data_2RI4
#
_model_server_result.job_id            kzSQdQDODkibG-4zxwuw5g 
_model_server_result.datetime_utc      '2024-10-19 16:44:12' 
_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          2ri4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":147}' 
#
_entry.id    2RI4 
#
_exptl.entry_id    2RI4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         110.64 
_cell.angle_beta          91.9 
_cell.angle_gamma         108.94 
_cell.entry_id            2RI4 
_cell.length_a            52.692 
_cell.length_b            68.325 
_cell.length_c            95.597 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2RI4 
_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
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_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,C,D,I,J,K,L,Q,R,S,T 1 1 
E,F,G,H,M,N,O,P,U,V,W,X 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
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P 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 I FE HEM . A HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc2 B NE2 HIS 91 B HIS 92 1_555 J FE HEM . B HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc3 C NE2 HIS 87 C HIS 87 1_555 K FE HEM . C HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc4 K FE HEM . C HEM 142 1_555 S O HOH . C HOH 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc5 D NE2 HIS 91 D HIS 92 1_555 L FE HEM . D HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc6 L FE HEM . D HEM 147 1_555 T O HOH . D HOH 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? 
metalc ? metalc7 E NE2 HIS 87 I HIS 87 1_555 M FE HEM . I HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc8 M FE HEM . I HEM 142 1_555 U O HOH . I HOH 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.587 ? 
metalc ? metalc9 F NE2 HIS 91 J HIS 92 1_555 N FE HEM . J HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc10 N FE HEM . J HEM 147 1_555 V O HOH . J HOH 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc11 G NE2 HIS 87 K HIS 87 1_555 O FE HEM . K HEM 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc12 H NE2 HIS 91 L HIS 92 1_555 P FE HEM . L HEM 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? 
#
_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                     2RI4 
_atom_sites.fract_transf_matrix[1][1]    0.018978 
_atom_sites.fract_transf_matrix[1][2]    0.006513 
_atom_sites.fract_transf_matrix[1][3]    0.003391 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015474 
_atom_sites.fract_transf_matrix[2][3]    0.006441 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011337 
_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
I 3 HEM A 1 142 142 HEM HEM . 
J 3 HEM B 1 147 147 HEM HEM . 
K 3 HEM C 1 142 142 HEM HEM . 
L 3 HEM D 1 147 147 HEM HEM . 
M 3 HEM I 1 142 142 HEM HEM . 
N 3 HEM J 1 147 147 HEM HEM . 
O 3 HEM K 1 142 142 HEM HEM . 
P 3 HEM L 1 147 147 HEM HEM . 
Q 4 HOH A 1 143 3 HOH HOH . 
Q 4 HOH A 2 144 13 HOH HOH . 
Q 4 HOH A 3 145 24 HOH HOH . 
Q 4 HOH A 4 146 41 HOH HOH . 
Q 4 HOH A 5 147 49 HOH HOH . 
R 4 HOH B 1 148 1 HOH HOH . 
R 4 HOH B 2 149 25 HOH HOH . 
R 4 HOH B 3 150 28 HOH HOH . 
R 4 HOH B 4 151 31 HOH HOH . 
R 4 HOH B 5 152 37 HOH HOH . 
R 4 HOH B 6 153 50 HOH HOH . 
S 4 HOH C 1 143 5 HOH HOH . 
S 4 HOH C 2 144 7 HOH HOH . 
S 4 HOH C 3 145 9 HOH HOH . 
S 4 HOH C 4 146 32 HOH HOH . 
S 4 HOH C 5 147 46 HOH HOH . 
T 4 HOH D 1 148 8 HOH HOH . 
T 4 HOH D 2 149 10 HOH HOH . 
T 4 HOH D 3 150 16 HOH HOH . 
T 4 HOH D 4 151 35 HOH HOH . 
T 4 HOH D 5 152 36 HOH HOH . 
