data_2YIU
#
_model_server_result.job_id            YUubTORbI4g-3ZeHMkOsKA 
_model_server_result.datetime_utc      '2024-11-13 20:48:20' 
_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          2yiu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":500}' 
#
_entry.id    2YIU 
#
_exptl.entry_id    2YIU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'HEME C' 
_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          103.18 
_cell.angle_gamma         90 
_cell.entry_id            2YIU 
_cell.length_a            85.3 
_cell.length_b            164.91 
_cell.length_c            100.61 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YIU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               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,L,M,N,O,P,Q,R,S,T 
_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
? 6 J N N 
? 6 O 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
disulf ? disulf1 C SG CYS 137 C CYS 137 1_555 C SG CYS 154 C CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf2 F SG CYS 137 F CYS 137 1_555 F SG CYS 154 F CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 B SG CYS 58 B CYS 82 1_555 J CAB HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? 
covale ? covale2 B SG CYS 61 B CYS 85 1_555 J CAC HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.673 ? 
covale ? covale3 E SG CYS 58 E CYS 82 1_555 O CAB HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? 
covale ? covale4 E SG CYS 61 E CYS 85 1_555 O CAC HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.664 ? 
metalc ? metalc1 A NE2 HIS 97 A HIS 97 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? 
metalc ? metalc2 A NE2 HIS 111 A HIS 111 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc3 A NE2 HIS 198 A HIS 198 1_555 G FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? 
metalc ? metalc4 A NE2 HIS 212 A HIS 212 1_555 H FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc5 B NE2 HIS 62 B HIS 86 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc6 B SD MET 186 B MET 210 1_555 J FE HEC . B HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc7 C SG CYS 132 C CYS 132 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc8 C ND1 HIS 134 C HIS 134 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc9 C SG CYS 152 C CYS 152 1_555 K FE2 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? 
metalc ? metalc10 C ND1 HIS 155 C HIS 155 1_555 K FE1 FES . C FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc11 D NE2 HIS 97 D HIS 97 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc12 D NE2 HIS 111 D HIS 111 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc13 D NE2 HIS 198 D HIS 198 1_555 L FE HEM . D HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? 
metalc ? metalc14 D NE2 HIS 212 D HIS 212 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? 
metalc ? metalc15 E NE2 HIS 62 E HIS 86 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc16 E SD MET 186 E MET 210 1_555 O FE HEC . E HEC 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc17 F SG CYS 132 F CYS 132 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc18 F ND1 HIS 134 F HIS 134 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc19 F SG CYS 152 F CYS 152 1_555 P FE2 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
