data_5X2T
#
_model_server_result.job_id            UuBO-jfHQJItGS7BM8PgJw 
_model_server_result.datetime_utc      '2024-11-27 19:58:01' 
_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          5x2t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":201}' 
#
_entry.id    5X2T 
#
_exptl.entry_id    5X2T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          103.38 
_cell.angle_gamma         90 
_cell.entry_id            5X2T 
_cell.length_a            228.494 
_cell.length_b            55.024 
_cell.length_c            138.504 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5X2T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 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
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_defined_assembly 2 
? tetrameric 4 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,M,N,O,P 1 1 
E,F,G,H,Q,R,S,T 2 1 
I,J,K,L,U,V,W,X,Y 3 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
? 4 N N N 
? 4 O N N 
? 4 R N N 
? 4 S N N 
? 4 W N N 
? 4 X 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 M NI HNI . A HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc2 B NE2 HIS 92 B HIS 92 1_555 N FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? 
metalc ? metalc3 C NE2 HIS 87 C HIS 87 1_555 O FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc4 D NE2 HIS 92 D HIS 92 1_555 P NI HNI . D HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc5 E NE2 HIS 87 E HIS 87 1_555 Q NI HNI . E HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? 
metalc ? metalc6 F NE2 HIS 92 F HIS 92 1_555 R FE HEM . F HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc7 G NE2 HIS 87 G HIS 87 1_555 S FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? 
metalc ? metalc8 H NE2 HIS 92 H HIS 92 1_555 T NI HNI . H HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc9 J NE2 HIS 92 J HIS 92 1_555 W FE HEM . J HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
#
_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                     5X2T 
_atom_sites.fract_transf_matrix[1][1]    0.004376 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001041 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018174 
_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]    0.007421 
_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
M 3 HNI A 1 201 142 HNI HNI . 
N 4 HEM B 1 201 147 HEM HEM . 
O 4 HEM C 1 201 142 HEM HEM . 
P 3 HNI D 1 201 147 HNI HNI . 
Q 3 HNI E 1 201 142 HNI HNI . 
R 4 HEM F 1 201 147 HEM HEM . 
S 4 HEM G 1 201 142 HEM HEM . 
T 3 HNI H 1 201 147 HNI HNI . 
U 3 HNI I 1 201 142 HNI HNI . 
V 5 PEM I 1 202 1 PEM PEM . 
W 4 HEM J 1 201 147 HEM HEM . 
X 4 HEM K 1 201 142 HEM HEM . 
Y 3 HNI L 1 201 147 HNI HNI . 
#
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 . . . W 4 29.087 -20.275 90.424 1 63.8 ? CHA HEM 201 J 1 
HETATM 2 C CHB HEM . . . W 4 27.1 -20.684 86.086 1 61.61 ? CHB HEM 201 J 1 
HETATM 3 C CHC HEM . . . W 4 26.379 -16.018 86.016 1 59.72 ? CHC HEM 201 J 1 
HETATM 4 C CHD HEM . . . W 4 28.143 -15.541 90.43 1 62.2 ? CHD HEM 201 J 1 
