data_4XYD
#
_model_server_result.job_id            SkB0H3-GnO3-HyynDVAuHQ 
_model_server_result.datetime_utc      '2024-11-21 14:30:16' 
_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          4xyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":504}' 
#
_entry.id    4XYD 
#
_exptl.entry_id    4XYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          3 
_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            4XYD 
_cell.length_a            86.22 
_cell.length_b            98.83 
_cell.length_c            126.78 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 21 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,E,F,G,H,I,J,K 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 F 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 B SG CYS 62 B CYS 62 1_555 H CAB HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? 
covale ? covale2 B SG CYS 65 B CYS 65 1_555 H CAC HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.719 ? 
metalc ? metalc1 A NE2 HIS 53 A HIS 53 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? 
metalc ? metalc2 A OE1 GLU 122 A GLU 122 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc3 A OE2 GLU 122 A GLU 122 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? 
metalc ? metalc4 A ND1 HIS 194 A HIS 194 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? 
metalc ? metalc5 A OE1 GLU 198 A GLU 198 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc6 A OE2 GLU 198 A GLU 198 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? 
metalc ? metalc7 A NE2 HIS 245 A HIS 245 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? 
metalc ? metalc8 A NE2 HIS 246 A HIS 246 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? 
metalc ? metalc9 A NE2 HIS 334 A HIS 334 1_555 F FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? 
metalc ? metalc10 A NE2 HIS 336 A HIS 336 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? 
metalc ? metalc11 C O1D HEM . A HEM 501 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc12 D O2 UNL . A UNL 502 1_555 F FE HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc13 D O2 UNL . A UNL 502 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc14 D O1 UNL . A UNL 502 1_555 G FE FE . A FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc15 E CA CA . A CA 503 1_555 F O1A HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc16 E CA CA . A CA 503 1_555 F O2A HEM . A HEM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.141 ? 
metalc ? metalc17 E CA CA . A CA 503 1_555 B O GLY 72 B GLY 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc18 E CA CA . A CA 503 1_555 B OH TYR 74 B TYR 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc19 B OE1 GLU 49 B GLU 49 1_555 I CU CU . B CU 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.918 ? 
metalc ? metalc20 B ND1 HIS 52 B HIS 52 1_555 I CU CU . B CU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc21 B NE2 HIS 66 B HIS 66 1_555 H FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? 
metalc ? metalc22 B SD MET 116 B MET 116 1_555 H FE HEC . B HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
metalc ? metalc23 B OE1 GLU 124 B GLU 124 1_555 I CU CU . B CU 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? 
metalc ? metalc24 I CU CU . B CU 202 1_555 K O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
