data_2D2M # _model_server_result.job_id dkGE_M9IijId8aojODbhmg _model_server_result.datetime_utc '2024-10-14 05:22:02' _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 2d2m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":200}' # _entry.id 2D2M # _exptl.entry_id 2D2M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 4 _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 2D2M _cell.length_a 111.498 _cell.length_b 111.498 _cell.length_c 276.835 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D2M _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _pdbx_struct_assembly.details author_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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 276.835 5 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 276.835 6 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 276.835 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 G N N ? 5 I N N ? 5 K 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 A SG CYS 2 A CYS 2 1_555 A SG CYS 130 A CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 121 A CYS 121 1_555 C SG CYS 126 C CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf3 B SG CYS 2 B CYS 2 1_555 B SG CYS 132 B CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 C SG CYS 4 C CYS 4 1_555 C SG CYS 135 C CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 D SG CYS 3 D CYS 3 1_555 D SG CYS 133 D CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A NE2 HIS 94 A HIS 94 1_555 E FE HEM . A HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc2 E FE HEM . A HEM 200 1_555 F O1 OXY . A OXY 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? metalc ? metalc3 E FE HEM . A HEM 200 1_555 F O2 OXY . A OXY 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc4 B NE2 HIS 94 B HIS 94 1_555 G FE HEM . B HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc5 G FE HEM . B HEM 200 1_555 H O2 OXY . B OXY 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc6 G FE HEM . B HEM 200 1_555 H O1 OXY . B OXY 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.801 ? metalc ? metalc7 C NE2 HIS 98 C HIS 98 1_555 I FE HEM . C HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc8 I FE HEM . C HEM 200 1_555 J O2 OXY . C OXY 2201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? metalc ? metalc9 I FE HEM . C HEM 200 1_555 J O1 OXY . C OXY 2201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.798 ? metalc ? metalc10 D NE2 HIS 96 D HIS 96 1_555 K FE HEM . D HEM 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc11 K FE HEM . D HEM 200 1_555 L O1 OXY . D OXY 3201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.799 ? metalc ? metalc12 K FE HEM . D HEM 200 1_555 L O2 OXY . D OXY 3201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? # _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 129 n n CHA C4D HEM doub 130 n n CHA HHA HEM sing 131 n n CHB C4A HEM sing 132 n n CHB C1B HEM doub 133 n n CHB HHB HEM sing 134 n n CHC C4B HEM sing 135 n n CHC C1C HEM doub 136 n n CHC HHC HEM sing 137 n n CHD C4C HEM doub 138 n n CHD C1D HEM sing 139 