data_1YCB
#
_model_server_result.job_id            '_MavIO9yl_4zD8-ypJvxkw' 
_model_server_result.datetime_utc      '2024-11-08 07:38:14' 
_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          1ycb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":154}' 
#
_entry.id    1YCB 
#
_exptl.entry_id    1YCB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          2 
_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          92 
_cell.angle_gamma         90 
_cell.entry_id            1YCB 
_cell.length_a            124.6 
_cell.length_b            42.5 
_cell.length_c            92 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YCB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 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
? 2 C N N 
? 2 D 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
metalc ? metalc1 A NE2 HIS 93 A HIS 93 1_555 C FE HEM . A HEM 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc2 C FE HEM . A HEM 154 1_555 E O HOH . A HOH 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? 
metalc ? metalc3 B NE2 HIS 93 B HIS 93 1_555 D FE HEM . B HEM 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc4 D FE HEM . B HEM 154 1_555 F O HOH . B HOH 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? 
#
_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 116 n n 
CHA C4D HEM doub 117 n n 
CHA HHA HEM sing 118 n n 
CHB C4A HEM sing 119 n n 
CHB C1B HEM doub 120 n n 
CHB HHB HEM sing 121 n n 
CHC C4B HEM sing 122 n n 
CHC C1C HEM doub 123 n n 
CHC HHC HEM sing 124 n n 
CHD C4C HEM doub 125 n n 
CHD C1D HEM sing 126 n n 
CHD HHD HEM sing 127 n n 
C1A C2A HEM doub 128 n y 
C1A NA HEM sing 129 n y 
C2A C3A HEM sing 130 n y 
C2A CAA HEM sing 131 n n 
C3A C4A HEM doub 132 n y 
C3A CMA HEM sing 133 n n 
C4A NA HEM sing 134 n y 
CMA HMA HEM sing 135 n n 
CMA HMAA HEM sing 136 n n 
CMA HMAB HEM sing 137 n n 
CAA CBA HEM sing 138 n n 
CAA HAA HEM sing 139 n n 
CAA HAAA HEM sing 140 n n 
CBA CGA HEM sing 141 n n 
CBA HBA HEM sing 142 n n 
CBA HBAA HEM sing 143 n n 
CGA O1A HEM doub 144 n n 
CGA O2A HEM sing 145 n n 
C1B C2B HEM sing 146 n n 
C1B NB HEM sing 147 n n 
C2B C3B HEM doub 148 n n 
C2B CMB HEM sing 149 n n 
C3B C4B HEM sing 150 n n 
C3B CAB HEM sing 151 n n 
C4B NB HEM doub 152 n n 
CMB HMB HEM sing 153 n n 
CMB HMBA HEM sing 154 n n 
CMB HMBB HEM sing 155 n n 
CAB CBB HEM doub 156 n n 
CAB HAB HEM sing 157 n n 
CBB HBB HEM sing 158 n n 
CBB HBBA HEM sing 159 n n 
C1C C2C HEM sing 160 n y 
C1C NC HEM sing 161 n y 
C2C C3C HEM doub 162 n y 
C2C CMC HEM sing 163 n n 
C3C C4C HEM sing 164 n y 
C3C CAC HEM sing 165 n n 
C4C NC HEM sing 166 n y 
CMC HMC HEM sing 167 n n 
CMC HMCA HEM sing 168 n n 
CMC HMCB HEM sing 169 n n 
CAC CBC HEM doub 170 n n 
CAC HAC HEM sing 171 n n 
CBC HBC HEM sing 172 n n 
CBC HBCA HEM sing 173 n n 
C1D C2D HEM sing 174 n n 
C1D ND HEM doub 175 n n 
C2D C3D HEM doub 176 n n 
C2D CMD HEM sing 177 n n 
C3D C4D HEM sing 178 n n 
C3D CAD HEM sing 179 n n 
C4D ND HEM sing 180 n n 
CMD HMD HEM sing 181 n n 
CMD HMDA HEM sing 182 n n 
CMD HMDB HEM sing 183 n n 
CAD CBD HEM sing 184 n n 
CAD HAD HEM sing 185 n n 
CAD HADA HEM sing 186 n n 
CBD CGD HEM sing 187 n n 
CBD HBD HEM sing 188 n n 
CBD HBDA HEM sing 189 n n 
CGD O1D HEM doub 190 n n 
CGD O2D HEM sing 191 n n 
O2A H2A HEM sing 192 n n 
O2D H2D HEM sing 193 n n 
FE NA HEM sing 194 n n 
FE NB HEM sing 195 n n 
FE NC HEM sing 196 n n 
FE ND HEM sing 197 n n 
#
_atom_sites.entry_id                     1YCB 
_atom_sites.fract_transf_matrix[1][1]    0.008026 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00028 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023529 
_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]    0.010876 
_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 2 HEM A 1 154 154 HEM HEM . 