metalc ? metalc20 F ND1 HIS 155 F HIS 155 1_555 P FE1 FES . F FES 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
#
_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 133 n n 
FE NB HEC sing 134 n n 
FE NC HEC sing 135 n n 
FE ND HEC sing 136 n n 
CHA C1A HEC doub 137 n n 
CHA C4D HEC sing 138 n n 
CHA HHA HEC sing 139 n n 
CHB C4A HEC doub 140 n n 
CHB C1B HEC sing 141 n n 
CHB HHB HEC sing 142 n n 
CHC C4B HEC doub 143 n n 
CHC C1C HEC sing 144 n n 
CHC HHC HEC sing 145 n n 
CHD C4C HEC doub 146 n n 
CHD C1D HEC sing 147 n n 
CHD HHD HEC sing 148 n n 
NA C1A HEC sing 149 n y 
NA C4A HEC sing 150 n y 
C1A C2A HEC sing 151 n y 
C2A C3A HEC doub 152 n y 
C2A CAA HEC sing 153 n n 
C3A C4A HEC sing 154 n y 
C3A CMA HEC sing 155 n n 
CMA HMA1 HEC sing 156 n n 
CMA HMA2 HEC sing 157 n n 
CMA HMA3 HEC sing 158 n n 
CAA CBA HEC sing 159 n n 
CAA HAA1 HEC sing 160 n n 
CAA HAA2 HEC sing 161 n n 
CBA CGA HEC sing 162 n n 
CBA HBA1 HEC sing 163 n n 
CBA HBA2 HEC sing 164 n n 
CGA O1A HEC doub 165 n n 
CGA O2A HEC sing 166 n n 
O2A H2A HEC sing 167 n n 
NB C1B HEC sing 168 n y 
NB C4B HEC sing 169 n y 
C1B C2B HEC doub 170 n y 
C2B C3B HEC sing 171 n y 
C2B CMB HEC sing 172 n n 
C3B C4B HEC sing 173 n y 
C3B CAB HEC doub 174 e n 
CMB HMB1 HEC sing 175 n n 
CMB HMB2 HEC sing 176 n n 
CMB HMB3 HEC sing 177 n n 
CAB CBB HEC sing 178 n n 
CAB HAB HEC sing 179 n n 
CBB HBB1 HEC sing 180 n n 
CBB HBB2 HEC sing 181 n n 
CBB HBB3 HEC sing 182 n n 
NC C1C HEC sing 183 n y 
NC C4C HEC sing 184 n y 
C1C C2C HEC doub 185 n y 
C2C C3C HEC sing 186 n y 
C2C CMC HEC sing 187 n n 
C3C C4C HEC sing 188 n y 
C3C CAC HEC doub 189 e n 
CMC HMC1 HEC sing 190 n n 
CMC HMC2 HEC sing 191 n n 
CMC HMC3 HEC sing 192 n n 
CAC CBC HEC sing 193 n n 
CAC HAC HEC sing 194 n n 
CBC HBC1 HEC sing 195 n n 
CBC HBC2 HEC sing 196 n n 
CBC HBC3 HEC sing 197 n n 
ND C1D HEC sing 198 n y 
ND C4D HEC sing 199 n y 
C1D C2D HEC doub 200 n y 
C2D C3D HEC sing 201 n y 
C2D CMD HEC sing 202 n n 
C3D C4D HEC doub 203 n y 
C3D CAD HEC sing 204 n n 
CMD HMD1 HEC sing 205 n n 
CMD HMD2 HEC sing 206 n n 
CMD HMD3 HEC sing 207 n n 
CAD CBD HEC sing 208 n n 
CAD HAD1 HEC sing 209 n n 
CAD HAD2 HEC sing 210 n n 
CBD CGD HEC sing 211 n n 
CBD HBD1 HEC sing 212 n n 
CBD HBD2 HEC sing 213 n n 
CGD O1D HEC doub 214 n n 
CGD O2D HEC sing 215 n n 
O2D H2D HEC sing 216 n n 
#
_atom_sites.entry_id                     2YIU 
_atom_sites.fract_transf_matrix[1][1]    0.011723 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002745 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006064 
_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]    0.010208 
_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
G 4 HEM A 1 500 500 HEM HEM . 
H 4 HEM A 1 501 501 HEM HEM . 
I 5 SMA A 1 502 502 SMA SMA . 
J 6 HEC B 1 500 500 HEC HEC . 
K 7 FES C 1 500 500 FES FES . 
L 4 HEM D 1 500 500 HEM HEM . 
M 4 HEM D 1 501 501 HEM HEM . 
N 5 SMA D 1 502 502 SMA SMA . 
O 6 HEC E 1 500 500 HEC HEC . 
P 7 FES F 1 500 500 FES FES . 
Q 8 HOH A 1 2001 2001 HOH HOH . 
Q 8 HOH A 2 2002 2002 HOH HOH . 
Q 8 HOH A 3 2003 2003 HOH HOH . 
R 8 HOH B 1 2001 2001 HOH HOH . 
S 8 HOH D 1 2001 2001 HOH HOH . 
T 8 HOH F 1 2001 2001 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 . . . O 6 -23.639 -10.853 -0.726 1 32.21 ? FE HEC 500 E 1 
