
J 3 HOH B 2 302 77 HOH HOH . 
J 3 HOH B 3 303 67 HOH HOH . 
J 3 HOH B 4 304 31 HOH HOH . 
J 3 HOH B 5 305 26 HOH HOH . 
J 3 HOH B 6 306 43 HOH HOH . 
J 3 HOH B 7 307 7 HOH HOH . 
J 3 HOH B 8 308 87 HOH HOH . 
J 3 HOH B 9 309 63 HOH HOH . 
J 3 HOH B 10 310 58 HOH HOH . 
J 3 HOH B 11 311 25 HOH HOH . 
J 3 HOH B 12 312 39 HOH HOH . 
J 3 HOH B 13 313 11 HOH HOH . 
J 3 HOH B 14 314 82 HOH HOH . 
J 3 HOH B 15 315 72 HOH HOH . 
J 3 HOH B 16 316 69 HOH HOH . 
J 3 HOH B 17 317 51 HOH HOH . 
K 3 HOH C 1 301 49 HOH HOH . 
K 3 HOH C 2 302 57 HOH HOH . 
K 3 HOH C 3 303 76 HOH HOH . 
K 3 HOH C 4 304 8 HOH HOH . 
K 3 HOH C 5 305 60 HOH HOH . 
K 3 HOH C 6 306 45 HOH HOH . 
K 3 HOH C 7 307 28 HOH HOH . 
K 3 HOH C 8 308 3 HOH HOH . 
K 3 HOH C 9 309 1 HOH HOH . 
K 3 HOH C 10 310 52 HOH HOH . 
K 3 HOH C 11 311 24 HOH HOH . 
K 3 HOH C 12 312 47 HOH HOH . 
K 3 HOH C 13 313 53 HOH HOH . 
K 3 HOH C 14 314 83 HOH HOH . 
K 3 HOH C 15 315 68 HOH HOH . 
K 3 HOH C 16 316 10 HOH HOH . 
K 3 HOH C 17 317 36 HOH HOH . 
K 3 HOH C 18 318 4 HOH HOH . 
K 3 HOH C 19 319 12 HOH HOH . 
K 3 HOH C 20 320 29 HOH HOH . 
K 3 HOH C 21 321 14 HOH HOH . 
K 3 HOH C 22 322 54 HOH HOH . 
K 3 HOH C 23 323 85 HOH HOH . 
K 3 HOH C 24 324 64 HOH HOH . 
L 3 HOH D 1 301 41 HOH HOH . 
L 3 HOH D 2 302 23 HOH HOH . 
L 3 HOH D 3 303 6 HOH HOH . 
L 3 HOH D 4 304 37 HOH HOH . 
L 3 HOH D 5 305 44 HOH HOH . 
L 3 HOH D 6 306 27 HOH HOH . 
L 3 HOH D 7 307 9 HOH HOH . 
L 3 HOH D 8 308 91 HOH HOH . 
L 3 HOH D 9 309 50 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 2 -12.43 21.017 -8.018 1 40.83 ? CHA HEM 201 B 1 
HETATM 2 C CHB HEM . . . F 2 -9.298 24.189 -9.94 1 40.12 ? CHB HEM 201 B 1 
HETATM 3 C CHC HEM . . . F 2 -5.817 22.269 -7.182 1 36.93 ? CHC HEM 201 B 1 
HETATM 4 C CHD HEM . . . F 2 -9.168 20.016 -4.503 1 35.76 ? CHD HEM 201 B 1 
HETATM 5 C C1A HEM . . . F 2 -11.91 22.048 -8.772 1 39.93 ? C1A HEM 201 B 1 
HETATM 6 C C2A HEM . . . F 2 -12.637 22.905 -9.688 1 48.77 ? C2A HEM 201 B 1 
HETATM 7 C C3A HEM . . . F 2 -11.768 23.775 -10.218 1 45.55 ? C3A HEM 201 B 1 
HETATM 8 C C4A HEM . . . F 2 -10.462 23.508 -9.654 1 38.65 ? C4A HEM 201 B 1 
HETATM 9 C CMA HEM . . . F 2 -12.08 24.881 -11.249 1 47.14 ? CMA HEM 201 B 1 
HETATM 10 C CAA HEM . . . F 2 -14.148 22.809 -9.999 1 43.73 ? CAA HEM 201 B 1 
HETATM 11 C CBA HEM . . . F 2 -14.915 23.929 -9.302 1 44.75 ? CBA HEM 201 B 1 
HETATM 12 C CGA HEM . . . F 2 -16.324 23.967 -9.833 1 57.98 ? CGA HEM 201 B 1 
HETATM 13 O O1A HEM . . . F 2 -16.669 23.108 -10.684 1 70.76 ? O1A HEM 201 B 1 
