data_3VP5
#
_model_server_result.job_id            jtJV-O_bW1skQwDhf0r2NQ 
_model_server_result.datetime_utc      '2024-11-05 00:55:59' 
_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          3vp5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    3VP5 
#
_exptl.entry_id    3VP5 
_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    1 
_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            3VP5 
_cell.length_a            48.14 
_cell.length_b            51.998 
_cell.length_c            87.477 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VP5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        17 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 2 2 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
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' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 43.7385 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 72 A HIS 72 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc2 A NE2 HIS 149 A HIS 149 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
#
_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 139 n n 
CHA C4D HEM doub 140 n n 
CHA HHA HEM sing 141 n n 
CHB C4A HEM sing 142 n n 
CHB C1B HEM doub 143 n n 
CHB HHB HEM sing 144 n n 
CHC C4B HEM sing 145 n n 
CHC C1C HEM doub 146 n n 
CHC HHC HEM sing 147 n n 
CHD C4C HEM doub 148 n n 
CHD C1D HEM sing 149 n n 
CHD HHD HEM sing 150 n n 
C1A C2A HEM doub 151 n y 
C1A NA HEM sing 152 n y 
C2A C3A HEM sing 153 n y 
C2A CAA HEM sing 154 n n 
C3A C4A HEM doub 155 n y 
C3A CMA HEM sing 156 n n 
C4A NA HEM sing 157 n y 
CMA HMA HEM sing 158 n n 
CMA HMAA HEM sing 159 n n 
CMA HMAB HEM sing 160 n n 
CAA CBA HEM sing 161 n n 
CAA HAA HEM sing 162 n n 
CAA HAAA HEM sing 163 n n 
CBA CGA HEM sing 164 n n 
CBA HBA HEM sing 165 n n 
CBA HBAA HEM sing 166 n n 
CGA O1A HEM doub 167 n n 
CGA O2A HEM sing 168 n n 
C1B C2B HEM sing 169 n n 
C1B NB HEM sing 170 n n 
C2B C3B HEM doub 171 n n 
C2B CMB HEM sing 172 n n 
C3B C4B HEM sing 173 n n 
C3B CAB HEM sing 174 n n 
C4B NB HEM doub 175 n n 
CMB HMB HEM sing 176 n n 
CMB HMBA HEM sing 177 n n 
CMB HMBB HEM sing 178 n n 
CAB CBB HEM doub 179 n n 
CAB HAB HEM sing 180 n n 
CBB HBB HEM sing 181 n n 
CBB HBBA HEM sing 182 n n 
C1C C2C HEM sing 183 n y 
C1C NC HEM sing 184 n y 
C2C C3C HEM doub 185 n y 
C2C CMC HEM sing 186 n n 
C3C C4C HEM sing 187 n y 
C3C CAC HEM sing 188 n n 
C4C NC HEM sing 189 n y 
CMC HMC HEM sing 190 n n 
CMC HMCA HEM sing 191 n n 
CMC HMCB HEM sing 192 n n 
CAC CBC HEM doub 193 n n 
CAC HAC HEM sing 194 n n 
CBC HBC HEM sing 195 n n 
CBC HBCA HEM sing 196 n n 
C1D C2D HEM sing 197 n n 
C1D ND HEM doub 198 n n 
C2D C3D HEM doub 199 n n 
C2D CMD HEM sing 200 n n 
C3D C4D HEM sing 201 n n 
C3D CAD HEM sing 202 n n 
C4D ND HEM sing 203 n n 
CMD HMD HEM sing 204 n n 
CMD HMDA HEM sing 205 n n 
CMD HMDB HEM sing 206 n n 
CAD CBD HEM sing 207 n n 
CAD HAD HEM sing 208 n n 
CAD HADA HEM sing 209 n n 
CBD CGD HEM sing 210 n n 
CBD HBD HEM sing 211 n n 
CBD HBDA HEM sing 212 n n 
CGD O1D HEM doub 213 n n 
CGD O2D HEM sing 214 n n 
O2A H2A HEM sing 215 n n 
O2D H2D HEM sing 216 n n 
FE NA HEM sing 217 n n 
FE NB HEM sing 218 n n 
FE NC HEM sing 219 n n 
FE ND HEM sing 220 n n 
#
_atom_sites.entry_id                     3VP5 
_atom_sites.fract_transf_matrix[1][1]    0.020773 
_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]    0.019232 
_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]    0.011432 
_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
B 2 HEM A 1 201 201 HEM HEM . 