T 4 HOH D 6 153 43 HOH HOH . 
T 4 HOH D 7 154 47 HOH HOH . 
T 4 HOH D 8 155 51 HOH HOH . 
U 4 HOH I 1 143 2 HOH HOH . 
U 4 HOH I 2 144 6 HOH HOH . 
U 4 HOH I 3 145 11 HOH HOH . 
U 4 HOH I 4 146 15 HOH HOH . 
U 4 HOH I 5 147 18 HOH HOH . 
U 4 HOH I 6 148 19 HOH HOH . 
U 4 HOH I 7 149 29 HOH HOH . 
U 4 HOH I 8 150 34 HOH HOH . 
U 4 HOH I 9 151 38 HOH HOH . 
V 4 HOH J 1 148 12 HOH HOH . 
V 4 HOH J 2 149 17 HOH HOH . 
V 4 HOH J 3 150 22 HOH HOH . 
V 4 HOH J 4 151 23 HOH HOH . 
V 4 HOH J 5 152 26 HOH HOH . 
V 4 HOH J 6 153 48 HOH HOH . 
W 4 HOH K 1 143 14 HOH HOH . 
W 4 HOH K 2 144 27 HOH HOH . 
W 4 HOH K 3 145 30 HOH HOH . 
W 4 HOH K 4 146 39 HOH HOH . 
W 4 HOH K 5 147 40 HOH HOH . 
W 4 HOH K 6 148 42 HOH HOH . 
W 4 HOH K 7 149 44 HOH HOH . 
X 4 HOH L 1 148 4 HOH HOH . 
X 4 HOH L 2 149 20 HOH HOH . 
X 4 HOH L 3 150 21 HOH HOH . 
X 4 HOH L 4 151 33 HOH HOH . 
X 4 HOH L 5 152 45 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 . . . P 3 10.477 -5.027 32.381 1 38.91 ? CHA HEM 147 L 1 
HETATM 2 C CHB HEM . . . P 3 10.434 -4.806 37.258 1 40.62 ? CHB HEM 147 L 1 
HETATM 3 C CHC HEM . . . P 3 14.075 -8.066 37.461 1 42.95 ? CHC HEM 147 L 1 
HETATM 4 C CHD HEM . . . P 3 14.5 -7.643 32.632 1 39.78 ? CHD HEM 147 L 1 
HETATM 5 C C1A HEM . . . P 3 10.158 -4.73 33.689 1 40.55 ? C1A HEM 147 L 1 
HETATM 6 C C2A HEM . . . P 3 9.068 -3.851 34.088 1 39.85 ? C2A HEM 147 L 1 
HETATM 7 C C3A HEM . . . P 3 9.038 -3.79 35.419 1 42.22 ? C3A HEM 147 L 1 
HETATM 8 C C4A HEM . . . P 3 10.128 -4.625 35.927 1 42.35 ? C4A HEM 147 L 1 
HETATM 9 C CMA HEM . . . P 3 8.039 -2.964 36.275 1 40.21 ? CMA HEM 147 L 1 
HETATM 10 C CAA HEM . . . P 3 8.107 -3.113 33.148 1 38.54 ? CAA HEM 147 L 1 
HETATM 11 C CBA HEM . . . P 3 7.023 -4.069 32.647 1 37.79 ? CBA HEM 147 L 1 
HETATM 12 C CGA HEM . . . P 3 5.764 -3.29 32.359 1 35.86 ? CGA HEM 147 L 1 
HETATM 13 O O1A HEM . . . P 3 4.841 -3.874 31.745 1 35.42 ? O1A HEM 147 L 1 
HETATM 14 O O2A HEM . . . P 3 5.692 -2.091 32.754 1 34.58 ? O2A HEM 147 L 1 
HETATM 15 C C1B HEM . . . P 3 11.413 -5.636 37.74 1 40.93 ? C1B HEM 147 L 1 
HETATM 16 C C2B HEM . . . P 3 11.738 -5.838 39.136 1 40.6 ? C2B HEM 147 L 1 
