data_3R1A
#
_model_server_result.job_id            slGzXyLr-9VYv5y5F6tgYQ 
_model_server_result.datetime_utc      '2024-11-29 10:21:40' 
_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          3r1a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":500}' 
#
_entry.id    3R1A 
#
_exptl.entry_id    3R1A 
_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            3R1A 
_cell.length_a            134.381 
_cell.length_b            144.549 
_cell.length_c            229.275 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3R1A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
PISA monomeric 1 author_and_software_defined_assembly 5 
PISA monomeric 1 author_and_software_defined_assembly 6 
PISA monomeric 1 author_and_software_defined_assembly 7 
PISA monomeric 1 author_and_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,I,J,Y 1 1 
B,K,L,Z 2 1 
C,M,N,AA 3 1 
D,O,P,BA 4 1 
E,Q,R,CA 5 1 
F,S,T,DA 6 1 
G,U,V,EA 7 1 
H,W,X,FA 8 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 I N N 
? 2 K N N 
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 S N N 
? 2 U N N 
? 2 W 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
covale ? covale1 A OG1 THR 283 A THR 302 1_555 J C1 TB2 . A TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.27 ? 
covale ? covale2 B OG1 THR 283 B THR 302 1_555 L C1 TB2 . B TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale3 C OG1 THR 283 C THR 302 1_555 N C1 TB2 . C TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? 
covale ? covale4 D OG1 THR 283 D THR 302 1_555 P C1 TB2 . D TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale5 E OG1 THR 283 E THR 302 1_555 R C1 TB2 . E TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
covale ? covale6 F OG1 THR 283 F THR 302 1_555 T C1 TB2 . F TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 ? 
covale ? covale7 G OG1 THR 283 G THR 302 1_555 V C1 TB2 . G TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? 
covale ? covale8 H OG1 THR 283 H THR 302 1_555 X C1 TB2 . H TB2 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? 
metalc ? metalc1 A SG CYS 417 A CYS 436 1_555 I FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc2 B SG CYS 417 B CYS 436 1_555 K FE HEM . B HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? 
metalc ? metalc3 C SG CYS 417 C CYS 436 1_555 M FE HEM . C HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? 
metalc ? metalc4 D SG CYS 417 D CYS 436 1_555 O FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? 
metalc ? metalc5 CA O HOH . E HOH 5 1_555 Q FE HEM . E HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc6 E SG CYS 417 E CYS 436 1_555 Q FE HEM . E HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? 
metalc ? metalc7 F SG CYS 417 F CYS 436 1_555 S FE HEM . F HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc8 G SG CYS 417 G CYS 436 1_555 U FE HEM . G HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? 
#
_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                     3R1A 
_atom_sites.fract_transf_matrix[1][1]    0.007442 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006918 
_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]    0.004362 
_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 2 HEM A 1 500 500 HEM HEM . 
J 3 TB2 A 1 501 501 TB2 TB2 . 
K 2 HEM B 1 500 500 HEM HEM . 
L 3 TB2 B 1 501 501 TB2 TB2 . 
M 2 HEM C 1 500 500 HEM HEM . 
N 3 TB2 C 1 501 501 TB2 TB2 . 
O 2 HEM D 1 500 500 HEM HEM . 
P 3 TB2 D 1 501 501 TB2 TB2 . 
Q 2 HEM E 1 500 500 HEM HEM . 
R 3 TB2 E 1 501 501 TB2 TB2 . 
S 2 HEM F 1 500 500 HEM HEM . 
T 3 TB2 F 1 501 501 TB2 TB2 . 
U 2 HEM G 1 500 500 HEM HEM . 
V 3 TB2 G 1 501 501 TB2 TB2 . 
W 2 HEM H 1 500 500 HEM HEM . 
X 3 TB2 H 1 501 501 TB2 TB2 . 
Y 4 HOH A 1 1 1 HOH HOH . 
Z 4 HOH B 1 2 2 HOH HOH . 
AA 4 HOH C 1 4 4 HOH HOH . 
BA 4 HOH D 1 3 3 HOH HOH . 
CA 4 HOH E 1 5 5 HOH HOH . 
DA 4 HOH F 1 6 6 HOH HOH . 
EA 4 HOH G 1 7 7 HOH HOH . 
