data_5NVI
#
_model_server_result.job_id            hSy6xEQFt8Ow0juZinlfVA 
_model_server_result.datetime_utc      '2024-11-01 08:17:30' 
_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          5nvi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    5NVI 
#
_exptl.entry_id    5NVI 
_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         120 
_cell.entry_id            5NVI 
_cell.length_a            89.198 
_cell.length_b            89.198 
_cell.length_c            115.348 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NVI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_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 62 A HIS 64 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc2 A NE2 HIS 94 A HIS 96 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
#
_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                     5NVI 
_atom_sites.fract_transf_matrix[1][1]    0.011211 
_atom_sites.fract_transf_matrix[1][2]    0.006473 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012945 
_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]    0.008669 
_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 SO4 A 1 202 202 SO4 SO4 . 
D 4 AR A 1 205 205 AR AR . 
E 5 HOH A 1 301 319 HOH HOH . 
E 5 HOH A 2 302 386 HOH HOH . 
E 5 HOH A 3 303 327 HOH HOH . 
E 5 HOH A 4 304 318 HOH HOH . 
E 5 HOH A 5 305 330 HOH HOH . 
E 5 HOH A 6 306 371 HOH HOH . 
E 5 HOH A 7 307 311 HOH HOH . 
E 5 HOH A 8 308 326 HOH HOH . 
E 5 HOH A 9 309 347 HOH HOH . 
E 5 HOH A 10 310 394 HOH HOH . 
E 5 HOH A 11 311 416 HOH HOH . 
E 5 HOH A 12 312 344 HOH HOH . 
E 5 HOH A 13 313 306 HOH HOH . 
E 5 HOH A 14 314 369 HOH HOH . 
E 5 HOH A 15 315 309 HOH HOH . 
E 5 HOH A 16 316 379 HOH HOH . 
E 5 HOH A 17 317 413 HOH HOH . 
E 5 HOH A 18 318 314 HOH HOH . 
E 5 HOH A 19 319 307 HOH HOH . 
E 5 HOH A 20 320 354 HOH HOH . 
E 5 HOH A 21 321 305 HOH HOH . 
E 5 HOH A 22 322 343 HOH HOH . 
E 5 HOH A 23 323 321 HOH HOH . 
E 5 HOH A 24 324 355 HOH HOH . 
E 5 HOH A 25 325 303 HOH HOH . 
E 5 HOH A 26 326 308 HOH HOH . 
E 5 HOH A 27 327 368 HOH HOH . 
E 5 HOH A 28 328 301 HOH HOH . 
E 5 HOH A 29 329 383 HOH HOH . 
E 5 HOH A 30 330 417 HOH HOH . 
E 5 HOH A 31 331 339 HOH HOH . 
E 5 HOH A 32 332 398 HOH HOH . 
E 5 HOH A 33 333 410 HOH HOH . 
E 5 HOH A 34 334 340 HOH HOH . 
E 5 HOH A 35 335 325 HOH HOH . 
E 5 HOH A 36 336 396 HOH HOH . 
E 5 HOH A 37 337 320 HOH HOH . 
E 5 HOH A 38 338 346 HOH HOH . 
E 5 HOH A 39 339 335 HOH HOH . 
E 5 HOH A 40 340 316 HOH HOH . 
E 5 HOH A 41 341 373 HOH HOH . 
E 5 HOH A 42 342 315 HOH HOH . 
E 5 HOH A 43 343 345 HOH HOH . 
E 5 HOH A 44 344 342 HOH HOH . 
E 5 HOH A 45 345 317 HOH HOH . 
E 5 HOH A 46 346 402 HOH HOH . 
E 5 HOH A 47 347 381 HOH HOH . 
E 5 HOH A 48 348 328 HOH HOH . 
E 5 HOH A 49 349 409 HOH HOH . 
E 5 HOH A 50 350 363 HOH HOH . 
E 5 HOH A 51 351 302 HOH HOH . 
E 5 HOH A 52 352 357 HOH HOH . 
E 5 HOH A 53 353 333 HOH HOH . 
E 5 HOH A 54 354 352 HOH HOH . 
E 5 HOH A 55 355 361 HOH HOH . 
E 5 HOH A 56 356 412 HOH HOH . 
E 5 HOH A 57 357 401 HOH HOH . 
E 5 HOH A 58 358 331 HOH HOH . 
E 5 HOH A 59 359 304 HOH HOH . 
E 5 HOH A 60 360 392 HOH HOH . 
E 5 HOH A 61 361 370 HOH HOH . 
E 5 HOH A 62 362 376 HOH HOH . 
