data_5VVA
#
_model_server_result.job_id            lhtDmDPvnutivFPqbG-h-A 
_model_server_result.datetime_utc      '2024-11-25 06:53:00' 
_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          5vva 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":501}' 
#
_entry.id    5VVA 
#
_exptl.entry_id    5VVA 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            5VVA 
_cell.length_a            57.27 
_cell.length_b            105.95 
_cell.length_c            155.41 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VVA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_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 
_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 
#
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 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
covale ? covale1 A C VAL 344 A VAL 383 1_555 A N CAS 345 A CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 A C CAS 345 A CAS 384 1_555 A N MET 346 A MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 B C VAL 344 B VAL 383 1_555 B N CAS 345 B CAS 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale4 B C CAS 345 B CAS 384 1_555 B N MET 346 B MET 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
metalc ? metalc1 A SG CYS 57 A CYS 96 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? 
metalc ? metalc2 A SG CYS 62 A CYS 101 1_555 G ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? 
metalc ? metalc3 A SG CYS 147 A CYS 186 1_555 C FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc4 G ZN ZN . A ZN 505 1_555 B SG CYS 57 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
metalc ? metalc5 G ZN ZN . A ZN 505 1_555 B SG CYS 62 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc6 B SG CYS 147 B CYS 186 1_555 H FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? 
#
_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 245 n n 
CHA C4D HEM doub 246 n n 
CHA HHA HEM sing 247 n n 
CHB C4A HEM sing 248 n n 
CHB C1B HEM doub 249 n n 
CHB HHB HEM sing 250 n n 
CHC C4B HEM sing 251 n n 
CHC C1C HEM doub 252 n n 
CHC HHC HEM sing 253 n n 
CHD C4C HEM doub 254 n n 
CHD C1D HEM sing 255 n n 
CHD HHD HEM sing 256 n n 
C1A C2A HEM doub 257 n y 
C1A NA HEM sing 258 n y 
C2A C3A HEM sing 259 n y 
C2A CAA HEM sing 260 n n 
C3A C4A HEM doub 261 n y 
C3A CMA HEM sing 262 n n 
C4A NA HEM sing 263 n y 
CMA HMA HEM sing 264 n n 
CMA HMAA HEM sing 265 n n 
CMA HMAB HEM sing 266 n n 
CAA CBA HEM sing 267 n n 
CAA HAA HEM sing 268 n n 
CAA HAAA HEM sing 269 n n 
CBA CGA HEM sing 270 n n 
CBA HBA HEM sing 271 n n 
CBA HBAA HEM sing 272 n n 
CGA O1A HEM doub 273 n n 
CGA O2A HEM sing 274 n n 
C1B C2B HEM sing 275 n n 
C1B NB HEM sing 276 n n 
C2B C3B HEM doub 277 n n 
C2B CMB HEM sing 278 n n 
C3B C4B HEM sing 279 n n 
C3B CAB HEM sing 280 n n 
C4B NB HEM doub 281 n n 
CMB HMB HEM sing 282 n n 
CMB HMBA HEM sing 283 n n 
CMB HMBB HEM sing 284 n n 
CAB CBB HEM doub 285 n n 
CAB HAB HEM sing 286 n n 
CBB HBB HEM sing 287 n n 
CBB HBBA HEM sing 288 n n 
C1C C2C HEM sing 289 n y 
C1C NC HEM sing 290 n y 
C2C C3C HEM doub 291 n y 
C2C CMC HEM sing 292 n n 
C3C C4C HEM sing 293 n y 
C3C CAC HEM sing 294 n n 
C4C NC HEM sing 295 n y 
CMC HMC HEM sing 296 n n 
CMC HMCA HEM sing 297 n n 
CMC HMCB HEM sing 298 n n 
CAC CBC HEM doub 299 n n 
CAC HAC HEM sing 300 n n 
CBC HBC HEM sing 301 n n 
CBC HBCA HEM sing 302 n n 
C1D C2D HEM sing 303 n n 
C1D ND HEM doub 304 n n 
C2D C3D HEM doub 305 n n 
C2D CMD HEM sing 306 n n 
C3D C4D HEM sing 307 n n 
C3D CAD HEM sing 308 n n 
C4D ND HEM sing 309 n n 
CMD HMD HEM sing 310 n n 
CMD HMDA HEM sing 311 n n 
CMD HMDB HEM sing 312 n n 
CAD CBD HEM sing 313 n n 
CAD HAD HEM sing 314 n n 
CAD HADA HEM sing 315 n n 
CBD CGD HEM sing 316 n n 
CBD HBD HEM sing 317 n n 
CBD HBDA HEM sing 318 n n 
CGD O1D HEM doub 319 n n 
CGD O2D HEM sing 320 n n 
O2A H2A HEM sing 321 n n 
O2D H2D HEM sing 322 n n 
FE NA HEM sing 323 n n 
FE NB HEM sing 324 n n 
FE NC HEM sing 325 n n 
FE ND HEM sing 326 n n 
#
_atom_sites.entry_id                     5VVA 
_atom_sites.fract_transf_matrix[1][1]    0.017461 
_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]    0.009438 
_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]    0.006435 
_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 1 501 500 HEM HEM . 
D 3 H4B A 1 502 600 H4B BH4 . 
E 4 9OJ A 1 503 800 9OJ 3P8 . 
F 5 GOL A 1 504 880 GOL GOL . 
G 6 ZN A 1 505 900 ZN ZN . 
H 2 HEM B 1 501 500 HEM HEM . 
