data_3VRA
#
_model_server_result.job_id            sGlpLySNFRT4MIx_76QLfQ 
_model_server_result.datetime_utc      '2024-11-24 13:44:17' 
_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          3vra 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":201}' 
#
_entry.id    3VRA 
#
_exptl.entry_id    3VRA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          10 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_entity.pdbx_number_of_molecules    2 
_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            3VRA 
_cell.length_a            122.823 
_cell.length_b            132.25 
_cell.length_c            220.577 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VRA 
_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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_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,M,N,O,P 1 1 
E,F,G,H,Q,R,S,T,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
? 10 N N N 
? 10 V 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 NE2 HIS 79 A HIS 79 1_555 J C8M FAD . A FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.666 ? 
covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? 
metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc6 B SG CYS 188 B CYS 188 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc7 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc8 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc9 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc10 B SG CYS 249 B CYS 249 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc11 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc12 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc13 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc14 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc15 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc16 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc17 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc18 F SG CYS 188 F CYS 188 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc19 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? 
metalc ? metalc20 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc21 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc22 F SG CYS 249 F CYS 249 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
metalc ? metalc23 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc24 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
#
_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 393 n n 
CHA C4D HEM doub 394 n n 
CHA HHA HEM sing 395 n n 
CHB C4A HEM sing 396 n n 
CHB C1B HEM doub 397 n n 
CHB HHB HEM sing 398 n n 
CHC C4B HEM sing 399 n n 
CHC C1C HEM doub 400 n n 
CHC HHC HEM sing 401 n n 
CHD C4C HEM doub 402 n n 
CHD C1D HEM sing 403 n n 
CHD HHD HEM sing 404 n n 
C1A C2A HEM doub 405 n y 
C1A NA HEM sing 406 n y 
C2A C3A HEM sing 407 n y 
C2A CAA HEM sing 408 n n 
C3A C4A HEM doub 409 n y 
C3A CMA HEM sing 410 n n 
C4A NA HEM sing 411 n y 
CMA HMA HEM sing 412 n n 
CMA HMAA HEM sing 413 n n 
CMA HMAB HEM sing 414 n n 
CAA CBA HEM sing 415 n n 
CAA HAA HEM sing 416 n n 
CAA HAAA HEM sing 417 n n 
CBA CGA HEM sing 418 n n 
CBA HBA HEM sing 419 n n 
CBA HBAA HEM sing 420 n n 
CGA O1A HEM doub 421 n n 
CGA O2A HEM sing 422 n n 
C1B C2B HEM sing 423 n n 
C1B NB HEM sing 424 n n 
C2B C3B HEM doub 425 n n 
C2B CMB HEM sing 426 n n 
C3B C4B HEM sing 427 n n 
C3B CAB HEM sing 428 n n 
C4B NB HEM doub 429 n n 
CMB HMB HEM sing 430 n n 
CMB HMBA HEM sing 431 n n 
CMB HMBB HEM sing 432 n n 
CAB CBB HEM doub 433 n n 
CAB HAB HEM sing 434 n n 
CBB HBB HEM sing 435 n n 
CBB HBBA HEM sing 436 n n 
C1C C2C HEM sing 437 n y 
C1C NC HEM sing 438 n y 
C2C C3C HEM doub 439 n y 
C2C CMC HEM sing 440 n n 
C3C C4C HEM sing 441 n y 
C3C CAC HEM sing 442 n n 
C4C NC HEM sing 443 n y 
CMC HMC HEM sing 444 n n 
CMC HMCA HEM sing 445 n n 
CMC HMCB HEM sing 446 n n 
CAC CBC HEM doub 447 n n 
CAC HAC HEM sing 448 n n 
CBC HBC HEM sing 449 n n 
CBC HBCA HEM sing 450 n n 
C1D C2D HEM sing 451 n n 
C1D ND HEM doub 452 n n 
C2D C3D HEM doub 453 n n 
C2D CMD HEM sing 454 n n 
C3D C4D HEM sing 455 n n 
C3D CAD HEM sing 456 n n 
C4D ND HEM sing 457 n n 
CMD HMD HEM sing 458 n n 
CMD HMDA HEM sing 459 n n 
CMD HMDB HEM sing 460 n n 
CAD CBD HEM sing 461 n n 
CAD HAD HEM sing 462 n n 
CAD HADA HEM sing 463 n n 
CBD CGD HEM sing 464 n n 
CBD HBD HEM sing 465 n n 
CBD HBDA HEM sing 466 n n 
CGD O1D HEM doub 467 n n 
CGD O2D HEM sing 468 n n 
O2A H2A HEM sing 469 n n 
O2D H2D HEM sing 470 n n 
FE NA HEM sing 471 n n 
FE NB HEM sing 472 n n 
FE NC HEM sing 473 n n 
FE ND HEM sing 474 n n 
#
_atom_sites.entry_id                     3VRA 
_atom_sites.fract_transf_matrix[1][1]    0.008142 
_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]    0.007561 
_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]    0.004534 
_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 5 MLI A 1 701 300 MLI MLI . 
