data_3KSW
#
_model_server_result.job_id            rpl_K-I5x9zFNDKRA38Dtg 
_model_server_result.datetime_utc      '2024-10-13 15:23:35' 
_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          3ksw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":488}' 
#
_entry.id    3KSW 
#
_exptl.entry_id    3KSW 
_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    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            3KSW 
_cell.length_a            66.468 
_cell.length_b            66.468 
_cell.length_c            234.281 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KSW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_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                      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
metalc ? metalc1 A SG CYS 393 A CYS 422 1_555 B FE HEM . A HEM 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc2 B FE HEM . A HEM 488 1_555 C NAT VNF . A VNF 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? 
#
_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                     3KSW 
_atom_sites.fract_transf_matrix[1][1]    0.015045 
_atom_sites.fract_transf_matrix[1][2]    0.008686 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017372 
_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]    0.004268 
_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 HEM A 1 488 488 HEM HEM . 
C 3 VNF A 1 490 490 VNF VNF . 
#
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 . . . B 2 3.898 26.226 14.431 1 74.18 ? CHA HEM 488 A 1 
HETATM 2 C CHB HEM . . . B 2 8.245 24.753 16.065 1 64.01 ? CHB HEM 488 A 1 
HETATM 3 C CHC HEM . . . B 2 9.416 29.378 16.978 1 69.64 ? CHC HEM 488 A 1 
HETATM 4 C CHD HEM . . . B 2 4.694 30.459 16.758 1 77.22 ? CHD HEM 488 A 1 
HETATM 5 C C1A HEM . . . B 2 4.968 25.423 14.775 1 73.41 ? C1A HEM 488 A 1 
HETATM 6 C C2A HEM . . . B 2 5.039 23.983 14.642 1 76 ? C2A HEM 488 A 1 
HETATM 7 C C3A HEM . . . B 2 6.232 23.576 15.085 1 71.41 ? C3A HEM 488 A 1 
HETATM 8 C C4A HEM . . . B 2 6.97 24.742 15.533 1 69.78 ? C4A HEM 488 A 1 
HETATM 9 C CMA HEM . . . B 2 6.728 22.115 15.116 1 70.24 ? CMA HEM 488 A 1 
HETATM 10 C CAA HEM . . . B 2 3.93 23.081 14.063 1 83.51 ? CAA HEM 488 A 1 
HETATM 11 C CBA HEM . . . B 2 3.365 22.193 15.163 1 96.91 ? CBA HEM 488 A 1 
HETATM 12 C CGA HEM . . . B 2 2.105 21.541 14.659 1 107 ? CGA HEM 488 A 1 
HETATM 13 O O1A HEM . . . B 2 2.124 20.986 13.528 1 110.53 ? O1A HEM 488 A 1 
HETATM 14 O O2A HEM . . . B 2 1.086 21.57 15.394 1 107.49 ? O2A HEM 488 A 1 
HETATM 15 C C1B HEM . . . B 2 8.961 25.877 16.423 1 69.58 ? C1B HEM 488 A 1 
HETATM 16 C C2B HEM . . . B 2 10.344 25.919 16.862 1 71.11 ? C2B HEM 488 A 1 
HETATM 17 C C3B HEM . . . B 2 10.666 27.19 17.113 1 70.27 ? C3B HEM 488 A 1 
HETATM 18 C C4B HEM . . . B 2 9.502 28.009 16.843 1 70.14 ? C4B HEM 488 A 1 
HETATM 19 C CMB HEM . . . B 2 11.288 24.706 17.016 1 61.45 ? CMB HEM 488 A 1 
HETATM 20 C CAB HEM . . . B 2 12.039 27.698 17.604 1 69.52 ? CAB HEM 488 A 1 
HETATM 21 C CBB HEM . . . B 2 13.04 26.836 17.807 1 74.88 ? CBB HEM 488 A 1 
HETATM 22 C C1C HEM . . . B 2 8.237 30.09 17.008 1 71.57 ? C1C HEM 488 A 1 
HETATM 23 C C2C HEM . . . B 2 8.086 31.508 17.27 1 74.6 ? C2C HEM 488 A 1 
HETATM 24 C C3C HEM . . . B 2 6.785 31.805 17.209 1 76.28 ? C3C HEM 488 A 1 
HETATM 25 C C4C HEM . . . B 2 6.058 30.587 16.906 1 73.85 ? C4C HEM 488 A 1 
HETATM 26 C CMC HEM . . . B 2 9.226 32.506 17.567 1 69.49 ? CMC HEM 488 A 1 
HETATM 27 C CAC HEM . . . B 2 6.163 33.202 17.423 1 73.17 ? CAC HEM 488 A 1 
HETATM 28 C CBC HEM . . . B 2 6.94 34.255 17.698 1 74.66 ? CBC HEM 488 A 1 
HETATM 29 C C1D HEM . . . B 2 4.034 29.471 16.057 1 77.1 ? C1D HEM 488 A 1 
HETATM 30 C C2D HEM . . . B 2 2.657 29.532 15.628 1 79.13 ? C2D HEM 488 A 1 
HETATM 31 C C3D HEM . . . B 2 2.391 28.211 14.895 1 80.27 ? C3D HEM 488 A 1 
HETATM 32 C C4D HEM . . . B 2 3.641 27.478 14.955 1 76.93 ? C4D HEM 488 A 1 
HETATM 33 C CMD HEM . . . B 2 1.656 30.686 15.856 1 79.75 ? CMD HEM 488 A 1 
HETATM 34 C CAD HEM . . . B 2 1.048 27.812 14.253 1 84.88 ? CAD HEM 488 A 1 
HETATM 35 C CBD HEM . . . B 2 1.168 26.565 13.389 1 99.12 ? CBD HEM 488 A 1 
HETATM 36 C CGD HEM . . . B 2 0.063 26.636 12.37 1 107.99 ? CGD HEM 488 A 1 
HETATM 37 O O1D HEM . . . B 2 0.13 27.523 11.478 1 108.67 ? O1D HEM 488 A 1 
HETATM 38 O O2D HEM . . . B 2 -0.878 25.806 12.447 1 108.95 ? O2D HEM 488 A 1 
HETATM 39 N NA HEM . . . B 2 6.163 25.847 15.328 1 71.34 ? NA HEM 488 A 1 
HETATM 40 N NB HEM . . . B 2 8.481 27.174 16.424 1 67.34 ? NB HEM 488 A 1 
HETATM 41 N NC HEM . . . B 2 6.978 29.564 16.792 1 70.72 ? NC HEM 488 A 1 
HETATM 42 N ND HEM . . . B 2 4.569 28.256 15.644 1 72.97 ? ND HEM 488 A 1 
HETATM 43 FE FE HEM . . . B 2 6.519 27.72 16.036 1 71.25 ? FE HEM 488 A 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           560 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           43 
#