C 3 CAC A 1 202 202 CAC CAC . 
D 4 HOH A 1 301 301 HOH HOH . 
D 4 HOH A 2 302 302 HOH HOH . 
D 4 HOH A 3 303 303 HOH HOH . 
D 4 HOH A 4 304 304 HOH HOH . 
D 4 HOH A 5 305 305 HOH HOH . 
D 4 HOH A 6 306 306 HOH HOH . 
D 4 HOH A 7 307 307 HOH HOH . 
D 4 HOH A 8 308 308 HOH HOH . 
D 4 HOH A 9 309 309 HOH HOH . 
D 4 HOH A 10 310 310 HOH HOH . 
D 4 HOH A 11 311 311 HOH HOH . 
D 4 HOH A 12 312 312 HOH HOH . 
D 4 HOH A 13 313 313 HOH HOH . 
D 4 HOH A 14 314 314 HOH HOH . 
D 4 HOH A 15 315 315 HOH HOH . 
D 4 HOH A 16 316 316 HOH HOH . 
D 4 HOH A 17 317 317 HOH HOH . 
D 4 HOH A 18 318 318 HOH HOH . 
D 4 HOH A 19 319 319 HOH HOH . 
D 4 HOH A 20 320 320 HOH HOH . 
D 4 HOH A 21 321 321 HOH HOH . 
D 4 HOH A 22 322 322 HOH HOH . 
D 4 HOH A 23 323 323 HOH HOH . 
D 4 HOH A 24 324 324 HOH HOH . 
D 4 HOH A 25 325 325 HOH HOH . 
D 4 HOH A 26 326 326 HOH HOH . 
D 4 HOH A 27 327 327 HOH HOH . 
D 4 HOH A 28 328 328 HOH HOH . 
D 4 HOH A 29 329 329 HOH HOH . 
D 4 HOH A 30 330 330 HOH HOH . 
D 4 HOH A 31 331 331 HOH HOH . 
D 4 HOH A 32 332 332 HOH HOH . 
D 4 HOH A 33 333 333 HOH HOH . 
D 4 HOH A 34 334 334 HOH HOH . 
D 4 HOH A 35 335 335 HOH HOH . 
D 4 HOH A 36 336 336 HOH HOH . 
D 4 HOH A 37 337 337 HOH HOH . 
D 4 HOH A 38 338 338 HOH HOH . 
D 4 HOH A 39 339 339 HOH HOH . 
D 4 HOH A 40 340 340 HOH HOH . 
D 4 HOH A 41 341 341 HOH HOH . 
D 4 HOH A 42 342 342 HOH HOH . 
D 4 HOH A 43 343 343 HOH HOH . 
D 4 HOH A 44 344 344 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 . . . B 2 9.91 12.266 23.539 1 39.63 ? CHA HEM 201 A 1 
HETATM 2 C CHB HEM . . . B 2 9.653 7.501 24.32 1 33.89 ? CHB HEM 201 A 1 
HETATM 3 C CHC HEM . . . B 2 7.868 8.157 28.768 1 29.91 ? CHC HEM 201 A 1 
HETATM 4 C CHD HEM . . . B 2 8.257 12.915 28.066 1 35.16 ? CHD HEM 201 A 1 
HETATM 5 C C1A HEM . . . B 2 9.986 10.896 23.394 1 35.08 ? C1A HEM 201 A 1 
HETATM 6 C C2A HEM . . . B 2 10.503 10.254 22.219 1 42.91 ? C2A HEM 201 A 1 
HETATM 7 C C3A HEM . . . B 2 10.426 8.919 22.42 1 44.83 ? C3A HEM 201 A 1 
HETATM 8 C C4A HEM . . . B 2 9.872 8.71 23.738 1 35.49 ? C4A HEM 201 A 1 
HETATM 9 C CMA HEM . . . B 2 10.882 7.819 21.438 1 43.95 ? CMA HEM 201 A 1 
HETATM 10 C CAA HEM . . . B 2 11.032 10.987 20.969 1 53.77 ? CAA HEM 201 A 1 
HETATM 11 C CBA HEM . . . B 2 9.948 10.924 19.894 1 72.01 ? CBA HEM 201 A 1 
HETATM 12 C CGA HEM . . . B 2 10.573 10.899 18.522 1 84.18 ? CGA HEM 201 A 1 