HETATM 5 C C1A HEM . . . W 4 28.647 -20.8 89.247 1 62.94 ? C1A HEM 201 J 1 
HETATM 6 C C2A HEM . . . W 4 28.793 -22.182 88.82 1 63.99 ? C2A HEM 201 J 1 
HETATM 7 C C3A HEM . . . W 4 28.207 -22.285 87.601 1 63.37 ? C3A HEM 201 J 1 
HETATM 8 C C4A HEM . . . W 4 27.729 -20.982 87.26 1 61.85 ? C4A HEM 201 J 1 
HETATM 9 C CMA HEM . . . W 4 28.142 -23.532 86.755 1 65.18 ? CMA HEM 201 J 1 
HETATM 10 C CAA HEM . . . W 4 29.477 -23.332 89.539 1 66.67 ? CAA HEM 201 J 1 
HETATM 11 C CBA HEM . . . W 4 28.963 -23.537 90.968 1 69.18 ? CBA HEM 201 J 1 
HETATM 12 C CGA HEM . . . W 4 28.967 -24.984 91.45 1 72.01 ? CGA HEM 201 J 1 
HETATM 13 O O1A HEM . . . W 4 28.027 -25.721 91.233 1 74.01 ? O1A HEM 201 J 1 
HETATM 14 O O2A HEM . . . W 4 30.02 -25.467 92.147 1 73.65 ? O2A HEM 201 J 1 
HETATM 15 C C1B HEM . . . W 4 26.672 -19.425 85.744 1 60.4 ? C1B HEM 201 J 1 
HETATM 16 C C2B HEM . . . W 4 26.084 -19.146 84.448 1 60.06 ? C2B HEM 201 J 1 
HETATM 17 C C3B HEM . . . W 4 25.894 -17.811 84.374 1 59.69 ? C3B HEM 201 J 1 
HETATM 18 C C4B HEM . . . W 4 26.382 -17.321 85.702 1 59.47 ? C4B HEM 201 J 1 
HETATM 19 C CMB HEM . . . W 4 25.777 -20.138 83.342 1 62.01 ? CMB HEM 201 J 1 
HETATM 20 C CAB HEM . . . W 4 25.337 -17.041 83.222 1 60.24 ? CAB HEM 201 J 1 
HETATM 21 C CBB HEM . . . W 4 24.341 -16.143 83.273 1 56.72 ? CBB HEM 201 J 1 
HETATM 22 C C1C HEM . . . W 4 26.803 -15.514 87.193 1 59.41 ? C1C HEM 201 J 1 
HETATM 23 C C2C HEM . . . W 4 26.771 -14.138 87.473 1 59.94 ? C2C HEM 201 J 1 
HETATM 24 C C3C HEM . . . W 4 27.229 -13.973 88.756 1 60.62 ? C3C HEM 201 J 1 
HETATM 25 C C4C HEM . . . W 4 27.577 -15.289 89.211 1 60.7 ? C4C HEM 201 J 1 
HETATM 26 C CMC HEM . . . W 4 26.318 -13.093 86.487 1 60.88 ? CMC HEM 201 J 1 
HETATM 27 C CAC HEM . . . W 4 27.445 -12.725 89.535 1 61.92 ? CAC HEM 201 J 1 
HETATM 28 C CBC HEM . . . W 4 27.735 -11.529 89.033 1 63.66 ? CBC HEM 201 J 1 
HETATM 29 C C1D HEM . . . W 4 28.501 -16.824 90.785 1 62.31 ? C1D HEM 201 J 1 
HETATM 30 C C2D HEM . . . W 4 29.24 -17.093 92.032 1 63.73 ? C2D HEM 201 J 1 
HETATM 31 C C3D HEM . . . W 4 29.507 -18.386 92.021 1 64.26 ? C3D HEM 201 J 1 
HETATM 32 C C4D HEM . . . W 4 28.941 -18.941 90.766 1 63.05 ? C4D HEM 201 J 1 
HETATM 33 C CMD HEM . . . W 4 29.624 -16.109 93.083 1 65.94 ? CMD HEM 201 J 1 
HETATM 34 C CAD HEM . . . W 4 30.305 -19.179 93.012 1 66.47 ? CAD HEM 201 J 1 
HETATM 35 C CBD HEM . . . W 4 31.807 -18.909 92.707 1 67.62 ? CBD HEM 201 J 1 
HETATM 36 C CGD HEM . . . W 4 32.72 -19.398 93.826 1 70.57 ? CGD HEM 201 J 1 
HETATM 37 O O1D HEM . . . W 4 32.976 -20.599 93.98 1 71.92 ? O1D HEM 201 J 1 
HETATM 38 O O2D HEM . . . W 4 33.233 -18.459 94.654 1 72.08 ? O2D HEM 201 J 1 
HETATM 39 N NA HEM . . . W 4 27.985 -20.044 88.278 1 61.86 ? NA HEM 201 J 1 
HETATM 40 N NB HEM . . . W 4 26.816 -18.321 86.503 1 59.83 ? NB HEM 201 J 1 
HETATM 41 N NC HEM . . . W 4 27.289 -16.252 88.239 1 60.12 ? NC HEM 201 J 1 
HETATM 42 N ND HEM . . . W 4 28.346 -17.955 90.04 1 61.87 ? ND HEM 201 J 1 
HETATM 43 FE FE HEM . . . W 4 27.477 -18.17 88.33 1 60.77 ? FE HEM 201 J 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#