J 6 FAD A 1 702 301 FAD FAD . 
K 7 FES B 1 301 302 FES FES . 
L 8 SF4 B 1 302 303 SF4 FS4 . 
M 9 F3S B 1 303 304 F3S F3S . 
N 10 HEM C 1 201 305 HEM HEM . 
O 11 AT5 C 1 202 811 AT5 AT5 . 
P 12 EPH D 1 201 306 EPH EPH . 
Q 5 MLI E 1 701 300 MLI MLI . 
R 6 FAD E 1 702 301 FAD FAD . 
S 7 FES F 1 301 302 FES FES . 
T 8 SF4 F 1 302 303 SF4 FS4 . 
U 9 F3S F 1 303 304 F3S F3S . 
V 10 HEM G 1 201 305 HEM HEM . 
W 11 AT5 G 1 202 811 AT5 AT5 . 
X 12 EPH H 1 201 306 EPH EPH . 
#
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 . . . V 10 66.468 -9.841 -81.668 1 119.83 ? CHA HEM 201 G 1 
HETATM 2 C CHB HEM . . . V 10 67.794 -5.248 -82.131 1 122.13 ? CHB HEM 201 G 1 
HETATM 3 C CHC HEM . . . V 10 72.447 -6.47 -81.586 1 118.9 ? CHC HEM 201 G 1 
HETATM 4 C CHD HEM . . . V 10 71.14 -11.12 -81.922 1 117.45 ? CHD HEM 201 G 1 
HETATM 5 C C1A HEM . . . V 10 66.41 -8.465 -81.632 1 120.32 ? C1A HEM 201 G 1 
HETATM 6 C C2A HEM . . . V 10 65.278 -7.623 -81.212 1 121.05 ? C2A HEM 201 G 1 
HETATM 7 C C3A HEM . . . V 10 65.664 -6.36 -81.351 1 120.76 ? C3A HEM 201 G 1 
HETATM 8 C C4A HEM . . . V 10 67.025 -6.361 -81.87 1 121.06 ? C4A HEM 201 G 1 
HETATM 9 C CMA HEM . . . V 10 64.821 -5.108 -81.023 1 120.81 ? CMA HEM 201 G 1 
HETATM 10 C CAA HEM . . . V 10 63.894 -8.064 -80.667 1 122.86 ? CAA HEM 201 G 1 
HETATM 11 C CBA HEM . . . V 10 62.801 -8.097 -81.737 1 126.86 ? CBA HEM 201 G 1 
HETATM 12 C CGA HEM . . . V 10 61.738 -9.144 -81.411 1 129.01 ? CGA HEM 201 G 1 
HETATM 13 O O1A HEM . . . V 10 61.98 -10.084 -80.577 1 129.43 ? O1A HEM 201 G 1 
HETATM 14 O O2A HEM . . . V 10 60.632 -9.024 -82.021 1 129.98 ? O2A HEM 201 G 1 
HETATM 15 C C1B HEM . . . V 10 69.173 -5.166 -81.943 1 122.06 ? C1B HEM 201 G 1 
HETATM 16 C C2B HEM . . . V 10 69.944 -3.924 -81.815 1 122.63 ? C2B HEM 201 G 1 
HETATM 17 C C3B HEM . . . V 10 71.239 -4.256 -81.667 1 122.33 ? C3B HEM 201 G 1 
HETATM 18 C C4B HEM . . . V 10 71.322 -5.713 -81.69 1 120.52 ? C4B HEM 201 G 1 
HETATM 19 C CMB HEM . . . V 10 69.374 -2.478 -81.846 1 121.51 ? CMB HEM 201 G 1 