#
_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 213 n n 
CHA C4D HEM doub 214 n n 
CHA HHA HEM sing 215 n n 
CHB C4A HEM sing 216 n n 
CHB C1B HEM doub 217 n n 
CHB HHB HEM sing 218 n n 
CHC C4B HEM sing 219 n n 
CHC C1C HEM doub 220 n n 
CHC HHC HEM sing 221 n n 
CHD C4C HEM doub 222 n n 
CHD C1D HEM sing 223 n n 
CHD HHD HEM sing 224 n n 
C1A C2A HEM doub 225 n y 
C1A NA HEM sing 226 n y 
C2A C3A HEM sing 227 n y 
C2A CAA HEM sing 228 n n 
C3A C4A HEM doub 229 n y 
C3A CMA HEM sing 230 n n 
C4A NA HEM sing 231 n y 
CMA HMA HEM sing 232 n n 
CMA HMAA HEM sing 233 n n 
CMA HMAB HEM sing 234 n n 
CAA CBA HEM sing 235 n n 
CAA HAA HEM sing 236 n n 
CAA HAAA HEM sing 237 n n 
CBA CGA HEM sing 238 n n 
CBA HBA HEM sing 239 n n 
CBA HBAA HEM sing 240 n n 
CGA O1A HEM doub 241 n n 
CGA O2A HEM sing 242 n n 
C1B C2B HEM sing 243 n n 
C1B NB HEM sing 244 n n 
C2B C3B HEM doub 245 n n 
C2B CMB HEM sing 246 n n 
C3B C4B HEM sing 247 n n 
C3B CAB HEM sing 248 n n 
C4B NB HEM doub 249 n n 
CMB HMB HEM sing 250 n n 
CMB HMBA HEM sing 251 n n 
CMB HMBB HEM sing 252 n n 
CAB CBB HEM doub 253 n n 
CAB HAB HEM sing 254 n n 
CBB HBB HEM sing 255 n n 
CBB HBBA HEM sing 256 n n 
C1C C2C HEM sing 257 n y 
C1C NC HEM sing 258 n y 
C2C C3C HEM doub 259 n y 
C2C CMC HEM sing 260 n n 
C3C C4C HEM sing 261 n y 
C3C CAC HEM sing 262 n n 
C4C NC HEM sing 263 n y 
CMC HMC HEM sing 264 n n 
CMC HMCA HEM sing 265 n n 
CMC HMCB HEM sing 266 n n 
CAC CBC HEM doub 267 n n 
CAC HAC HEM sing 268 n n 
CBC HBC HEM sing 269 n n 
CBC HBCA HEM sing 270 n n 
C1D C2D HEM sing 271 n n 
C1D ND HEM doub 272 n n 
C2D C3D HEM doub 273 n n 
C2D CMD HEM sing 274 n n 
C3D C4D HEM sing 275 n n 
C3D CAD HEM sing 276 n n 
C4D ND HEM sing 277 n n 
CMD HMD HEM sing 278 n n 
CMD HMDA HEM sing 279 n n 
CMD HMDB HEM sing 280 n n 
CAD CBD HEM sing 281 n n 
CAD HAD HEM sing 282 n n 
CAD HADA HEM sing 283 n n 
CBD CGD HEM sing 284 n n 
CBD HBD HEM sing 285 n n 
CBD HBDA HEM sing 286 n n 
CGD O1D HEM doub 287 n n 
CGD O2D HEM sing 288 n n 
O2A H2A HEM sing 289 n n 
O2D H2D HEM sing 290 n n 
FE NA HEM sing 291 n n 
FE NB HEM sing 292 n n 
FE NC HEM sing 293 n n 
FE ND HEM sing 294 n n 
#
_atom_sites.entry_id                     4XYD 
_atom_sites.fract_transf_matrix[1][1]    0.011598 
_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]    0.010118 
_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]    0.007888 
_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
C 3 HEM A 1 501 500 HEM HEM . 
D 4 UNL A 1 502 1 UNL UNL . 
E 5 CA A 1 503 700 CA CA . 
F 3 HEM A 1 504 600 HEM HEM . 
G 6 FE A 1 505 601 FE FE . 
H 7 HEC B 1 201 500 HEC HEC . 
I 8 CU B 1 202 600 CU CU . 
J 9 HOH A 1 601 13 HOH HOH . 
J 9 HOH A 2 602 17 HOH HOH . 
J 9 HOH A 3 603 11 HOH HOH . 
J 9 HOH A 4 604 15 HOH HOH . 
J 9 HOH A 5 605 2 HOH HOH . 
J 9 HOH A 6 606 12 HOH HOH . 
J 9 HOH A 7 607 8 HOH HOH . 
J 9 HOH A 8 608 5 HOH HOH . 
J 9 HOH A 9 609 4 HOH HOH . 
J 9 HOH A 10 610 14 HOH HOH . 
J 9 HOH A 11 611 1 HOH HOH . 
J 9 HOH A 12 612 3 HOH HOH . 
K 9 HOH B 1 301 10 HOH HOH . 
K 9 HOH B 2 302 7 HOH HOH . 
K 9 HOH B 3 303 9 HOH HOH . 
K 9 HOH B 4 304 6 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 . . . F 3 15.655 -11.502 -33.269 1 57.84 ? CHA HEM 504 A 1 
HETATM 2 C CHB HEM . . . F 3 17.412 -15.968 -32.584 1 55.14 ? CHB HEM 504 A 1 