HETATM 17 C C3B HEM . . . P 3 12.739 -6.735 39.199 1 41.01 ? C3B HEM 147 L 1 
HETATM 18 C C4B HEM . . . P 3 13.091 -7.146 37.845 1 42.72 ? C4B HEM 147 L 1 
HETATM 19 C CMB HEM . . . P 3 11.031 -5.139 40.323 1 38.84 ? CMB HEM 147 L 1 
HETATM 20 C CAB HEM . . . P 3 13.416 -7.256 40.484 1 41.5 ? CAB HEM 147 L 1 
HETATM 21 C CBB HEM . . . P 3 13.901 -6.421 41.414 1 40.5 ? CBB HEM 147 L 1 
HETATM 22 C C1C HEM . . . P 3 14.576 -8.197 36.173 1 42.6 ? C1C HEM 147 L 1 
HETATM 23 C C2C HEM . . . P 3 15.82 -8.821 35.728 1 42.25 ? C2C HEM 147 L 1 
HETATM 24 C C3C HEM . . . P 3 15.91 -8.68 34.396 1 43.07 ? C3C HEM 147 L 1 
HETATM 25 C C4C HEM . . . P 3 14.744 -7.963 33.946 1 42.25 ? C4C HEM 147 L 1 
HETATM 26 C CMC HEM . . . P 3 16.872 -9.519 36.608 1 40.7 ? CMC HEM 147 L 1 
HETATM 27 C CAC HEM . . . P 3 17.041 -9.178 33.462 1 43.68 ? CAC HEM 147 L 1 
HETATM 28 C CBC HEM . . . P 3 18.32 -9.072 33.852 1 43.93 ? CBC HEM 147 L 1 
HETATM 29 C C1D HEM . . . P 3 13.472 -6.899 32.113 1 38.59 ? C1D HEM 147 L 1 
HETATM 30 C C2D HEM . . . P 3 13.333 -6.61 30.708 1 39.05 ? C2D HEM 147 L 1 
HETATM 31 C C3D HEM . . . P 3 12.063 -5.776 30.576 1 39.36 ? C3D HEM 147 L 1 
HETATM 32 C C4D HEM . . . P 3 11.588 -5.661 31.946 1 37.32 ? C4D HEM 147 L 1 
HETATM 33 C CMD HEM . . . P 3 14.266 -7.033 29.539 1 38.47 ? CMD HEM 147 L 1 
HETATM 34 C CAD HEM . . . P 3 11.588 -5.276 29.17 1 43.03 ? CAD HEM 147 L 1 
HETATM 35 C CBD HEM . . . P 3 10.425 -4.286 29.036 1 48.34 ? CBD HEM 147 L 1 
HETATM 36 C CGD HEM . . . P 3 9.308 -4.876 28.178 1 51.62 ? CGD HEM 147 L 1 
HETATM 37 O O1D HEM . . . P 3 9.614 -5.43 27.078 1 53.86 ? O1D HEM 147 L 1 
HETATM 38 O O2D HEM . . . P 3 8.1 -4.806 28.578 1 51.97 ? O2D HEM 147 L 1 
HETATM 39 N NA HEM . . . P 3 10.794 -5.19 34.84 1 41.45 ? NA HEM 147 L 1 
HETATM 40 N NB HEM . . . P 3 12.245 -6.448 36.992 1 41.5 ? NB HEM 147 L 1 
HETATM 41 N NC HEM . . . P 3 13.959 -7.687 35.051 1 41.96 ? NC HEM 147 L 1 
HETATM 42 N ND HEM . . . P 3 12.425 -6.324 32.817 1 38.38 ? ND HEM 147 L 1 
HETATM 43 FE FE HEM . . . P 3 12.25 -6.734 35.128 1 43.64 ? FE HEM 147 L 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           43 
#