HETATM 2 C CHA HEC . . . O 6 -22.003 -13.026 1.4 1 29.52 ? CHA HEC 500 E 1 
HETATM 3 C CHB HEC . . . O 6 -25.714 -13.381 -1.569 1 30.13 ? CHB HEC 500 E 1 
HETATM 4 C CHC HEC . . . O 6 -25.527 -8.739 -2.646 1 28.21 ? CHC HEC 500 E 1 
HETATM 5 C CHD HEC . . . O 6 -21.456 -8.341 -0.062 1 30.4 ? CHD HEC 500 E 1 
HETATM 6 N NA HEC . . . O 6 -23.782 -12.814 -0.201 1 29.56 ? NA HEC 500 E 1 
HETATM 7 C C1A HEC . . . O 6 -23.065 -13.542 0.722 1 30.42 ? C1A HEC 500 E 1 
HETATM 8 C C2A HEC . . . O 6 -23.633 -14.88 0.807 1 32 ? C2A HEC 500 E 1 
HETATM 9 C C3A HEC . . . O 6 -24.643 -14.926 -0.037 1 31.75 ? C3A HEC 500 E 1 
HETATM 10 C C4A HEC . . . O 6 -24.745 -13.651 -0.673 1 30.54 ? C4A HEC 500 E 1 
HETATM 11 C CMA HEC . . . O 6 -25.562 -16.128 -0.319 1 31.02 ? CMA HEC 500 E 1 
HETATM 12 C CAA HEC . . . O 6 -23.28 -16.116 1.646 1 32.99 ? CAA HEC 500 E 1 
HETATM 13 C CBA HEC . . . O 6 -21.815 -16.232 2.004 1 34.13 ? CBA HEC 500 E 1 
HETATM 14 C CGA HEC . . . O 6 -21.654 -17.414 2.949 1 35.77 ? CGA HEC 500 E 1 
HETATM 15 O O1A HEC . . . O 6 -20.491 -17.51 3.44 1 36.89 ? O1A HEC 500 E 1 
HETATM 16 O O2A HEC . . . O 6 -22.625 -18.221 3.219 1 30.9 ? O2A HEC 500 E 1 
HETATM 17 N NB HEC . . . O 6 -25.316 -11.01 -1.814 1 29.33 ? NB HEC 500 E 1 
HETATM 18 C C1B HEC . . . O 6 -25.991 -12.168 -2.074 1 28.75 ? C1B HEC 500 E 1 
HETATM 19 C C2B HEC . . . O 6 -27.076 -11.918 -2.975 1 27.7 ? C2B HEC 500 E 1 
HETATM 20 C C3B HEC . . . O 6 -27.017 -10.636 -3.309 1 27.78 ? C3B HEC 500 E 1 
HETATM 21 C C4B HEC . . . O 6 -25.925 -10.036 -2.575 1 28.56 ? C4B HEC 500 E 1 
HETATM 22 C CMB HEC . . . O 6 -28.032 -12.986 -3.537 1 24.98 ? CMB HEC 500 E 1 
HETATM 23 C CAB HEC . . . O 6 -27.958 -9.938 -4.291 1 27.71 ? CAB HEC 500 E 1 
HETATM 24 C CBB HEC . . . O 6 -29.168 -9.48 -3.482 1 28.01 ? CBB HEC 500 E 1 
HETATM 25 N NC HEC . . . O 6 -23.508 -8.92 -1.246 1 28.76 ? NC HEC 500 E 1 
HETATM 26 C C1C HEC . . . O 6 -24.403 -8.233 -2.043 1 28.87 ? C1C HEC 500 E 1 
HETATM 27 C C2C HEC . . . O 6 -23.931 -6.873 -2.216 1 29.14 ? C2C HEC 500 E 1 
HETATM 28 C C3C HEC . . . O 6 -22.879 -6.721 -1.396 1 30.45 ? C3C HEC 500 E 1 
HETATM 29 C C4C HEC . . . O 6 -22.545 -8.026 -0.842 1 29.93 ? C4C HEC 500 E 1 
HETATM 30 C CMC HEC . . . O 6 -24.742 -5.74 -2.9 1 24.84 ? CMC HEC 500 E 1 
HETATM 31 C CAC HEC . . . O 6 -22.061 -5.408 -1.226 1 33.39 ? CAC HEC 500 E 1 
HETATM 32 C CBC HEC . . . O 6 -22.984 -4.175 -1.094 1 32.24 ? CBC HEC 500 E 1 
HETATM 33 N ND HEC . . . O 6 -22 -10.72 0.447 1 29.37 ? ND HEC 500 E 1 
HETATM 34 C C1D HEC . . . O 6 -21.24 -9.556 0.567 1 30.93 ? C1D HEC 500 E 1 
HETATM 35 C C2D HEC . . . O 6 -20.168 -9.817 1.511 1 31.16 ? C2D HEC 500 E 1 
HETATM 36 C C3D HEC . . . O 6 -20.34 -11.276 1.938 1 29.66 ? C3D HEC 500 E 1 
HETATM 37 C C4D HEC . . . O 6 -21.509 -11.749 1.257 1 29 ? C4D HEC 500 E 1 
HETATM 38 C CMD HEC . . . O 6 -19.064 -8.848 1.971 1 31.63 ? CMD HEC 500 E 1 
HETATM 39 C CAD HEC . . . O 6 -19.489 -12.057 2.941 1 29.1 ? CAD HEC 500 E 1 
HETATM 40 C CBD HEC . . . O 6 -20.387 -12.29 4.142 1 29.6 ? CBD HEC 500 E 1 
HETATM 41 C CGD HEC . . . O 6 -19.546 -12.96 5.171 1 31.24 ? CGD HEC 500 E 1 
HETATM 42 O O1D HEC . . . O 6 -19.248 -14.175 5.058 1 33.53 ? O1D HEC 500 E 1 
HETATM 43 O O2D HEC . . . O 6 -19.148 -12.254 6.108 1 34.08 ? O2D HEC 500 E 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#