data_7KVM
#
_model_server_result.job_id            Ym8gy-KGf7phCS_RSiwDbg 
_model_server_result.datetime_utc      '2024-11-04 23:04:29' 
_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          7kvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    7KVM 
#
_exptl.entry_id    7KVM 
_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         90 
_cell.entry_id            7KVM 
_cell.length_a            77.65 
_cell.length_b            101.2 
_cell.length_c            129.26 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KVM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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' 3_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -77.65 0 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 422 A CYS 442 1_555 B FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc2 B FE HEM . A HEM 601 1_555 C N29 X71 . A X71 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
#
_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                     7KVM 
_atom_sites.fract_transf_matrix[1][1]    0.012878 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009881 
_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]    0.007736 
_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 1 601 500 HEM HEM . 
C 3 X71 A 1 602 700 X71 390 . 
#
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 -15.372 -19.918 -9.862 1 89.58 ? CHA HEM 601 A 1 
HETATM 2 C CHB HEM . . . B 2 -15.945 -22.559 -13.891 1 90.23 ? CHB HEM 601 A 1 
HETATM 3 C CHC HEM . . . B 2 -16.501 -26.497 -11.124 1 96.89 ? CHC HEM 601 A 1 
HETATM 4 C CHD HEM . . . B 2 -15.586 -23.92 -7.113 1 96.97 ? CHD HEM 601 A 1 
HETATM 5 C C1A HEM . . . B 2 -15.483 -20.277 -11.186 1 92.44 ? C1A HEM 601 A 1 
HETATM 6 C C2A HEM . . . B 2 -15.388 -19.383 -12.323 1 91.35 ? C2A HEM 601 A 1 
HETATM 7 C C3A HEM . . . B 2 -15.544 -20.111 -13.434 1 93.18 ? C3A HEM 601 A 1 
HETATM 8 C C4A HEM . . . B 2 -15.748 -21.491 -13.042 1 82.2 ? C4A HEM 601 A 1 
HETATM 9 C CMA HEM . . . B 2 -15.519 -19.598 -14.889 1 101.93 ? CMA HEM 601 A 1 
HETATM 10 C CAA HEM . . . B 2 -15.141 -17.862 -12.243 1 76.94 ? CAA HEM 601 A 1 
HETATM 11 C CBA HEM . . . B 2 -13.647 -17.604 -12.413 1 80.69 ? CBA HEM 601 A 1 
HETATM 12 C CGA HEM . . . B 2 -13.415 -16.139 -12.669 1 97.29 ? CGA HEM 601 A 1 
HETATM 13 O O1A HEM . . . B 2 -12.375 -15.801 -13.291 1 108.35 ? O1A HEM 601 A 1 
HETATM 14 O O2A HEM . . . B 2 -14.273 -15.313 -12.261 1 90.05 ? O2A HEM 601 A 1 
HETATM 15 C C1B HEM . . . B 2 -16.13 -23.866 -13.497 1 95.5 ? C1B HEM 601 A 1 
HETATM 16 C C2B HEM . . . B 2 -16.305 -25.009 -14.371 1 106.55 ? C2B HEM 601 A 1 
HETATM 17 C C3B HEM . . . B 2 -16.45 -26.102 -13.6 1 110.28 ? C3B HEM 601 A 1 
HETATM 18 C C4B HEM . . . B 2 -16.387 -25.672 -12.22 1 99.58 ? C4B HEM 601 A 1 
HETATM 19 C CMB HEM . . . B 2 -16.292 -24.906 -15.913 1 97.2 ? CMB HEM 601 A 1 
HETATM 20 C CAB HEM . . . B 2 -16.681 -27.588 -13.981 1 96.63 ? CAB HEM 601 A 1 
HETATM 21 C CBB HEM . . . B 2 -17.013 -28.02 -15.2 1 104.42 ? CBB HEM 601 A 1 
HETATM 22 C C1C HEM . . . B 2 -16.252 -26.161 -9.812 1 97.28 ? C1C HEM 601 A 1 
HETATM 23 C C2C HEM . . . B 2 -16.16 -27.092 -8.712 1 102.39 ? C2C HEM 601 A 1 
HETATM 24 C C3C HEM . . . B 2 -15.906 -26.407 -7.598 1 96.79 ? C3C HEM 601 A 1 
HETATM 25 C C4C HEM . . . B 2 -15.825 -24.994 -7.95 1 92.08 ? C4C HEM 601 A 1 
HETATM 26 C CMC HEM . . . B 2 -16.324 -28.624 -8.81 1 108.55 ? CMC HEM 601 A 1 
HETATM 27 C CAC HEM . . . B 2 -15.744 -27.081 -6.215 1 100.14 ? CAC HEM 601 A 1 
HETATM 28 C CBC HEM . . . B 2 -15.465 -26.399 -5.103 1 103.89 ? CBC HEM 601 A 1 
HETATM 29 C C1D HEM . . . B 2 -15.476 -22.6 -7.502 1 96.56 ? C1D HEM 601 A 1 
HETATM 30 C C2D HEM . . . B 2 -15.285 -21.457 -6.632 1 87.55 ? C2D HEM 601 A 1 
HETATM 31 C C3D HEM . . . B 2 -15.23 -20.362 -7.393 1 89.82 ? C3D HEM 601 A 1 
HETATM 32 C C4D HEM . . . B 2 -15.376 -20.764 -8.774 1 92.66 ? C4D HEM 601 A 1 
HETATM 33 C CMD HEM . . . B 2 -15.173 -21.493 -5.092 1 85.31 ? CMD HEM 601 A 1 
HETATM 34 C CAD HEM . . . B 2 -15.023 -18.912 -6.902 1 88.71 ? CAD HEM 601 A 1 
HETATM 35 C CBD HEM . . . B 2 -13.52 -18.659 -6.824 1 94.59 ? CBD HEM 601 A 1 
HETATM 36 C CGD HEM . . . B 2 -13.222 -17.318 -6.207 1 106.63 ? CGD HEM 601 A 1 
HETATM 37 O O1D HEM . . . B 2 -12.144 -17.192 -5.571 1 107.1 ? O1D HEM 601 A 1 
HETATM 38 O O2D HEM . . . B 2 -14.052 -16.382 -6.338 1 107.98 ? O2D HEM 601 A 1 
HETATM 39 N NA HEM . . . B 2 -15.703 -21.552 -11.663 1 89.42 ? NA HEM 601 A 1 
HETATM 40 N NB HEM . . . B 2 -16.188 -24.31 -12.193 1 92.8 ? NB HEM 601 A 1 
HETATM 41 N NC HEM . . . B 2 -16.044 -24.894 -9.312 1 99.4 ? NC HEM 601 A 1 
HETATM 42 N ND HEM . . . B 2 -15.526 -22.134 -8.802 1 101.43 ? ND HEM 601 A 1 
HETATM 43 FE FE HEM . . . B 2 -15.856 -23.228 -10.504 1 71.57 ? FE HEM 601 A 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           43 
#