data_5VBU
#
_model_server_result.job_id            9ZMevec7BZ2WN5iEt2Rw5A 
_model_server_result.datetime_utc      '2024-10-12 14:33:00' 
_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          5vbu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    5VBU 
#
_exptl.entry_id    5VBU 
_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    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          102.37 
_cell.angle_gamma         90 
_cell.entry_id            5VBU 
_cell.length_a            152.431 
_cell.length_b            88.385 
_cell.length_c            111.417 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VBU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA trimeric 3 software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,J 1 1 
B,F,G,K 2 1 
C,H,I 3 1 
A,B,C,D,E,F,G,H,I,J,K 4 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 D N N 
? 2 F N N 
? 2 H 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 SG CYS 410 A CYS 429 1_555 D FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
metalc ? metalc2 B SG CYS 410 B CYS 429 1_555 F FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc3 C SG CYS 410 C CYS 429 1_555 H FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
#
_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 186 n n 
CHA C4D HEM doub 187 n n 
CHA HHA HEM sing 188 n n 
CHB C4A HEM sing 189 n n 
CHB C1B HEM doub 190 n n 
CHB HHB HEM sing 191 n n 
CHC C4B HEM sing 192 n n 
CHC C1C HEM doub 193 n n 
CHC HHC HEM sing 194 n n 
CHD C4C HEM doub 195 n n 
CHD C1D HEM sing 196 n n 
CHD HHD HEM sing 197 n n 
C1A C2A HEM doub 198 n y 
C1A NA HEM sing 199 n y 
C2A C3A HEM sing 200 n y 
C2A CAA HEM sing 201 n n 
C3A C4A HEM doub 202 n y 
C3A CMA HEM sing 203 n n 
C4A NA HEM sing 204 n y 
CMA HMA HEM sing 205 n n 
CMA HMAA HEM sing 206 n n 
CMA HMAB HEM sing 207 n n 
CAA CBA HEM sing 208 n n 
CAA HAA HEM sing 209 n n 
CAA HAAA HEM sing 210 n n 
CBA CGA HEM sing 211 n n 
CBA HBA HEM sing 212 n n 
CBA HBAA HEM sing 213 n n 
CGA O1A HEM doub 214 n n 
CGA O2A HEM sing 215 n n 
C1B C2B HEM sing 216 n n 
C1B NB HEM sing 217 n n 
C2B C3B HEM doub 218 n n 
C2B CMB HEM sing 219 n n 
C3B C4B HEM sing 220 n n 
C3B CAB HEM sing 221 n n 
C4B NB HEM doub 222 n n 
CMB HMB HEM sing 223 n n 
CMB HMBA HEM sing 224 n n 
CMB HMBB HEM sing 225 n n 
CAB CBB HEM doub 226 n n 
CAB HAB HEM sing 227 n n 
CBB HBB HEM sing 228 n n 
CBB HBBA HEM sing 229 n n 
C1C C2C HEM sing 230 n y 
C1C NC HEM sing 231 n y 
C2C C3C HEM doub 232 n y 
C2C CMC HEM sing 233 n n 
C3C C4C HEM sing 234 n y 
C3C CAC HEM sing 235 n n 
C4C NC HEM sing 236 n y 
CMC HMC HEM sing 237 n n 
CMC HMCA HEM sing 238 n n 
CMC HMCB HEM sing 239 n n 
CAC CBC HEM doub 240 n n 
CAC HAC HEM sing 241 n n 
CBC HBC HEM sing 242 n n 
CBC HBCA HEM sing 243 n n 
C1D C2D HEM sing 244 n n 
C1D ND HEM doub 245 n n 
C2D C3D HEM doub 246 n n 
C2D CMD HEM sing 247 n n 
C3D C4D HEM sing 248 n n 
C3D CAD HEM sing 249 n n 
C4D ND HEM sing 250 n n 
CMD HMD HEM sing 251 n n 
CMD HMDA HEM sing 252 n n 
CMD HMDB HEM sing 253 n n 
CAD CBD HEM sing 254 n n 
CAD HAD HEM sing 255 n n 
CAD HADA HEM sing 256 n n 
CBD CGD HEM sing 257 n n 
CBD HBD HEM sing 258 n n 
CBD HBDA HEM sing 259 n n 
CGD O1D HEM doub 260 n n 
CGD O2D HEM sing 261 n n 
O2A H2A HEM sing 262 n n 
O2D H2D HEM sing 263 n n 
FE NA HEM sing 264 n n 
FE NB HEM sing 265 n n 
FE NC HEM sing 266 n n 
FE ND HEM sing 267 n n 
#
_atom_sites.entry_id                     5VBU 
_atom_sites.fract_transf_matrix[1][1]    0.00656 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001439 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011314 
_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]    0.009189 
_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
D 2 HEM A 1 501 501 HEM HEM . 
E 3 3QZ A 1 502 502 3QZ 3QZ . 
F 2 HEM B 1 501 501 HEM HEM . 
G 3 3QZ B 1 502 502 3QZ 3QZ . 
H 2 HEM C 1 501 501 HEM HEM . 
I 3 3QZ C 1 502 502 3QZ 3QZ . 
J 4 HOH A 1 601 2 HOH HOH . 
K 4 HOH B 1 601 3 HOH HOH . 
K 4 HOH B 2 602 4 HOH HOH . 
K 4 HOH B 3 603 5 HOH HOH . 
