data_3VRB
#
_model_server_result.job_id            zX-8Jgz6gMh5095mQYiMng 
_model_server_result.datetime_utc      '2024-11-24 14:43:31' 
_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          3vrb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":201}' 
#
_entry.id    3VRB 
#
_exptl.entry_id    3VRB 
_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            3VRB 
_cell.length_a            124.306 
_cell.length_b            131.649 
_cell.length_c            222.519 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VRB 
_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 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 NE2 HIS 79 A HIS 79 1_555 J C8M FAD . A FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.788 ? 
covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? 
metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc6 B SG CYS 185 B CYS 185 1_555 L FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.685 ? 
metalc ? metalc7 B SG CYS 188 B CYS 188 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc8 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc9 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc10 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? 
metalc ? metalc11 B SG CYS 249 B CYS 249 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? 
metalc ? metalc12 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc13 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc14 F SG CYS 89 F CYS 89 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc15 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc16 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.735 ? 
metalc ? metalc17 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc18 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? 
metalc ? metalc19 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc20 F SG CYS 188 F CYS 188 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
metalc ? metalc21 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc22 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc23 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc24 F SG CYS 249 F CYS 249 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc25 G NE2 HIS 131 G HIS 131 1_555 W FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc26 W FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
#
_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 400 n n 
CHA C4D HEM doub 401 n n 
CHA HHA HEM sing 402 n n 
CHB C4A HEM sing 403 n n 
CHB C1B HEM doub 404 n n 
CHB HHB HEM sing 405 n n 
CHC C4B HEM sing 406 n n 
CHC C1C HEM doub 407 n n 
CHC HHC HEM sing 408 n n 
CHD C4C HEM doub 409 n n 
CHD C1D HEM sing 410 n n 
CHD HHD HEM sing 411 n n 
C1A C2A HEM doub 412 n y 
C1A NA HEM sing 413 n y 
C2A C3A HEM sing 414 n y 
C2A CAA HEM sing 415 n n 
C3A C4A HEM doub 416 n y 
C3A CMA HEM sing 417 n n 
C4A NA HEM sing 418 n y 
CMA HMA HEM sing 419 n n 
CMA HMAA HEM sing 420 n n 
CMA HMAB HEM sing 421 n n 
CAA CBA HEM sing 422 n n 
CAA HAA HEM sing 423 n n 
CAA HAAA HEM sing 424 n n 
CBA CGA HEM sing 425 n n 
CBA HBA HEM sing 426 n n 
CBA HBAA HEM sing 427 n n 
CGA O1A HEM doub 428 n n 
CGA O2A HEM sing 429 n n 
C1B C2B HEM sing 430 n n 
C1B NB HEM sing 431 n n 
C2B C3B HEM doub 432 n n 
C2B CMB HEM sing 433 n n 
C3B C4B HEM sing 434 n n 
C3B CAB HEM sing 435 n n 
C4B NB HEM doub 436 n n 
CMB HMB HEM sing 437 n n 
CMB HMBA HEM sing 438 n n 
CMB HMBB HEM sing 439 n n 
CAB CBB HEM doub 440 n n 
CAB HAB HEM sing 441 n n 
CBB HBB HEM sing 442 n n 
CBB HBBA HEM sing 443 n n 
C1C C2C HEM sing 444 n y 
C1C NC HEM sing 445 n y 
C2C C3C HEM doub 446 n y 
C2C CMC HEM sing 447 n n 
C3C C4C HEM sing 448 n y 
C3C CAC HEM sing 449 n n 
C4C NC HEM sing 450 n y 
CMC HMC HEM sing 451 n n 
CMC HMCA HEM sing 452 n n 
CMC HMCB HEM sing 453 n n 
CAC CBC HEM doub 454 n n 
CAC HAC HEM sing 455 n n 
CBC HBC HEM sing 456 n n 
CBC HBCA HEM sing 457 n n 
C1D C2D HEM sing 458 n n 
C1D ND HEM doub 459 n n 
C2D C3D HEM doub 460 n n 
C2D CMD HEM sing 461 n n 
C3D C4D HEM sing 462 n n 
C3D CAD HEM sing 463 n n 
C4D ND HEM sing 464 n n 
CMD HMD HEM sing 465 n n 
CMD HMDA HEM sing 466 n n 
CMD HMDB HEM sing 467 n n 
CAD CBD HEM sing 468 n n 
CAD HAD HEM sing 469 n n 
CAD HADA HEM sing 470 n n 
CBD CGD HEM sing 471 n n 
CBD HBD HEM sing 472 n n 
CBD HBDA HEM sing 473 n n 
CGD O1D HEM doub 474 n n 
CGD O2D HEM sing 475 n n 
O2A H2A HEM sing 476 n n 
O2D H2D HEM sing 477 n n 
FE NA HEM sing 478 n n 
FE NB HEM sing 479 n n 
FE NC HEM sing 480 n n 
FE ND HEM sing 481 n n 
#
_atom_sites.entry_id                     3VRB 
_atom_sites.fract_transf_matrix[1][1]    0.008045 
_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]    0.007596 
_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]    0.004494 
_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 FUM A 1 701 300 FUM FMR . 
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 FTN C 1 202 810 FTN FTN . 
P 12 EPH D 1 201 306 EPH EPH . 
Q 5 FUM E 1 701 300 FUM FMR . 
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 11 FTN F 1 304 810 FTN FTN . 
W 10 HEM G 1 201 305 HEM HEM . 