E 5 HOH A 63 363 341 HOH HOH . 
E 5 HOH A 64 364 324 HOH HOH . 
E 5 HOH A 65 365 385 HOH HOH . 
E 5 HOH A 66 366 358 HOH HOH . 
E 5 HOH A 67 367 380 HOH HOH . 
E 5 HOH A 68 368 404 HOH HOH . 
E 5 HOH A 69 369 403 HOH HOH . 
E 5 HOH A 70 370 337 HOH HOH . 
E 5 HOH A 71 371 397 HOH HOH . 
E 5 HOH A 72 372 356 HOH HOH . 
E 5 HOH A 73 373 338 HOH HOH . 
E 5 HOH A 74 374 312 HOH HOH . 
E 5 HOH A 75 375 367 HOH HOH . 
E 5 HOH A 76 376 313 HOH HOH . 
E 5 HOH A 77 377 375 HOH HOH . 
E 5 HOH A 78 378 350 HOH HOH . 
E 5 HOH A 79 379 382 HOH HOH . 
E 5 HOH A 80 380 351 HOH HOH . 
E 5 HOH A 81 381 362 HOH HOH . 
E 5 HOH A 82 382 360 HOH HOH . 
E 5 HOH A 83 383 414 HOH HOH . 
E 5 HOH A 84 384 390 HOH HOH . 
E 5 HOH A 85 385 393 HOH HOH . 
E 5 HOH A 86 386 348 HOH HOH . 
E 5 HOH A 87 387 405 HOH HOH . 
E 5 HOH A 88 388 359 HOH HOH . 
E 5 HOH A 89 389 336 HOH HOH . 
E 5 HOH A 90 390 384 HOH HOH . 
E 5 HOH A 91 391 406 HOH HOH . 
E 5 HOH A 92 392 374 HOH HOH . 
E 5 HOH A 93 393 364 HOH HOH . 
E 5 HOH A 94 394 322 HOH HOH . 
E 5 HOH A 95 395 310 HOH HOH . 
E 5 HOH A 96 396 323 HOH HOH . 
E 5 HOH A 97 397 415 HOH HOH . 
E 5 HOH A 98 398 407 HOH HOH . 
E 5 HOH A 99 399 332 HOH HOH . 
E 5 HOH A 100 400 399 HOH HOH . 
E 5 HOH A 101 401 334 HOH HOH . 
E 5 HOH A 102 402 366 HOH HOH . 
E 5 HOH A 103 403 389 HOH HOH . 
E 5 HOH A 104 404 391 HOH HOH . 
E 5 HOH A 105 405 400 HOH HOH . 
E 5 HOH A 106 406 353 HOH HOH . 
E 5 HOH A 107 407 349 HOH HOH . 
E 5 HOH A 108 408 365 HOH HOH . 
E 5 HOH A 109 409 329 HOH HOH . 
E 5 HOH A 110 410 372 HOH HOH . 
E 5 HOH A 111 411 411 HOH HOH . 
E 5 HOH A 112 412 388 HOH HOH . 
E 5 HOH A 113 413 408 HOH HOH . 
E 5 HOH A 114 414 395 HOH HOH . 
E 5 HOH A 115 415 387 HOH HOH . 
E 5 HOH A 116 416 378 HOH HOH . 