D 2 HEM B 1 154 154 HEM HEM . 
E 3 HOH A 1 155 1 HOH HOH . 
E 3 HOH A 2 156 4 HOH HOH . 
E 3 HOH A 3 157 7 HOH HOH . 
E 3 HOH A 4 158 8 HOH HOH . 
E 3 HOH A 5 159 9 HOH HOH . 
E 3 HOH A 6 160 13 HOH HOH . 
E 3 HOH A 7 161 1 HOH HOH . 
E 3 HOH A 8 162 2 HOH HOH . 
E 3 HOH A 9 163 3 HOH HOH . 
E 3 HOH A 10 164 4 HOH HOH . 
E 3 HOH A 11 165 5 HOH HOH . 
E 3 HOH A 12 166 6 HOH HOH . 
E 3 HOH A 13 167 7 HOH HOH . 
E 3 HOH A 14 168 8 HOH HOH . 
E 3 HOH A 15 169 9 HOH HOH . 
E 3 HOH A 16 170 10 HOH HOH . 
E 3 HOH A 17 171 11 HOH HOH . 
E 3 HOH A 18 172 12 HOH HOH . 
E 3 HOH A 19 173 13 HOH HOH . 
E 3 HOH A 20 174 14 HOH HOH . 
E 3 HOH A 21 175 15 HOH HOH . 
E 3 HOH A 22 176 16 HOH HOH . 
E 3 HOH A 23 177 17 HOH HOH . 
E 3 HOH A 24 178 18 HOH HOH . 
E 3 HOH A 25 179 19 HOH HOH . 
E 3 HOH A 26 180 20 HOH HOH . 
E 3 HOH A 27 181 21 HOH HOH . 
E 3 HOH A 28 182 22 HOH HOH . 
E 3 HOH A 29 183 23 HOH HOH . 
E 3 HOH A 30 184 24 HOH HOH . 
E 3 HOH A 31 185 25 HOH HOH . 
E 3 HOH A 32 186 26 HOH HOH . 
E 3 HOH A 33 187 27 HOH HOH . 
E 3 HOH A 34 188 28 HOH HOH . 
E 3 HOH A 35 189 29 HOH HOH . 
E 3 HOH A 36 190 30 HOH HOH . 
E 3 HOH A 37 191 31 HOH HOH . 
E 3 HOH A 38 192 32 HOH HOH . 
E 3 HOH A 39 193 33 HOH HOH . 
E 3 HOH A 40 194 34 HOH HOH . 
E 3 HOH A 41 195 35 HOH HOH . 
E 3 HOH A 42 196 36 HOH HOH . 
E 3 HOH A 43 197 37 HOH HOH . 
F 3 HOH B 1 155 2 HOH HOH . 
F 3 HOH B 2 156 3 HOH HOH . 
F 3 HOH B 3 157 5 HOH HOH . 
F 3 HOH B 4 158 6 HOH HOH . 
F 3 HOH B 5 159 10 HOH HOH . 
F 3 HOH B 6 160 11 HOH HOH . 
F 3 HOH B 7 161 12 HOH HOH . 
F 3 HOH B 8 162 1 HOH HOH . 
F 3 HOH B 9 163 2 HOH HOH . 
F 3 HOH B 10 164 3 HOH HOH . 
F 3 HOH B 11 165 4 HOH HOH . 
F 3 HOH B 12 166 5 HOH HOH . 
F 3 HOH B 13 167 6 HOH HOH . 
F 3 HOH B 14 168 7 HOH HOH . 
F 3 HOH B 15 169 8 HOH HOH . 
F 3 HOH B 16 170 9 HOH HOH . 
F 3 HOH B 17 171 10 HOH HOH . 
F 3 HOH B 18 172 11 HOH HOH . 
F 3 HOH B 19 173 12 HOH HOH . 
F 3 HOH B 20 174 13 HOH HOH . 