n n CHD HHD HEM sing 140 n n C1A C2A HEM doub 141 n y C1A NA HEM sing 142 n y C2A C3A HEM sing 143 n y C2A CAA HEM sing 144 n n C3A C4A HEM doub 145 n y C3A CMA HEM sing 146 n n C4A NA HEM sing 147 n y CMA HMA HEM sing 148 n n CMA HMAA HEM sing 149 n n CMA HMAB HEM sing 150 n n CAA CBA HEM sing 151 n n CAA HAA HEM sing 152 n n CAA HAAA HEM sing 153 n n CBA CGA HEM sing 154 n n CBA HBA HEM sing 155 n n CBA HBAA HEM sing 156 n n CGA O1A HEM doub 157 n n CGA O2A HEM sing 158 n n C1B C2B HEM sing 159 n n C1B NB HEM sing 160 n n C2B C3B HEM doub 161 n n C2B CMB HEM sing 162 n n C3B C4B HEM sing 163 n n C3B CAB HEM sing 164 n n C4B NB HEM doub 165 n n CMB HMB HEM sing 166 n n CMB HMBA HEM sing 167 n n CMB HMBB HEM sing 168 n n CAB CBB HEM doub 169 n n CAB HAB HEM sing 170 n n CBB HBB HEM sing 171 n n CBB HBBA HEM sing 172 n n C1C C2C HEM sing 173 n y C1C NC HEM sing 174 n y C2C C3C HEM doub 175 n y C2C CMC HEM sing 176 n n C3C C4C HEM sing 177 n y C3C CAC HEM sing 178 n n C4C NC HEM sing 179 n y CMC HMC HEM sing 180 n n CMC HMCA HEM sing 181 n n CMC HMCB HEM sing 182 n n CAC CBC HEM doub 183 n n CAC HAC HEM sing 184 n n CBC HBC HEM sing 185 n n CBC HBCA HEM sing 186 n n C1D C2D HEM sing 187 n n C1D ND HEM doub 188 n n C2D C3D HEM doub 189 n n C2D CMD HEM sing 190 n n C3D C4D HEM sing 191 n n C3D CAD HEM sing 192 n n C4D ND HEM sing 193 n n CMD HMD HEM sing 194 n n CMD HMDA HEM sing 195 n n CMD HMDB HEM sing 196 n n CAD CBD HEM sing 197 n n CAD HAD HEM sing 198 n n CAD HADA HEM sing 199 n n CBD CGD HEM sing 200 n n CBD HBD HEM sing 201 n n CBD HBDA HEM sing 202 n n CGD O1D HEM doub 203 n n CGD O2D HEM sing 204 n n O2A H2A HEM sing 205 n n O2D H2D HEM sing 206 n n FE NA HEM sing 207 n n FE NB HEM sing 208 n n FE NC HEM sing 209 n n FE ND HEM sing 210 n n # _atom_sites.entry_id 2D2M _atom_sites.fract_transf_matrix[1][1] 0.008969 _atom_sites.fract_transf_matrix[1][2] 0.005178 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010356 _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] 0.003612 _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 E 5 HEM A 1 200 200 HEM HEM . F 6 OXY A 1 201 201 OXY O2 . G 5 HEM B 1 200 200 HEM HEM . H 6 OXY B 1 1201 1201 OXY O2 . I 5 HEM C 1 200 200 HEM HEM . J 6 OXY C 1 2201 2201 OXY O2 . K 5 HEM D 1 200 200 HEM HEM . L 6 OXY D 1 3201 3201 OXY O2 . M 7 HOH A 1 1002 1002 HOH HOH . M 7 HOH A 2 1003 1003 HOH HOH . M 7 HOH A 3 1004 1004 HOH HOH . M 7 HOH A 4 1007 1007 HOH HOH . M 7 HOH A 5 1009 1009 HOH HOH . M 7 HOH A 6 1013 1013 HOH HOH . N 7 HOH B 1 1008 1008 HOH HOH . O 7 HOH C 1 1001 1001 HOH HOH . O 7 HOH C 2 1005 1005 HOH HOH . O 7 HOH C 3 1012 1012 HOH HOH . P 7 HOH D 1 1006 1006 HOH HOH . P 7 HOH D 2 1010 1010 HOH HOH . P 7 HOH D 3 1011 1011 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 . . . K 5 -5.172 48.773 120.099 1 87.77 ? CHA HEM 200 D 1 HETATM 2 C CHB HEM . . . K 5 -6.826 44.232 120.645 1 87.77 ? CHB HEM 200 D 1 HETATM 3 C CHC HEM . . . K 5 -10.363 45.125 117.45 1 87.77 ? CHC HEM 200 D 1 HETATM 4 C CHD HEM . . . K 5 -8.286 49.39 116.406 1 87.77 ? CHD HEM 200 D 1 HETATM 