data_4CDY
#
_model_server_result.job_id            D4gh7QdO0Dx_x0WXERLoKQ 
_model_server_result.datetime_utc      '2024-11-22 17:55:37' 
_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          4cdy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1127}' 
#
_entry.id    4CDY 
#
_exptl.entry_id    4CDY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          2 
_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         120 
_cell.entry_id            4CDY 
_cell.length_a            53.623 
_cell.length_b            53.623 
_cell.length_c            181.724 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4CDY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 26.8115 46.43888 30.287333 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 A C PCA 1 A PCA 1 1_555 A N PHE 2 A PHE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
metalc ? metalc1 A NE2 HIS 120 A HIS 120 1_555 B FE HEC . A HEC 1127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? 
#
_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                     4CDY 
_atom_sites.fract_transf_matrix[1][1]    0.018649 
_atom_sites.fract_transf_matrix[1][2]    0.010767 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021534 
_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]    0.005503 
_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
B 2 HEC A 1 1127 1127 HEC HEC . 
C 3 HOH A 1 2001 2001 HOH HOH . 
C 3 HOH A 2 2002 2002 HOH HOH . 
C 3 HOH A 3 2003 2003 HOH HOH . 
C 3 HOH A 4 2004 2004 HOH HOH . 
C 3 HOH A 5 2005 2005 HOH HOH . 
C 3 HOH A 6 2006 2006 HOH HOH . 
C 3 HOH A 7 2007 2007 HOH HOH . 
C 3 HOH A 8 2008 2008 HOH HOH . 
C 3 HOH A 9 2009 2009 HOH HOH . 
C 3 HOH A 10 2010 2010 HOH HOH . 
C 3 HOH A 11 2011 2011 HOH HOH . 
C 3 HOH A 12 2012 2012 HOH HOH . 
C 3 HOH A 13 2013 2013 HOH HOH . 
C 3 HOH A 14 2014 2014 HOH HOH . 
C 3 HOH A 15 2015 2015 HOH HOH . 
C 3 HOH A 16 2016 2016 HOH HOH . 
C 3 HOH A 17 2017 2017 HOH HOH . 
C 3 HOH A 18 2018 2018 HOH HOH . 
C 3 HOH A 19 2019 2019 HOH HOH . 
C 3 HOH A 20 2020 2020 HOH HOH . 
C 3 HOH A 21 2021 2021 HOH HOH . 
C 3 HOH A 22 2022 2022 HOH HOH . 
C 3 HOH A 23 2023 2023 HOH HOH . 
C 3 HOH A 24 2024 2024 HOH HOH . 
C 3 HOH A 25 2025 2025 HOH HOH . 
C 3 HOH A 26 2026 2026 HOH HOH . 
C 3 HOH A 27 2027 2027 HOH HOH . 
C 3 HOH A 28 2028 2028 HOH HOH . 
C 3 HOH A 29 2029 2029 HOH HOH . 
C 3 HOH A 30 2030 2030 HOH HOH . 
C 3 HOH A 31 2031 2031 HOH HOH . 
C 3 HOH A 32 2032 2032 HOH HOH . 
C 3 HOH A 33 2033 2033 HOH HOH . 
C 3 HOH A 34 2034 2034 HOH HOH . 
C 3 HOH A 35 2035 2035 HOH HOH . 
C 3 HOH A 36 2036 2036 HOH HOH . 
C 3 HOH A 37 2037 2037 HOH HOH . 
C 3 HOH A 38 2038 2038 HOH HOH . 
C 3 HOH A 39 2039 2039 HOH HOH . 
C 3 HOH A 40 2040 2040 HOH HOH . 
C 3 HOH A 41 2041 2041 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 . . . B 2 7.005 39.332 21.732 1 25.74 ? FE HEC 1127 A 1 
HETATM 2 C CHA HEC . . . B 2 8.526 36.341 21.69 1 25.37 ? CHA HEC 1127 A 1 
HETATM 3 C CHB HEC . . . B 2 7.001 39.357 18.334 1 28.43 ? CHB HEC 1127 A 1 
HETATM 4 C CHC HEC . . . B 2 4.68 41.807 21.743 1 31.44 ? CHC HEC 1127 A 1 
HETATM 5 C CHD HEC . . . B 2 6.667 39.079 25.095 1 24.89 ? CHD HEC 1127 A 1 
HETATM 6 N NA HEC . . . B 2 7.619 38.064 20.264 1 26.74 ? NA HEC 1127 A 1 
HETATM 7 C C1A HEC . . . B 2 8.263 36.855 20.421 1 25.97 ? C1A HEC 1127 A 1 
HETATM 8 C C2A HEC . . . B 2 8.644 36.27 19.204 1 26.92 ? C2A HEC 1127 A 1 
HETATM 9 C C3A HEC . . . B 2 8.166 37.15 18.227 1 29.68 ? C3A HEC 1127 A 1 
HETATM 10 C C4A HEC . . . B 2 7.607 38.231 18.919 1 28.8 ? C4A HEC 1127 A 1 
HETATM 11 C CMA HEC . . . B 2 8.092 36.912 16.751 1 32.54 ? CMA HEC 1127 A 1 
HETATM 12 C CAA HEC . . . B 2 9.4 34.98 18.944 1 30.34 ? CAA HEC 1127 A 1 
HETATM 13 C CBA HEC . . . B 2 8.388 33.851 18.908 1 29.04 ? CBA HEC 1127 A 1 
HETATM 14 C CGA HEC . . . B 2 9.064 32.573 18.427 1 37.66 ? CGA HEC 1127 A 1 
HETATM 15 O O1A HEC . . . B 2 9.637 31.831 19.251 1 34.79 ? O1A HEC 1127 A 1 
HETATM 16 O O2A HEC . . . B 2 8.996 32.286 17.226 1 41.03 ? O2A HEC 1127 A 1 
HETATM 17 N NB HEC . . . B 2 6.069 40.45 20.275 1 29.11 ? NB HEC 1127 A 1 
HETATM 18 C C1B HEC . . . B 2 6.283 40.381 18.976 1 28.25 ? C1B HEC 1127 A 1 
HETATM 19 C C2B HEC . . . B 2 5.616 41.426 18.309 1 35.43 ? C2B HEC 1127 A 1 
HETATM 20 C C3B HEC . . . B 2 4.862 42.102 19.287 1 34.85 ? C3B HEC 1127 A 1 
HETATM 21 C C4B HEC . . . B 2 5.218 41.475 20.486 1 32.32 ? C4B HEC 1127 A 1 
HETATM 22 C CMB HEC . . . B 2 5.791 41.739 16.836 1 42.65 ? CMB HEC 1127 A 1 
HETATM 23 C CAB HEC . . . B 2 3.754 43.126 19.186 1 37.77 ? CAB HEC 1127 A 1 
HETATM 24 C CBB HEC . . . B 2 3.24 43.413 17.801 1 40.18 ? CBB HEC 1127 A 1 
HETATM 25 N NC HEC . . . B 2 5.947 40.281 23.146 1 26.79 ? NC HEC 1127 A 1 
HETATM 26 C C1C HEC . . . B 2 5.07 41.294 23.015 1 28.5 ? C1C HEC 1127 A 1 
HETATM 27 C C2C HEC . . . B 2 4.548 41.78 24.199 1 30.14 ? C2C HEC 1127 A 1 
HETATM 28 C C3C HEC . . . B 2 5.105 40.998 25.192 1 29.36 ? C3C HEC 1127 A 1 
HETATM 29 C C4C HEC . . . B 2 5.97 40.119 24.483 1 27.17 ? C4C HEC 1127 A 1 
HETATM 30 C CMC HEC . . . B 2 3.611 42.942 24.346 1 31.26 ? CMC HEC 1127 A 1 
HETATM 31 C CAC HEC . . . B 2 4.765 40.887 26.644 1 30.95 ? CAC HEC 1127 A 1 
HETATM 32 C CBC HEC . . . B 2 3.589 41.699 27.187 1 31.2 ? CBC HEC 1127 A 1 
HETATM 33 N ND HEC . . . B 2 7.516 37.927 23.184 1 24.9 ? ND HEC 1127 A 1 
HETATM 34 C C1D HEC . . . B 2 7.361 38.02 24.507 1 24.55 ? C1D HEC 1127 A 1 
HETATM 35 C C2D HEC . . . B 2 7.958 36.909 25.185 1 24.4 ? C2D HEC 1127 A 1 
HETATM 36 C C3D HEC . . . B 2 8.464 36.106 24.192 1 24.17 ? C3D HEC 1127 A 1 
HETATM 37 C C4D HEC . . . B 2 8.171 36.782 22.976 1 22.6 ? C4D HEC 1127 A 1 
HETATM 38 C CMD HEC . . . B 2 8.02 36.653 26.665 1 25.26 ? CMD HEC 1127 A 1 
HETATM 39 C CAD HEC . . . B 2 9.131 34.739 24.399 1 22.82 ? CAD HEC 1127 A 1 
HETATM 40 C CBD HEC . . . B 2 8.104 33.622 24.316 1 25.23 ? CBD HEC 1127 A 1 
HETATM 41 C CGD HEC . . . B 2 8.709 32.241 24.409 1 28.05 ? CGD HEC 1127 A 1 
HETATM 42 O O1D HEC . . . B 2 9.726 31.968 23.724 1 26.83 ? O1D HEC 1127 A 1 
HETATM 43 O O2D HEC . . . B 2 8.163 31.446 25.166 1 27.64 ? O2D HEC 1127 A 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           43 
#