F 3 HOH B 21 175 14 HOH HOH . 
F 3 HOH B 22 176 15 HOH HOH . 
F 3 HOH B 23 177 16 HOH HOH . 
F 3 HOH B 24 178 17 HOH HOH . 
F 3 HOH B 25 179 18 HOH HOH . 
F 3 HOH B 26 180 19 HOH HOH . 
F 3 HOH B 27 181 20 HOH HOH . 
F 3 HOH B 28 182 21 HOH HOH . 
F 3 HOH B 29 183 22 HOH HOH . 
F 3 HOH B 30 184 23 HOH HOH . 
F 3 HOH B 31 185 24 HOH HOH . 
F 3 HOH B 32 186 25 HOH HOH . 
F 3 HOH B 33 187 26 HOH HOH . 
F 3 HOH B 34 188 27 HOH HOH . 
F 3 HOH B 35 189 28 HOH HOH . 
F 3 HOH B 36 190 29 HOH HOH . 
F 3 HOH B 37 191 30 HOH HOH . 
F 3 HOH B 38 192 31 HOH HOH . 
F 3 HOH B 39 193 32 HOH HOH . 
F 3 HOH B 40 194 33 HOH HOH . 
F 3 HOH B 41 195 34 HOH HOH . 
F 3 HOH B 42 196 35 HOH HOH . 
F 3 HOH B 43 197 36 HOH HOH . 
F 3 HOH B 44 198 37 HOH HOH . 
F 3 HOH B 45 199 38 HOH HOH . 
F 3 HOH B 46 200 39 HOH HOH . 
F 3 HOH B 47 201 40 HOH HOH . 
F 3 HOH B 48 202 41 HOH HOH . 
F 3 HOH B 49 203 42 HOH HOH . 
F 3 HOH B 50 204 43 HOH HOH . 
F 3 HOH B 51 205 44 HOH HOH . 
F 3 HOH B 52 206 45 HOH HOH . 
F 3 HOH B 53 207 46 HOH HOH . 
F 3 HOH B 54 208 47 HOH HOH . 
F 3 HOH B 55 209 48 HOH HOH . 
F 3 HOH B 56 210 49 HOH HOH . 
F 3 HOH B 57 211 50 HOH HOH . 
F 3 HOH B 58 212 51 HOH HOH . 
F 3 HOH B 59 213 52 HOH HOH . 
F 3 HOH B 60 214 53 HOH HOH . 
F 3 HOH B 61 215 54 HOH HOH . 
F 3 HOH B 62 216 55 HOH HOH . 
F 3 HOH B 63 217 56 HOH HOH . 
F 3 HOH B 64 218 57 HOH HOH . 
F 3 HOH B 65 219 58 HOH HOH . 
F 3 HOH B 66 220 59 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 . . . D 2 16.034 -13.731 53.21 1 16.13 ? CHA HEM 154 B 1 
HETATM 2 C CHB HEM . . . D 2 13.382 -14.255 49.16 1 13.66 ? CHB HEM 154 B 1 
HETATM 3 C CHC HEM . . . D 2 13.325 -19.004 49.842 1 13.05 ? CHC HEM 154 B 1 
HETATM 4 C CHD HEM . . . D 2 15.891 -18.599 53.951 1 15.19 ? CHD HEM 154 B 1 
HETATM 5 C C1A HEM . . . D 2 15.34 -13.425 52.059 1 15.52 ? C1A HEM 154 B 1 
HETATM 6 C C2A HEM . . . D 2 15.086 -12.134 51.441 1 15.62 ? C2A HEM 154 B 1 
HETATM 7 C C3A HEM . . . D 2 14.356 -12.306 50.349 1 14.72 ? C3A HEM 154 B 1 
HETATM 8 C C4A HEM . . . D 2 14.102 -13.739 50.241 1 14.67 ? C4A HEM 154 B 1 
HETATM 9 C CMA HEM . . . D 2 13.823 -11.381 49.238 1 14.21 ? CMA HEM 154 B 1 
HETATM 10 C CAA HEM . . . D 2 15.638 -10.761 51.928 1 17.74 ? CAA HEM 154 B 1 
HETATM 11 C CBA HEM . . . D 2 17.008 -10.323 51.408 1 17.78 ? CBA HEM 154 B 1 
HETATM 12 C CGA HEM . . . D 2 18.093 -11.289 51.18 1 18.64 ? CGA HEM 154 B 1 
HETATM 13 O O1A HEM . . . D 2 18.93 -11.583 52.092 1 20 ? O1A HEM 154 B 1 