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 . . . W 10 -5.477 9.822 27.577 1 74.46 ? CHA HEM 201 G 1 
HETATM 2 C CHB HEM . . . W 10 -7.047 5.326 28.194 1 72.12 ? CHB HEM 201 G 1 
HETATM 3 C CHC HEM . . . W 10 -11.625 6.676 27.983 1 72.18 ? CHC HEM 201 G 1 
HETATM 4 C CHD HEM . . . W 10 -10.081 11.204 27.866 1 73.56 ? CHD HEM 201 G 1 
HETATM 5 C C1A HEM . . . W 10 -5.491 8.473 27.793 1 74.83 ? C1A HEM 201 G 1 
HETATM 6 C C2A HEM . . . W 10 -4.353 7.603 28.058 1 75.96 ? C2A HEM 201 G 1 
HETATM 7 C C3A HEM . . . W 10 -4.822 6.383 28.232 1 74.2 ? C3A HEM 201 G 1 
HETATM 8 C C4A HEM . . . W 10 -6.249 6.417 28.073 1 73.29 ? C4A HEM 201 G 1 
HETATM 9 C CMA HEM . . . W 10 -3.964 5.145 28.547 1 73.8 ? CMA HEM 201 G 1 
HETATM 10 C CAA HEM . . . W 10 -2.839 7.889 28.175 1 79.49 ? CAA HEM 201 G 1 
HETATM 11 C CBA HEM . . . W 10 -2.372 9.305 27.901 1 83.24 ? CBA HEM 201 G 1 
HETATM 12 C CGA HEM . . . W 10 -0.972 9.164 27.364 1 86.19 ? CGA HEM 201 G 1 
HETATM 13 O O1A HEM . . . W 10 -0.019 8.953 28.176 1 86.16 ? O1A HEM 201 G 1 
HETATM 14 O O2A HEM . . . W 10 -0.837 9.254 26.108 1 88.68 ? O2A HEM 201 G 1 
HETATM 15 C C1B HEM . . . W 10 -8.393 5.315 28.088 1 72.18 ? C1B HEM 201 G 1 
HETATM 16 C C2B HEM . . . W 10 -9.179 4.13 27.867 1 73.83 ? C2B HEM 201 G 1 
HETATM 17 C C3B HEM . . . W 10 -10.454 4.5 27.81 1 74.61 ? C3B HEM 201 G 1 
HETATM 18 C C4B HEM . . . W 10 -10.496 5.925 27.995 1 73.07 ? C4B HEM 201 G 1 
HETATM 19 C CMB HEM . . . W 10 -8.632 2.689 27.734 1 74.85 ? CMB HEM 201 G 1 
HETATM 20 C CAB HEM . . . W 10 -11.692 3.591 27.587 1 76.96 ? CAB HEM 201 G 1 
HETATM 21 C CBB HEM . . . W 10 -11.937 2.513 28.352 1 78.44 ? CBB HEM 201 G 1 
HETATM 22 C C1C HEM . . . W 10 -11.592 8.026 27.861 1 73.1 ? C1C HEM 201 G 1 
HETATM 23 C C2C HEM . . . W 10 -12.738 8.851 27.569 1 74.08 ? C2C HEM 201 G 1 
HETATM 24 C C3C HEM . . . W 10 -12.285 10.119 27.541 1 75.02 ? C3C HEM 201 G 1 
HETATM 25 C C4C HEM . . . W 10 -10.862 10.103 27.796 1 73.92 ? C4C HEM 201 G 1 
HETATM 26 C CMC HEM . . . W 10 -14.184 8.332 27.35 1 71.6 ? CMC HEM 201 G 1 
HETATM 27 C CAC HEM . . . W 10 -13.07 11.425 27.273 1 75.77 ? CAC HEM 201 G 1 
HETATM 28 C CBC HEM . . . W 10 -14.354 11.568 27.619 1 76.96 ? CBC HEM 201 G 1 
HETATM 29 C C1D HEM . . . W 10 -8.739 11.27 27.781 1 73.76 ? C1D HEM 201 G 1 
HETATM 30 C C2D HEM . . . W 10 -8.004 12.509 27.697 1 75.36 ? C2D HEM 201 G 1 
HETATM 31 C C3D HEM . . . W 10 -6.534 12.107 27.605 1 76.15 ? C3D HEM 201 G 1 
HETATM 32 C C4D HEM . . . W 10 -6.568 10.649 27.655 1 74.9 ? C4D HEM 201 G 1 
HETATM 33 C CMD HEM . . . W 10 -8.569 13.953 27.683 1 74.7 ? CMD HEM 201 G 1 
HETATM 34 C CAD HEM . . . W 10 -5.368 13.139 27.465 1 78.78 ? CAD HEM 201 G 1 
HETATM 35 C CBD HEM . . . W 10 -3.906 12.633 27.477 1 81.32 ? CBD HEM 201 G 1 
HETATM 36 C CGD HEM . . . W 10 -3.305 12.417 26.095 1 82.1 ? CGD HEM 201 G 1 
HETATM 37 O O1D HEM . . . W 10 -2.045 12.333 25.963 1 80.48 ? O1D HEM 201 G 1 
HETATM 38 O O2D HEM . . . W 10 -4.092 12.322 25.106 1 84.11 ? O2D HEM 201 G 1 
HETATM 39 N NA HEM . . . W 10 -6.643 7.712 27.805 1 73.77 ? NA HEM 201 G 1 
HETATM 40 N NB HEM . . . W 10 -9.217 6.403 28.149 1 72.45 ? NB HEM 201 G 1 
HETATM 41 N NC HEM . . . W 10 -10.46 8.819 27.992 1 73.4 ? NC HEM 201 G 1 
HETATM 42 N ND HEM . . . W 10 -7.886 10.198 27.754 1 73.65 ? ND HEM 201 G 1 
HETATM 43 FE FE HEM . . . W 10 -8.567 8.319 27.942 1 72.29 ? FE HEM 201 G 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           234 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#