FA 4 HOH H 1 8 8 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 . . . M 2 -135.99 -10.553 -26.745 1 58.21 ? CHA HEM 500 C 1 
HETATM 2 C CHB HEM . . . M 2 -136.461 -13.789 -23.159 1 50.84 ? CHB HEM 500 C 1 
HETATM 3 C CHC HEM . . . M 2 -131.924 -12.868 -21.714 1 58.07 ? CHC HEM 500 C 1 
HETATM 4 C CHD HEM . . . M 2 -131.471 -9.514 -25.185 1 66.89 ? CHD HEM 500 C 1 
HETATM 5 C C1A HEM . . . M 2 -136.529 -11.453 -25.855 1 55.42 ? C1A HEM 500 C 1 
HETATM 6 C C2A HEM . . . M 2 -137.918 -11.854 -25.791 1 50.3 ? C2A HEM 500 C 1 
HETATM 7 C C3A HEM . . . M 2 -138.051 -12.746 -24.808 1 54.08 ? C3A HEM 500 C 1 
HETATM 8 C C4A HEM . . . M 2 -136.749 -12.944 -24.206 1 52.89 ? C4A HEM 500 C 1 
HETATM 9 C CMA HEM . . . M 2 -139.36 -13.444 -24.382 1 59.63 ? CMA HEM 500 C 1 
HETATM 10 C CAA HEM . . . M 2 -139.043 -11.345 -26.713 1 45.92 ? CAA HEM 500 C 1 
HETATM 11 C CBA HEM . . . M 2 -139.162 -12.328 -27.872 1 47.98 ? CBA HEM 500 C 1 
HETATM 12 C CGA HEM . . . M 2 -140.326 -11.96 -28.75 1 50.87 ? CGA HEM 500 C 1 
HETATM 13 O O1A HEM . . . M 2 -140.524 -10.749 -29.02 1 54.58 ? O1A HEM 500 C 1 
HETATM 14 O O2A HEM . . . M 2 -141.052 -12.887 -29.19 1 46.65 ? O2A HEM 500 C 1 
HETATM 15 C C1B HEM . . . M 2 -135.27 -13.838 -22.471 1 55.8 ? C1B HEM 500 C 1 
HETATM 16 C C2B HEM . . . M 2 -134.969 -14.712 -21.356 1 57.87 ? C2B HEM 500 C 1 
HETATM 17 C C3B HEM . . . M 2 -133.717 -14.461 -20.956 1 54.43 ? C3B HEM 500 C 1 
HETATM 18 C C4B HEM . . . M 2 -133.186 -13.413 -21.807 1 52.16 ? C4B HEM 500 C 1 
HETATM 19 C CMB HEM . . . M 2 -135.95 -15.748 -20.763 1 61.3 ? CMB HEM 500 C 1 
HETATM 20 C CAB HEM . . . M 2 -132.942 -15.135 -19.797 1 53.47 ? CAB HEM 500 C 1 
HETATM 21 C CBB HEM . . . M 2 -133.496 -16.058 -19.002 1 50.42 ? CBB HEM 500 C 1 
HETATM 22 C C1C HEM . . . M 2 -131.386 -11.927 -22.562 1 64.04 ? C1C HEM 500 C 1 
HETATM 23 C C2C HEM . . . M 2 -130 -11.5 -22.594 1 64.63 ? C2C HEM 500 C 1 
HETATM 24 C C3C HEM . . . M 2 -129.878 -10.573 -23.555 1 65.65 ? C3C HEM 500 C 1 
HETATM 25 C C4C HEM . . . M 2 -131.183 -10.384 -24.158 1 65.07 ? C4C HEM 500 C 1 
HETATM 26 C CMC HEM . . . M 2 -128.889 -12.048 -21.67 1 60.92 ? CMC HEM 500 C 1 
HETATM 27 C CAC HEM . . . M 2 -128.603 -9.809 -23.987 1 69.31 ? CAC HEM 500 C 1 
HETATM 28 C CBC HEM . . . M 2 -127.418 -10 -23.396 1 72.89 ? CBC HEM 500 C 1 
HETATM 29 C C1D HEM . . . M 2 -132.63 -9.467 -25.926 1 65.53 ? C1D HEM 500 C 1 
HETATM 30 C C2D HEM . . . M 2 -132.866 -8.562 -27.026 1 64.05 ? C2D HEM 500 C 1 
HETATM 31 C C3D HEM . . . M 2 -134.277 -8.886 -27.52 1 56.56 ? C3D HEM 500 C 1 
HETATM 32 C C4D HEM . . . M 2 -134.754 -9.951 -26.663 1 55.4 ? C4D HEM 500 C 1 
HETATM 33 C CMD HEM . . . M 2 -131.902 -7.498 -27.593 1 55.93 ? CMD HEM 500 C 1 
HETATM 34 C CAD HEM . . . M 2 -135.007 -8.192 -28.686 1 56.01 ? CAD HEM 500 C 1 
HETATM 35 C CBD HEM . . . M 2 -135.524 -9.249 -29.651 1 56.8 ? CBD HEM 500 C 1 
HETATM 36 C CGD HEM . . . M 2 -136.241 -8.569 -30.783 1 62.08 ? CGD HEM 500 C 1 
HETATM 37 O O1D HEM . . . M 2 -136.043 -7.342 -30.984 1 59.53 ? O1D HEM 500 C 1 
HETATM 38 O O2D HEM . . . M 2 -137.01 -9.266 -31.487 1 67.28 ? O2D HEM 500 C 1 
HETATM 39 N NA HEM . . . M 2 -135.844 -12.136 -24.87 1 56.66 ? NA HEM 500 C 1 
HETATM 40 N NB HEM . . . M 2 -134.16 -13.055 -22.72 1 50.94 ? NB HEM 500 C 1 
HETATM 41 N NC HEM . . . M 2 -132.082 -11.223 -23.527 1 65.66 ? NC HEM 500 C 1 
HETATM 42 N ND HEM . . . M 2 -133.759 -10.262 -25.742 1 56.39 ? ND HEM 500 C 1 
HETATM 43 FE FE HEM . . . M 2 -134.051 -11.527 -24.114 1 52.5 ? FE HEM 500 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    54 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#