HETATM 14 O O2A HEM . . . D 2 18.229 -11.821 50.04 1 19.26 ? O2A HEM 154 B 1 
HETATM 15 C C1B HEM . . . D 2 13.201 -15.587 48.911 1 12.39 ? C1B HEM 154 B 1 
HETATM 16 C C2B HEM . . . D 2 12.543 -16.197 47.799 1 11.79 ? C2B HEM 154 B 1 
HETATM 17 C C3B HEM . . . D 2 12.534 -17.529 47.976 1 11.73 ? C3B HEM 154 B 1 
HETATM 18 C C4B HEM . . . D 2 13.15 -17.778 49.241 1 12.8 ? C4B HEM 154 B 1 
HETATM 19 C CMB HEM . . . D 2 12.02 -15.381 46.619 1 10.8 ? CMB HEM 154 B 1 
HETATM 20 C CAB HEM . . . D 2 11.937 -18.607 47.047 1 11.89 ? CAB HEM 154 B 1 
HETATM 21 C CBB HEM . . . D 2 10.629 -18.574 46.659 1 11.45 ? CBB HEM 154 B 1 
HETATM 22 C C1C HEM . . . D 2 14.095 -19.299 50.948 1 13.43 ? C1C HEM 154 B 1 
HETATM 23 C C2C HEM . . . D 2 14.058 -20.55 51.662 1 13.29 ? C2C HEM 154 B 1 
HETATM 24 C C3C HEM . . . D 2 14.689 -20.393 52.804 1 13.33 ? C3C HEM 154 B 1 
HETATM 25 C C4C HEM . . . D 2 15.149 -19.049 52.871 1 14.26 ? C4C HEM 154 B 1 
HETATM 26 C CMC HEM . . . D 2 13.363 -21.821 51.101 1 14.19 ? CMC HEM 154 B 1 
HETATM 27 C CAC HEM . . . D 2 14.92 -21.421 53.968 1 13.89 ? CAC HEM 154 B 1 
HETATM 28 C CBC HEM . . . D 2 14.349 -22.638 53.7 1 12.93 ? CBC HEM 154 B 1 
HETATM 29 C C1D HEM . . . D 2 16.145 -17.248 53.999 1 16.08 ? C1D HEM 154 B 1 
HETATM 30 C C2D HEM . . . D 2 16.744 -16.697 55.178 1 17.18 ? C2D HEM 154 B 1 
HETATM 31 C C3D HEM . . . D 2 16.786 -15.369 55 1 18.28 ? C3D HEM 154 B 1 
HETATM 32 C C4D HEM . . . D 2 16.177 -15.032 53.733 1 17.47 ? C4D HEM 154 B 1 
HETATM 33 C CMD HEM . . . D 2 17.275 -17.583 56.36 1 17.22 ? CMD HEM 154 B 1 
HETATM 34 C CAD HEM . . . D 2 17.352 -14.321 56.014 1 20.66 ? CAD HEM 154 B 1 
HETATM 35 C CBD HEM . . . D 2 16.214 -13.933 56.998 1 23.9 ? CBD HEM 154 B 1 
HETATM 36 C CGD HEM . . . D 2 16.653 -13.067 58.136 1 26.38 ? CGD HEM 154 B 1 
HETATM 37 O O1D HEM . . . D 2 17.284 -13.695 59.068 1 28.38 ? O1D HEM 154 B 1 
HETATM 38 O O2D HEM . . . D 2 16.352 -11.839 58.094 1 28.06 ? O2D HEM 154 B 1 
HETATM 39 N NA HEM . . . D 2 14.701 -14.405 51.318 1 14.42 ? NA HEM 154 B 1 
HETATM 40 N NB HEM . . . D 2 13.599 -16.575 49.829 1 13.68 ? NB HEM 154 B 1 
HETATM 41 N NC HEM . . . D 2 14.785 -18.353 51.7 1 14.16 ? NC HEM 154 B 1 
HETATM 42 N ND HEM . . . D 2 15.796 -16.241 53.149 1 15.89 ? ND HEM 154 B 1 
HETATM 43 FE FE HEM . . . D 2 14.867 -16.356 51.393 1 16.33 ? FE HEM 154 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           43 
#