HETATM 3 C CHC HEM . . . F 3 13.2 -17.107 -30.466 1 59.97 ? CHC HEM 504 A 1 
HETATM 4 C CHD HEM . . . F 3 12.468 -12.376 -29.646 1 61.5 ? CHD HEM 504 A 1 
HETATM 5 C C1A HEM . . . F 3 16.491 -12.601 -33.298 1 56.6 ? C1A HEM 504 A 1 
HETATM 6 C C2A HEM . . . F 3 17.755 -12.662 -33.945 1 54.5 ? C2A HEM 504 A 1 
HETATM 7 C C3A HEM . . . F 3 18.239 -13.93 -33.749 1 52.64 ? C3A HEM 504 A 1 
HETATM 8 C C4A HEM . . . F 3 17.29 -14.644 -32.987 1 54.27 ? C4A HEM 504 A 1 
HETATM 9 C CMA HEM . . . F 3 19.538 -14.509 -34.232 1 48.89 ? CMA HEM 504 A 1 
HETATM 10 C CAA HEM . . . F 3 18.411 -11.53 -34.709 1 51.14 ? CAA HEM 504 A 1 
HETATM 11 C CBA HEM . . . F 3 18.128 -11.755 -36.195 1 56.16 ? CBA HEM 504 A 1 
HETATM 12 C CGA HEM . . . F 3 18.912 -10.82 -37.081 1 62.79 ? CGA HEM 504 A 1 
HETATM 13 O O1A HEM . . . F 3 20.097 -11.103 -37.391 1 64.16 ? O1A HEM 504 A 1 
HETATM 14 O O2A HEM . . . F 3 18.387 -9.764 -37.522 1 65.81 ? O2A HEM 504 A 1 
HETATM 15 C C1B HEM . . . F 3 16.361 -16.709 -31.999 1 53.4 ? C1B HEM 504 A 1 
HETATM 16 C C2B HEM . . . F 3 16.398 -18.124 -31.809 1 51.88 ? C2B HEM 504 A 1 
HETATM 17 C C3B HEM . . . F 3 15.205 -18.467 -31.211 1 51.87 ? C3B HEM 504 A 1 
HETATM 18 C C4B HEM . . . F 3 14.461 -17.202 -31.047 1 53.19 ? C4B HEM 504 A 1 
HETATM 19 C CMB HEM . . . F 3 17.541 -19.038 -32.203 1 49.96 ? CMB HEM 504 A 1 
HETATM 20 C CAB HEM . . . F 3 14.702 -19.786 -30.771 1 48.82 ? CAB HEM 504 A 1 
HETATM 21 C CBB HEM . . . F 3 14.855 -20.877 -31.495 1 49.41 ? CBB HEM 504 A 1 
HETATM 22 C C1C HEM . . . F 3 12.682 -15.935 -29.917 1 60.44 ? C1C HEM 504 A 1 
HETATM 23 C C2C HEM . . . F 3 11.698 -15.859 -28.922 1 60.14 ? C2C HEM 504 A 1 
HETATM 24 C C3C HEM . . . F 3 11.473 -14.523 -28.665 1 61 ? C3C HEM 504 A 1 
HETATM 25 C C4C HEM . . . F 3 12.346 -13.757 -29.527 1 62.01 ? C4C HEM 504 A 1 
HETATM 26 C CMC HEM . . . F 3 11.01 -17.016 -28.243 1 58.7 ? CMC HEM 504 A 1 
HETATM 27 C CAC HEM . . . F 3 10.498 -14.091 -27.649 1 58.96 ? CAC HEM 504 A 1 
HETATM 28 C CBC HEM . . . F 3 9.95 -12.895 -27.694 1 61.68 ? CBC HEM 504 A 1 
HETATM 29 C C1D HEM . . . F 3 13.265 -11.787 -30.663 1 60.14 ? C1D HEM 504 A 1 
HETATM 30 C C2D HEM . . . F 3 13.192 -10.349 -30.976 1 57.6 ? C2D HEM 504 A 1 
HETATM 31 C C3D HEM . . . F 3 14.078 -10.113 -31.969 1 55.01 ? C3D HEM 504 A 1 
HETATM 32 C C4D HEM . . . F 3 14.681 -11.404 -32.281 1 55.91 ? C4D HEM 504 A 1 
HETATM 33 C CMD HEM . . . F 3 12.303 -9.339 -30.304 1 57.2 ? CMD HEM 504 A 1 
HETATM 34 C CAD HEM . . . F 3 14.386 -8.809 -32.663 1 51.31 ? CAD HEM 504 A 1 
HETATM 35 C CBD HEM . . . F 3 15.431 -7.976 -31.93 1 51.08 ? CBD HEM 504 A 1 
HETATM 36 C CGD HEM . . . F 3 15.584 -6.638 -32.619 1 53.75 ? CGD HEM 504 A 1 
HETATM 37 O O1D HEM . . . F 3 14.619 -6.07 -33.192 1 56.42 ? O1D HEM 504 A 1 
HETATM 38 O O2D HEM . . . F 3 16.699 -6.082 -32.626 1 53.33 ? O2D HEM 504 A 1 
HETATM 39 N NA HEM . . . F 3 16.215 -13.828 -32.724 1 55.53 ? NA HEM 504 A 1 
HETATM 40 N NB HEM . . . F 3 15.202 -16.227 -31.542 1 53.3 ? NB HEM 504 A 1 
HETATM 41 N NC HEM . . . F 3 13.053 -14.673 -30.28 1 59.25 ? NC HEM 504 A 1 
HETATM 42 N ND HEM . . . F 3 14.168 -12.377 -31.492 1 57.37 ? ND HEM 504 A 1 
HETATM 43 FE FE HEM . . . F 3 14.655 -14.211 -31.536 1 50.79 ? FE HEM 504 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          21 
_model_server_stats.element_count           43 
#