HETATM 13 O O1A HEM . . . B 2 11.602 11.61 18.337 1 86.75 ? O1A HEM 201 A 1 
HETATM 14 O O2A HEM . . . B 2 10.035 10.179 17.628 1 87.96 ? O2A HEM 201 A 1 
HETATM 15 C C1B HEM . . . B 2 9.182 7.275 25.569 1 31.41 ? C1B HEM 201 A 1 
HETATM 16 C C2B HEM . . . B 2 9.034 5.953 26.178 1 33.69 ? C2B HEM 201 A 1 
HETATM 17 C C3B HEM . . . B 2 8.535 6.133 27.417 1 31.31 ? C3B HEM 201 A 1 
HETATM 18 C C4B HEM . . . B 2 8.359 7.576 27.613 1 31.66 ? C4B HEM 201 A 1 
HETATM 19 C CMB HEM . . . B 2 9.45 4.672 25.41 1 35.77 ? CMB HEM 201 A 1 
HETATM 20 C CAB HEM . . . B 2 8.19 5.128 28.551 1 44.06 ? CAB HEM 201 A 1 
HETATM 21 C CBB HEM . . . B 2 8.207 3.809 28.347 1 46.32 ? CBB HEM 201 A 1 
HETATM 22 C C1C HEM . . . B 2 7.852 9.511 29.002 1 30.04 ? C1C HEM 201 A 1 
HETATM 23 C C2C HEM . . . B 2 7.423 10.183 30.203 1 34.28 ? C2C HEM 201 A 1 
HETATM 24 C C3C HEM . . . B 2 7.555 11.52 30.001 1 40.3 ? C3C HEM 201 A 1 
HETATM 25 C C4C HEM . . . B 2 8.035 11.695 28.643 1 38.87 ? C4C HEM 201 A 1 
HETATM 26 C CMC HEM . . . B 2 6.964 9.433 31.477 1 33.44 ? CMC HEM 201 A 1 
HETATM 27 C CAC HEM . . . B 2 7.249 12.756 30.913 1 38.2 ? CAC HEM 201 A 1 
HETATM 28 C CBC HEM . . . B 2 6.479 12.706 32.003 1 38.79 ? CBC HEM 201 A 1 
HETATM 29 C C1D HEM . . . B 2 8.725 13.178 26.815 1 34.52 ? C1D HEM 201 A 1 
HETATM 30 C C2D HEM . . . B 2 8.933 14.52 26.291 1 41.42 ? C2D HEM 201 A 1 
HETATM 31 C C3D HEM . . . B 2 9.45 14.352 24.855 1 41.17 ? C3D HEM 201 A 1 
HETATM 32 C C4D HEM . . . B 2 9.512 12.915 24.673 1 38.26 ? C4D HEM 201 A 1 
HETATM 33 C CMD HEM . . . B 2 8.638 15.812 27.071 1 39.7 ? CMD HEM 201 A 1 
HETATM 34 C CAD HEM . . . B 2 9.843 15.49 23.856 1 44.63 ? CAD HEM 201 A 1 
HETATM 35 C CBD HEM . . . B 2 9.136 15.401 22.514 1 66.17 ? CBD HEM 201 A 1 
HETATM 36 C CGD HEM . . . B 2 7.729 14.881 22.676 1 79.95 ? CGD HEM 201 A 1 
HETATM 37 O O1D HEM . . . B 2 6.938 15.497 23.446 1 83.42 ? O1D HEM 201 A 1 
HETATM 38 O O2D HEM . . . B 2 7.397 13.855 22.017 1 85.67 ? O2D HEM 201 A 1 
HETATM 39 N NA HEM . . . B 2 9.606 9.941 24.318 1 38.94 ? NA HEM 201 A 1 
HETATM 40 N NB HEM . . . B 2 8.748 8.193 26.449 1 30.26 ? NB HEM 201 A 1 
HETATM 41 N NC HEM . . . B 2 8.218 10.443 28.042 1 32.52 ? NC HEM 201 A 1 
HETATM 42 N ND HEM . . . B 2 9.079 12.274 25.826 1 39.55 ? ND HEM 201 A 1 
HETATM 43 FE FE HEM . . . B 2 8.892 10.233 26.265 1 35.3 ? FE HEM 201 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#