HETATM 14 O O2A HEM . . . F 2 -17.103 24.858 -9.408 1 60.84 ? O2A HEM 201 B 1 
HETATM 15 C C1B HEM . . . F 2 -8.076 23.967 -9.346 1 36.59 ? C1B HEM 201 B 1 
HETATM 16 C C2B HEM . . . F 2 -6.863 24.732 -9.567 1 40.82 ? C2B HEM 201 B 1 
HETATM 17 C C3B HEM . . . F 2 -5.892 24.198 -8.8 1 37.6 ? C3B HEM 201 B 1 
HETATM 18 C C4B HEM . . . F 2 -6.473 23.084 -8.078 1 35.27 ? C4B HEM 201 B 1 
HETATM 19 C CMB HEM . . . F 2 -6.783 25.937 -10.534 1 35.99 ? CMB HEM 201 B 1 
HETATM 20 C CAB HEM . . . F 2 -4.404 24.604 -8.632 1 39.31 ? CAB HEM 201 B 1 
HETATM 21 C CBB HEM . . . F 2 -3.815 25.631 -9.253 1 42.93 ? CBB HEM 201 B 1 
HETATM 22 C C1C HEM . . . F 2 -6.424 21.595 -6.146 1 35.12 ? C1C HEM 201 B 1 
HETATM 23 C C2C HEM . . . F 2 -5.795 21.186 -4.906 1 34.88 ? C2C HEM 201 B 1 
HETATM 24 C C3C HEM . . . F 2 -6.725 20.558 -4.16 1 33.72 ? C3C HEM 201 B 1 
HETATM 25 C C4C HEM . . . F 2 -7.967 20.558 -4.912 1 38.18 ? C4C HEM 201 B 1 
HETATM 26 C CMC HEM . . . F 2 -4.307 21.463 -4.584 1 25.69 ? CMC HEM 201 B 1 
HETATM 27 C CAC HEM . . . F 2 -6.604 19.921 -2.75 1 32.98 ? CAC HEM 201 B 1 
HETATM 28 C CBC HEM . . . F 2 -5.491 19.924 -2.008 1 35.02 ? CBC HEM 201 B 1 
HETATM 29 C C1D HEM . . . F 2 -10.373 20.076 -5.175 1 37.52 ? C1D HEM 201 B 1 
HETATM 30 C C2D HEM . . . F 2 -11.633 19.548 -4.693 1 44.99 ? C2D HEM 201 B 1 
HETATM 31 C C3D HEM . . . F 2 -12.659 19.864 -5.796 1 42.35 ? C3D HEM 201 B 1 
HETATM 32 C C4D HEM . . . F 2 -11.911 20.545 -6.83 1 44.2 ? C4D HEM 201 B 1 
HETATM 33 C CMD HEM . . . F 2 -11.875 18.83 -3.346 1 37.03 ? CMD HEM 201 B 1 
HETATM 34 C CAD HEM . . . F 2 -14.17 19.534 -5.83 1 41.31 ? CAD HEM 201 B 1 
HETATM 35 C CBD HEM . . . F 2 -14.402 18.032 -5.693 1 51.6 ? CBD HEM 201 B 1 
HETATM 36 C CGD HEM . . . F 2 -15.858 17.719 -5.927 1 53.54 ? CGD HEM 201 B 1 
HETATM 37 O O1D HEM . . . F 2 -16.284 16.576 -5.621 1 45.52 ? O1D HEM 201 B 1 
HETATM 38 O O2D HEM . . . F 2 -16.595 18.614 -6.417 1 48.24 ? O2D HEM 201 B 1 
HETATM 39 N NA HEM . . . F 2 -10.587 22.448 -8.777 1 40.89 ? NA HEM 201 B 1 
HETATM 40 N NB HEM . . . F 2 -7.801 22.971 -8.433 1 41.42 ? NB HEM 201 B 1 
HETATM 41 N NC HEM . . . F 2 -7.744 21.197 -6.115 1 41.17 ? NC HEM 201 B 1 
HETATM 42 N ND HEM . . . F 2 -10.582 20.648 -6.427 1 41.89 ? ND HEM 201 B 1 
HETATM 43 FE FE HEM . . . F 2 -9.16 21.696 -7.51 1 39.41 ? FE HEM 201 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           221 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           43 
#