E 5 HOH A 117 417 377 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 19.654 58.953 36.758 1 16.03 ? CHA HEM 201 A 1 
HETATM 2 C CHB HEM . . . B 2 15.249 58.087 34.972 1 17.81 ? CHB HEM 201 A 1 
HETATM 3 C CHC HEM . . . B 2 15.907 53.343 35.761 1 17.38 ? CHC HEM 201 A 1 
HETATM 4 C CHD HEM . . . B 2 20.497 54.158 36.86 1 16.73 ? CHD HEM 201 A 1 
HETATM 5 C C1A HEM . . . B 2 18.377 59.108 36.232 1 17.54 ? C1A HEM 201 A 1 
HETATM 6 C C2A HEM . . . B 2 17.818 60.334 35.893 1 17.53 ? C2A HEM 201 A 1 
HETATM 7 C C3A HEM . . . B 2 16.57 60.12 35.379 1 18.78 ? C3A HEM 201 A 1 
HETATM 8 C C4A HEM . . . B 2 16.386 58.724 35.395 1 16.92 ? C4A HEM 201 A 1 
HETATM 9 C CMA HEM . . . B 2 15.603 61.158 34.88 1 20.81 ? CMA HEM 201 A 1 
HETATM 10 C CAA HEM . . . B 2 18.468 61.693 36.031 1 20 ? CAA HEM 201 A 1 
HETATM 11 C CBA HEM . . . B 2 19.107 62.174 34.724 1 18.59 ? CBA HEM 201 A 1 
HETATM 12 C CGA HEM . . . B 2 20.214 61.305 34.206 1 21.6 ? CGA HEM 201 A 1 
HETATM 13 O O1A HEM . . . B 2 21.271 61.161 34.917 1 22.66 ? O1A HEM 201 A 1 
HETATM 14 O O2A HEM . . . B 2 20.12 60.751 33.088 1 20.59 ? O2A HEM 201 A 1 
HETATM 15 C C1B HEM . . . B 2 15.055 56.725 35.049 1 17.4 ? C1B HEM 201 A 1 
HETATM 16 C C2B HEM . . . B 2 13.822 56.088 34.748 1 18.56 ? C2B HEM 201 A 1 
HETATM 17 C C3B HEM . . . B 2 13.98 54.738 34.978 1 18.74 ? C3B HEM 201 A 1 
HETATM 18 C C4B HEM . . . B 2 15.353 54.543 35.425 1 18.11 ? C4B HEM 201 A 1 
HETATM 19 C CMB HEM . . . B 2 12.556 56.77 34.3 1 21.54 ? CMB HEM 201 A 1 
HETATM 20 C CAB HEM . . . B 2 13.009 53.59 34.841 1 22.36 ? CAB HEM 201 A 1 
HETATM 21 C CBB HEM . . . B 2 11.724 53.652 34.629 1 31.81 ? CBB HEM 201 A 1 
HETATM 22 C C1C HEM . . . B 2 17.207 53.109 36.12 1 17.6 ? C1C HEM 201 A 1 
HETATM 23 C C2C HEM . . . B 2 17.803 51.874 36.432 1 18.13 ? C2C HEM 201 A 1 
HETATM 24 C C3C HEM . . . B 2 19.121 52.099 36.744 1 18.7 ? C3C HEM 201 A 1 
HETATM 25 C C4C HEM . . . B 2 19.314 53.5 36.579 1 15.8 ? C4C HEM 201 A 1 
HETATM 26 C CMC HEM . . . B 2 17.055 50.538 36.369 1 20.02 ? CMC HEM 201 A 1 
HETATM 27 C CAC HEM . . . B 2 20.192 51.166 37.147 1 20.89 ? CAC HEM 201 A 1 
HETATM 28 C CBC HEM . . . B 2 20.014 49.908 37.463 1 27.5 ? CBC HEM 201 A 1 
HETATM 29 C C1D HEM . . . B 2 20.589 55.544 36.897 1 15.47 ? C1D HEM 201 A 1 
HETATM 30 C C2D HEM . . . B 2 21.834 56.207 37.337 1 16.8 ? C2D HEM 201 A 1 
HETATM 31 C C3D HEM . . . B 2 21.596 57.533 37.341 1 17.18 ? C3D HEM 201 A 1 
HETATM 32 C C4D HEM . . . B 2 20.215 57.705 36.919 1 16.65 ? C4D HEM 201 A 1 
HETATM 33 C CMD HEM . . . B 2 23.139 55.561 37.725 1 16.8 ? CMD HEM 201 A 1 
HETATM 34 C CAD HEM . . . B 2 22.587 58.618 37.749 1 20.35 ? CAD HEM 201 A 1 
HETATM 35 C CBD HEM . . . B 2 22.276 58.884 39.234 1 23.98 ? CBD HEM 201 A 1 
HETATM 36 C CGD HEM . . . B 2 23.035 60.046 39.894 1 27.87 ? CGD HEM 201 A 1 
HETATM 37 O O1D HEM . . . B 2 22.72 61.261 39.775 1 31.9 ? O1D HEM 201 A 1 
HETATM 38 O O2D HEM . . . B 2 23.996 59.727 40.575 1 25.98 ? O2D HEM 201 A 1 
HETATM 39 N NA HEM . . . B 2 17.487 58.085 35.908 1 17.46 ? NA HEM 201 A 1 
HETATM 40 N NB HEM . . . B 2 15.891 55.781 35.421 1 15.31 ? NB HEM 201 A 1 
HETATM 41 N NC HEM . . . B 2 18.148 54.111 36.247 1 18.32 ? NC HEM 201 A 1 
HETATM 42 N ND HEM . . . B 2 19.652 56.475 36.681 1 14.53 ? ND HEM 201 A 1 
HETATM 43 FE FE HEM . . . B 2 17.821 56.135 36.053 1 15.8 ? FE HEM 201 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#