HETATM 20 C CAB HEM . . . V 10 72.419 -3.259 -81.499 1 122.78 ? CAB HEM 201 G 1 
HETATM 21 C CBB HEM . . . V 10 72.198 -1.958 -81.246 1 123.28 ? CBB HEM 201 G 1 
HETATM 22 C C1C HEM . . . V 10 72.477 -7.817 -81.815 1 117.54 ? C1C HEM 201 G 1 
HETATM 23 C C2C HEM . . . V 10 73.623 -8.541 -82.311 1 116.83 ? C2C HEM 201 G 1 
HETATM 24 C C3C HEM . . . V 10 73.268 -9.811 -82.402 1 116.6 ? C3C HEM 201 G 1 
HETATM 25 C C4C HEM . . . V 10 71.879 -9.948 -81.974 1 117.04 ? C4C HEM 201 G 1 
HETATM 26 C CMC HEM . . . V 10 75.009 -7.95 -82.662 1 115.75 ? CMC HEM 201 G 1 
HETATM 27 C CAC HEM . . . V 10 74.219 -10.924 -82.872 1 116.46 ? CAC HEM 201 G 1 
HETATM 28 C CBC HEM . . . V 10 75.13 -11.4 -82.009 1 115.69 ? CBC HEM 201 G 1 
HETATM 29 C C1D HEM . . . V 10 69.767 -11.263 -81.947 1 116.79 ? C1D HEM 201 G 1 
HETATM 30 C C2D HEM . . . V 10 69.009 -12.495 -82.182 1 115.78 ? C2D HEM 201 G 1 
HETATM 31 C C3D HEM . . . V 10 67.532 -12.09 -82.11 1 116.39 ? C3D HEM 201 G 1 
HETATM 32 C C4D HEM . . . V 10 67.578 -10.651 -81.824 1 117.77 ? C4D HEM 201 G 1 
HETATM 33 C CMD HEM . . . V 10 69.548 -13.922 -82.451 1 114.66 ? CMD HEM 201 G 1 
HETATM 34 C CAD HEM . . . V 10 66.299 -13.043 -82.318 1 115.56 ? CAD HEM 201 G 1 
HETATM 35 C CBD HEM . . . V 10 64.89 -12.405 -82.468 1 113.99 ? CBD HEM 201 G 1 
HETATM 36 C CGD HEM . . . V 10 64.474 -12.077 -83.897 1 112.67 ? CGD HEM 201 G 1 
HETATM 37 O O1D HEM . . . V 10 63.338 -11.574 -84.131 1 111.51 ? O1D HEM 201 G 1 
HETATM 38 O O2D HEM . . . V 10 65.272 -12.324 -84.833 1 112.17 ? O2D HEM 201 G 1 
HETATM 39 N NA HEM . . . V 10 67.461 -7.666 -82.03 1 119.68 ? NA HEM 201 G 1 
HETATM 40 N NB HEM . . . V 10 70.057 -6.243 -81.86 1 120.03 ? NB HEM 201 G 1 
HETATM 41 N NC HEM . . . V 10 71.426 -8.696 -81.628 1 117.25 ? NC HEM 201 G 1 
HETATM 42 N ND HEM . . . V 10 68.895 -10.208 -81.744 1 117.41 ? ND HEM 201 G 1 
HETATM 43 FE FE HEM . . . V 10 69.538 -8.23 -82.064 1 116.65 ? FE HEM 201 G 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    262 
_model_server_stats.query_time_ms           409 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#