K 4 HOH B 4 604 1 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 -36.697 -2.232 31.329 1 91.45 ? CHA HEM 501 A 1 
HETATM 2 C CHB HEM . . . D 2 -33.246 -4.463 28.686 1 94.7 ? CHB HEM 501 A 1 
HETATM 3 C CHC HEM . . . D 2 -35.071 -2.336 24.663 1 92.84 ? CHC HEM 501 A 1 
HETATM 4 C CHD HEM . . . D 2 -38.475 -0.153 27.365 1 94.16 ? CHD HEM 501 A 1 
HETATM 5 C C1A HEM . . . D 2 -35.565 -3.048 30.953 1 90.87 ? C1A HEM 501 A 1 
HETATM 6 C C2A HEM . . . D 2 -34.839 -3.772 31.872 1 91.41 ? C2A HEM 501 A 1 
HETATM 7 C C3A HEM . . . D 2 -33.862 -4.407 31.106 1 90.96 ? C3A HEM 501 A 1 
HETATM 8 C C4A HEM . . . D 2 -34.092 -3.998 29.812 1 92.5 ? C4A HEM 501 A 1 
HETATM 9 C CMA HEM . . . D 2 -32.764 -5.345 31.537 1 89.14 ? CMA HEM 501 A 1 
HETATM 10 C CAA HEM . . . D 2 -35.054 -3.832 33.383 1 93.12 ? CAA HEM 501 A 1 
HETATM 11 C CBA HEM . . . D 2 -35.52 -5.18 33.936 1 97.55 ? CBA HEM 501 A 1 
HETATM 12 C CGA HEM . . . D 2 -35.73 -5.169 35.438 1 97.32 ? CGA HEM 501 A 1 
HETATM 13 O O1A HEM . . . D 2 -36.002 -4.102 36.025 1 99.16 ? O1A HEM 501 A 1 
HETATM 14 O O2A HEM . . . D 2 -35.609 -6.247 36.061 1 97.03 ? O2A HEM 501 A 1 
HETATM 15 C C1B HEM . . . D 2 -33.424 -4.066 27.273 1 94.82 ? C1B HEM 501 A 1 
HETATM 16 C C2B HEM . . . D 2 -32.599 -4.539 26.256 1 92.78 ? C2B HEM 501 A 1 
HETATM 17 C C3B HEM . . . D 2 -33.083 -3.93 25.11 1 92.79 ? C3B HEM 501 A 1 
HETATM 18 C C4B HEM . . . D 2 -34.234 -3.129 25.54 1 93.48 ? C4B HEM 501 A 1 
HETATM 19 C CMB HEM . . . D 2 -31.44 -5.486 26.391 1 92.18 ? CMB HEM 501 A 1 
HETATM 20 C CAB HEM . . . D 2 -32.623 -4.045 23.695 1 93.09 ? CAB HEM 501 A 1 
HETATM 21 C CBB HEM . . . D 2 -31.715 -4.901 23.248 1 93.56 ? CBB HEM 501 A 1 
HETATM 22 C C1C HEM . . . D 2 -36.216 -1.52 25.068 1 92.45 ? C1C HEM 501 A 1 
HETATM 23 C C2C HEM . . . D 2 -37.001 -0.821 24.161 1 92.77 ? C2C HEM 501 A 1 
HETATM 24 C C3C HEM . . . D 2 -37.964 -0.196 24.954 1 92.24 ? C3C HEM 501 A 1 
HETATM 25 C C4C HEM . . . D 2 -37.662 -0.572 26.244 1 93.01 ? C4C HEM 501 A 1 
HETATM 26 C CMC HEM . . . D 2 -36.758 -0.779 22.678 1 93.58 ? CMC HEM 501 A 1 
HETATM 27 C CAC HEM . . . D 2 -39.118 0.695 24.599 1 89.83 ? CAC HEM 501 A 1 
HETATM 28 C CBC HEM . . . D 2 -39.485 0.976 23.37 1 87.67 ? CBC HEM 501 A 1 
HETATM 29 C C1D HEM . . . D 2 -38.249 -0.557 28.717 1 91.56 ? C1D HEM 501 A 1 
HETATM 30 C C2D HEM . . . D 2 -39.122 -0.025 29.741 1 90.48 ? C2D HEM 501 A 1 
HETATM 31 C C3D HEM . . . D 2 -38.608 -0.672 30.918 1 89.57 ? C3D HEM 501 A 1 
HETATM 32 C C4D HEM . . . D 2 -37.499 -1.462 30.411 1 91.3 ? C4D HEM 501 A 1 
HETATM 33 C CMD HEM . . . D 2 -40.292 0.909 29.613 1 91.75 ? CMD HEM 501 A 1 
HETATM 34 C CAD HEM . . . D 2 -39.099 -0.537 32.323 1 89.19 ? CAD HEM 501 A 1 
HETATM 35 C CBD HEM . . . D 2 -40.157 -1.605 32.604 1 84.71 ? CBD HEM 501 A 1 
HETATM 36 C CGD HEM . . . D 2 -40.478 -1.73 34.082 1 80.85 ? CGD HEM 501 A 1 
HETATM 37 O O1D HEM . . . D 2 -39.881 -1.032 34.909 1 81.16 ? O1D HEM 501 A 1 
HETATM 38 O O2D HEM . . . D 2 -41.197 -2.654 34.475 1 77.14 ? O2D HEM 501 A 1 
HETATM 39 N NA HEM . . . D 2 -35.15 -3.181 29.7 1 91.29 ? NA HEM 501 A 1 
HETATM 40 N NB HEM . . . D 2 -34.403 -3.207 26.858 1 94.68 ? NB HEM 501 A 1 
HETATM 41 N NC HEM . . . D 2 -36.602 -1.364 26.324 1 91.77 ? NC HEM 501 A 1 
HETATM 42 N ND HEM . . . D 2 -37.301 -1.357 29.114 1 91.92 ? ND HEM 501 A 1 
HETATM 43 FE FE HEM . . . D 2 -35.871 -2.261 27.998 1 89.89 ? FE HEM 501 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#