5 C C1A HEM . . . K 5 -5.264 47.444 120.515 1 87.77 ? C1A HEM 200 D 1 HETATM 6 C C2A HEM . . . K 5 -4.334 46.74 121.42 1 87.77 ? C2A HEM 200 D 1 HETATM 7 C C3A HEM . . . K 5 -4.849 45.486 121.621 1 87.77 ? C3A HEM 200 D 1 HETATM 8 C C4A HEM . . . K 5 -6.034 45.381 120.774 1 87.77 ? C4A HEM 200 D 1 HETATM 9 C CMA HEM . . . K 5 -4.324 44.391 122.525 1 87.77 ? CMA HEM 200 D 1 HETATM 10 C CAA HEM . . . K 5 -3.052 47.307 121.995 1 87.77 ? CAA HEM 200 D 1 HETATM 11 C CBA HEM . . . K 5 -3.297 47.996 123.332 1 87.77 ? CBA HEM 200 D 1 HETATM 12 C CGA HEM . . . K 5 -2.691 49.383 123.481 1 87.77 ? CGA HEM 200 D 1 HETATM 13 O O1A HEM . . . K 5 -1.878 49.578 124.42 1 87.77 ? O1A HEM 200 D 1 HETATM 14 O O2A HEM . . . K 5 -3.031 50.275 122.653 1 87.77 ? O2A HEM 200 D 1 HETATM 15 C C1B HEM . . . K 5 -7.836 44.023 119.714 1 87.77 ? C1B HEM 200 D 1 HETATM 16 C C2B HEM . . . K 5 -8.449 42.744 119.392 1 87.77 ? C2B HEM 200 D 1 HETATM 17 C C3B HEM . . . K 5 -9.635 43.068 118.792 1 87.77 ? C3B HEM 200 D 1 HETATM 18 C C4B HEM . . . K 5 -9.513 44.451 118.349 1 87.77 ? C4B HEM 200 D 1 HETATM 19 C CMB HEM . . . K 5 -7.855 41.391 119.674 1 87.77 ? CMB HEM 200 D 1 HETATM 20 C CAB HEM . . . K 5 -10.856 42.253 118.615 1 87.77 ? CAB HEM 200 D 1 HETATM 21 C CBB HEM . . . K 5 -11 41.153 117.898 1 87.77 ? CBB HEM 200 D 1 HETATM 22 C C1C HEM . . . K 5 -10.162 46.389 116.886 1 87.77 ? C1C HEM 200 D 1 HETATM 23 C C2C HEM . . . K 5 -10.973 47.001 115.827 1 87.77 ? C2C HEM 200 D 1 HETATM 24 C C3C HEM . . . K 5 -10.436 48.251 115.596 1 87.77 ? C3C HEM 200 D 1 HETATM 25 C C4C HEM . . . K 5 -9.225 48.348 116.431 1 87.77 ? C4C HEM 200 D 1 HETATM 26 C CMC HEM . . . K 5 -12.169 46.334 115.168 1 87.77 ? CMC HEM 200 D 1 HETATM 27 C CAC HEM . . . K 5 -10.949 49.338 114.721 1 87.77 ? CAC HEM 200 D 1 HETATM 28 C CBC HEM . . . K 5 -10.95 49.365 113.389 1 87.77 ? CBC HEM 200 D 1 HETATM 29 C C1D HEM . . . K 5 -7.269 49.649 117.337 1 87.77 ? C1D HEM 200 D 1 HETATM 30 C C2D HEM . . . K 5 -6.448 50.846 117.385 1 87.77 ? C2D HEM 200 D 1 HETATM 31 C C3D HEM . . . K 5 -5.586 50.687 118.459 1 87.77 ? C3D HEM 200 D 1 HETATM 32 C C4D HEM . . . K 5 -5.853 49.374 119.029 1 87.77 ? C4D HEM 200 D 1 HETATM 33 C CMD HEM . . . K 5 -6.543 52.014 116.436 1 87.77 ? CMD HEM 200 D 1 HETATM 34 C CAD HEM . . . K 5 -4.572 51.686 118.949 1 87.77 ? CAD HEM 200 D 1 HETATM 35 C CBD HEM . . . K 5 -3.237 51.612 118.179 1 87.77 ? CBD HEM 200 D 1 HETATM 36 C CGD HEM . . . K 5 -2.185 52.414 118.937 1 87.77 ? CGD HEM 200 D 1 HETATM 37 O O1D HEM . . . K 5 -1.517 51.841 119.84 1 87.77 ? O1D HEM 200 D 1 HETATM 38 O O2D HEM . . . K 5 -2.04 53.628 118.604 1 87.77 ? O2D HEM 200 D 1 HETATM 39 N NA HEM . . . K 5 -6.256 46.567 120.118 1 87.77 ? NA HEM 200 D 1 HETATM 40 N NB HEM . . . K 5 -8.419 45.013 118.95 1 87.77 ? NB HEM 200 D 1 HETATM 41 N NC HEM . . . K 5 -9.158 47.256 117.247 1 87.77 ? NC HEM 200 D 1 HETATM 42 N ND HEM . . . K 5 -6.895 48.789 118.351 1 87.77 ? ND HEM 200 D 1 HETATM 43 FE FE HEM . . . K 5 -7.751 46.966 118.753 1 76.03 ? FE HEM 200 D 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #