data_4XYD
#
_model_server_result.job_id            Z-S6UEDw5Yocia9682cyEA 
_model_server_result.datetime_utc      '2024-11-21 13:44:24' 
_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":"H","auth_seq_id":201}' 
#
_entry.id    4XYD 
#
_exptl.entry_id    4XYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'HEME C' 
_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            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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             H 
_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
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 H34 Fe N4 O4' 
_chem_comp.formula_weight    618.503 
_chem_comp.id                HEC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'HEME C' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
FE NA HEC sing 129 n n 
FE NB HEC sing 130 n n 
FE NC HEC sing 131 n n 
FE ND HEC sing 132 n n 
CHA C1A HEC doub 133 n n 
CHA C4D HEC sing 134 n n 
CHA HHA HEC sing 135 n n 
CHB C4A HEC doub 136 n n 
CHB C1B HEC sing 137 n n 
CHB HHB HEC sing 138 n n 
CHC C4B HEC doub 139 n n 
CHC C1C HEC sing 140 n n 
CHC HHC HEC sing 141 n n 
CHD C4C HEC doub 142 n n 
CHD C1D HEC sing 143 n n 
CHD HHD HEC sing 144 n n 
NA C1A HEC sing 145 n y 
NA C4A HEC sing 146 n y 
C1A C2A HEC sing 147 n y 
C2A C3A HEC doub 148 n y 
C2A CAA HEC sing 149 n n 
C3A C4A HEC sing 150 n y 
C3A CMA HEC sing 151 n n 
CMA HMA1 HEC sing 152 n n 
CMA HMA2 HEC sing 153 n n 
CMA HMA3 HEC sing 154 n n 
CAA CBA HEC sing 155 n n 
CAA HAA1 HEC sing 156 n n 
CAA HAA2 HEC sing 157 n n 
CBA CGA HEC sing 158 n n 
CBA HBA1 HEC sing 159 n n 
CBA HBA2 HEC sing 160 n n 
CGA O1A HEC doub 161 n n 
CGA O2A HEC sing 162 n n 
O2A H2A HEC sing 163 n n 
NB C1B HEC sing 164 n y 
NB C4B HEC sing 165 n y 
C1B C2B HEC doub 166 n y 
C2B C3B HEC sing 167 n y 
C2B CMB HEC sing 168 n n 
C3B C4B HEC sing 169 n y 
C3B CAB HEC doub 170 e n 
CMB HMB1 HEC sing 171 n n 
CMB HMB2 HEC sing 172 n n 
CMB HMB3 HEC sing 173 n n 
CAB CBB HEC sing 174 n n 
CAB HAB HEC sing 175 n n 
CBB HBB1 HEC sing 176 n n 
CBB HBB2 HEC sing 177 n n 
CBB HBB3 HEC sing 178 n n 
NC C1C HEC sing 179 n y 
NC C4C HEC sing 180 n y 
C1C C2C HEC doub 181 n y 
C2C C3C HEC sing 182 n y 
C2C CMC HEC sing 183 n n 
C3C C4C HEC sing 184 n y 
C3C CAC HEC doub 185 e n 
CMC HMC1 HEC sing 186 n n 
CMC HMC2 HEC sing 187 n n 
CMC HMC3 HEC sing 188 n n 
CAC CBC HEC sing 189 n n 
CAC HAC HEC sing 190 n n 
CBC HBC1 HEC sing 191 n n 
CBC HBC2 HEC sing 192 n n 
CBC HBC3 HEC sing 193 n n 
ND C1D HEC sing 194 n y 
ND C4D HEC sing 195 n y 
C1D C2D HEC doub 196 n y 
C2D C3D HEC sing 197 n y 
C2D CMD HEC sing 198 n n 
C3D C4D HEC doub 199 n y 
C3D CAD HEC sing 200 n n 
CMD HMD1 HEC sing 201 n n 
CMD HMD2 HEC sing 202 n n 
CMD HMD3 HEC sing 203 n n 
CAD CBD HEC sing 204 n n 
CAD HAD1 HEC sing 205 n n 
CAD HAD2 HEC sing 206 n n 
CBD CGD HEC sing 207 n n 
CBD HBD1 HEC sing 208 n n 
CBD HBD2 HEC sing 209 n n 
CGD O1D HEC doub 210 n n 
CGD O2D HEC sing 211 n n 
O2D H2D HEC sing 212 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 FE FE HEC . . . H 7 30.573 1.433 -44.029 1 42.09 ? FE HEC 201 B 1 
HETATM 2 C CHA HEC . . . H 7 30.788 4.209 -41.94 1 41.87 ? CHA HEC 201 B 1 
HETATM 3 C CHB HEC . . . H 7 28.541 3.196 -46.204 1 39.57 ? CHB HEC 201 B 1 
HETATM 4 C CHC HEC . . . H 7 30.368 -1.344 -46.085 1 38.03 ? CHC HEC 201 B 1 
HETATM 5 C CHD HEC . . . H 7 32.583 -0.363 -41.832 1 40.33 ? CHD HEC 201 B 1 
HETATM 6 N NA HEC . . . H 7 29.799 3.369 -44.075 1 39.56 ? NA HEC 201 B 1 
HETATM 7 C C1A HEC . . . H 7 29.971 4.356 -43.169 1 42.39 ? C1A HEC 201 B 1 
HETATM 8 C C2A HEC . . . H 7 29.285 5.63 -43.502 1 42.26 ? C2A HEC 201 B 1 
HETATM 9 C C3A HEC . . . H 7 28.607 5.308 -44.761 1 40.41 ? C3A HEC 201 B 1 
HETATM 10 C C4A HEC . . . H 7 28.996 3.906 -45.001 1 39.89 ? C4A HEC 201 B 1 
HETATM 11 C CMA HEC . . . H 7 27.749 6.171 -45.632 1 40.59 ? CMA HEC 201 B 1 
HETATM 12 C CAA HEC . . . H 7 29.255 6.893 -42.697 1 44.09 ? CAA HEC 201 B 1 
HETATM 13 C CBA HEC . . . H 7 28.145 6.55 -41.694 1 47.95 ? CBA HEC 201 B 1 
HETATM 14 C CGA HEC . . . H 7 28.136 7.367 -40.416 1 55.33 ? CGA HEC 201 B 1 
HETATM 15 O O1A HEC . . . H 7 29.208 7.882 -40.031 1 64.36 ? O1A HEC 201 B 1 
HETATM 16 O O2A HEC . . . H 7 27.066 7.513 -39.771 1 56.38 ? O2A HEC 201 B 1 
HETATM 17 N NB HEC . . . H 7 29.614 1.014 -45.838 1 38.85 ? NB HEC 201 B 1 
HETATM 18 C C1B HEC . . . H 7 28.833 1.817 -46.596 1 39.36 ? C1B HEC 201 B 1 
HETATM 19 C C2B HEC . . . H 7 28.286 1.213 -47.853 1 41.77 ? C2B HEC 201 B 1 
HETATM 20 C C3B HEC . . . H 7 28.871 -0.128 -47.755 1 41.29 ? C3B HEC 201 B 1 
HETATM 21 C C4B HEC . . . H 7 29.654 -0.143 -46.515 1 39.53 ? C4B HEC 201 B 1 
HETATM 22 C CMB HEC . . . H 7 27.402 1.779 -48.945 1 40.94 ? CMB HEC 201 B 1 
HETATM 23 C CAB HEC . . . H 7 28.721 -1.286 -48.736 1 41.4 ? CAB HEC 201 B 1 
HETATM 24 C CBB HEC . . . H 7 28.925 -0.918 -50.178 1 41.23 ? CBB HEC 201 B 1 
HETATM 25 N NC HEC . . . H 7 31.343 -0.511 -43.984 1 38.16 ? NC HEC 201 B 1 
HETATM 26 C C1C HEC . . . H 7 31.166 -1.498 -44.872 1 38.25 ? C1C HEC 201 B 1 
HETATM 27 C C2C HEC . . . H 7 31.843 -2.781 -44.566 1 40.2 ? C2C HEC 201 B 1 
HETATM 28 C C3C HEC . . . H 7 32.519 -2.455 -43.317 1 39.93 ? C3C HEC 201 B 1 
HETATM 29 C C4C HEC . . . H 7 32.116 -1.07 -43.031 1 39.9 ? C4C HEC 201 B 1 
HETATM 30 C CMC HEC . . . H 7 31.853 -4.063 -45.345 1 41.12 ? CMC HEC 201 B 1 
HETATM 31 C CAC HEC . . . H 7 33.302 -3.407 -42.397 1 40.25 ? CAC HEC 201 B 1 
HETATM 32 C CBC HEC . . . H 7 34.478 -4.25 -42.803 1 40.17 ? CBC HEC 201 B 1 
HETATM 33 N ND HEC . . . H 7 31.534 1.85 -42.217 1 40.88 ? ND HEC 201 B 1 
HETATM 34 C C1D HEC . . . H 7 32.296 1.027 -41.475 1 40.64 ? C1D HEC 201 B 1 
HETATM 35 C C2D HEC . . . H 7 32.836 1.607 -40.238 1 42.35 ? C2D HEC 201 B 1 
HETATM 36 C C3D HEC . . . H 7 32.287 2.963 -40.263 1 44.09 ? C3D HEC 201 B 1 
HETATM 37 C C4D HEC . . . H 7 31.517 3.003 -41.516 1 42.68 ? C4D HEC 201 B 1 
HETATM 38 C CMD HEC . . . H 7 33.71 0.967 -39.203 1 41.78 ? CMD HEC 201 B 1 
HETATM 39 C CAD HEC . . . H 7 32.519 4.056 -39.277 1 47.81 ? CAD HEC 201 B 1 
HETATM 40 C CBD HEC . . . H 7 33.809 4.649 -39.842 1 50.33 ? CBD HEC 201 B 1 
HETATM 41 C CGD HEC . . . H 7 34.326 5.847 -39.074 1 54.66 ? CGD HEC 201 B 1 
HETATM 42 O O1D HEC . . . H 7 33.543 6.445 -38.288 1 53.66 ? O1D HEC 201 B 1 
HETATM 43 O O2D HEC . . . H 7 35.529 6.193 -39.259 1 55.09 ? O2D HEC 201 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#