I 3 H4B B 1 502 600 H4B BH4 . 
J 4 9OJ B 1 503 800 9OJ 3P8 . 
K 5 GOL B 1 504 880 GOL GOL . 
L 7 HOH A 1 601 13 HOH HOH . 
L 7 HOH A 2 602 11 HOH HOH . 
L 7 HOH A 3 603 6 HOH HOH . 
L 7 HOH A 4 604 12 HOH HOH . 
L 7 HOH A 5 605 8 HOH HOH . 
L 7 HOH A 6 606 5 HOH HOH . 
L 7 HOH A 7 607 10 HOH HOH . 
L 7 HOH A 8 608 20 HOH HOH . 
L 7 HOH A 9 609 14 HOH HOH . 
L 7 HOH A 10 610 17 HOH HOH . 
L 7 HOH A 11 611 21 HOH HOH . 
L 7 HOH A 12 612 19 HOH HOH . 
L 7 HOH A 13 613 9 HOH HOH . 
L 7 HOH A 14 614 7 HOH HOH . 
M 7 HOH B 1 601 4 HOH HOH . 
M 7 HOH B 2 602 15 HOH HOH . 
M 7 HOH B 3 603 1 HOH HOH . 
M 7 HOH B 4 604 2 HOH HOH . 
M 7 HOH B 5 605 3 HOH HOH . 
M 7 HOH B 6 606 23 HOH HOH . 
M 7 HOH B 7 607 18 HOH HOH . 
M 7 HOH B 8 608 16 HOH HOH . 
M 7 HOH B 9 609 22 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 . . . H 2 3.605 7.9 64.01 1 68.03 ? CHA HEM 501 B 1 
HETATM 2 C CHB HEM . . . H 2 2.05 12.451 64.536 1 67.83 ? CHB HEM 501 B 1 
HETATM 3 C CHC HEM . . . H 2 3.196 12.147 69.254 1 75.71 ? CHC HEM 501 B 1 
HETATM 4 C CHD HEM . . . H 2 5.69 8.113 68.422 1 59.91 ? CHD HEM 501 B 1 
HETATM 5 C C1A HEM . . . H 2 3.013 9.111 63.763 1 75.86 ? C1A HEM 501 B 1 
HETATM 6 C C2A HEM . . . H 2 2.336 9.498 62.536 1 78.42 ? C2A HEM 501 B 1 
HETATM 7 C C3A HEM . . . H 2 1.898 10.757 62.686 1 64.74 ? C3A HEM 501 B 1 
HETATM 8 C C4A HEM . . . H 2 2.293 11.206 64 1 66.05 ? C4A HEM 501 B 1 
HETATM 9 C CMA HEM . . . H 2 1.119 11.608 61.659 1 60.49 ? CMA HEM 501 B 1 
HETATM 10 C CAA HEM . . . H 2 2.132 8.58 61.305 1 71.55 ? CAA HEM 501 B 1 
HETATM 11 C CBA HEM . . . H 2 1.236 7.439 61.794 1 71.36 ? CBA HEM 501 B 1 
HETATM 12 C CGA HEM . . . H 2 0.265 6.943 60.756 1 78.7 ? CGA HEM 501 B 1 
HETATM 13 O O1A HEM . . . H 2 0.137 7.579 59.683 1 88.33 ? O1A HEM 501 B 1 
HETATM 14 O O2A HEM . . . H 2 -0.394 5.904 61.004 1 62.56 ? O2A HEM 501 B 1 
HETATM 15 C C1B HEM . . . H 2 2.172 12.749 65.865 1 62.85 ? C1B HEM 501 B 1 
HETATM 16 C C2B HEM . . . H 2 1.653 13.918 66.523 1 59.52 ? C2B HEM 501 B 1 
HETATM 17 C C3B HEM . . . H 2 1.973 13.855 67.821 1 64.01 ? C3B HEM 501 B 1 
HETATM 18 C C4B HEM . . . H 2 2.7 12.612 68.038 1 75.33 ? C4B HEM 501 B 1 
HETATM 19 C CMB HEM . . . H 2 0.887 15.049 65.816 1 59.87 ? CMB HEM 501 B 1 
HETATM 20 C CAB HEM . . . H 2 1.592 14.923 68.882 1 63.8 ? CAB HEM 501 B 1 
HETATM 21 C CBB HEM . . . H 2 2.208 15.075 70.063 1 60.68 ? CBB HEM 501 B 1 
HETATM 22 C C1C HEM . . . H 2 3.918 10.991 69.468 1 63.85 ? C1C HEM 501 B 1 
HETATM 23 C C2C HEM . . . H 2 4.311 10.444 70.745 1 59.81 ? C2C HEM 501 B 1 
HETATM 24 C C3C HEM . . . H 2 5.002 9.316 70.507 1 58.85 ? C3C HEM 501 B 1 
HETATM 25 C C4C HEM . . . H 2 5.071 9.138 69.08 1 54.84 ? C4C HEM 501 B 1 
HETATM 26 C CMC HEM . . . H 2 3.942 11.095 72.096 1 62.65 ? CMC HEM 501 B 1 
HETATM 27 C CAC HEM . . . H 2 5.674 8.324 71.484 1 56.8 ? CAC HEM 501 B 1 
HETATM 28 C CBC HEM . . . H 2 5.839 8.598 72.779 1 63.36 ? CBC HEM 501 B 1 
HETATM 29 C C1D HEM . . . H 2 5.319 7.647 67.177 1 65.76 ? C1D HEM 501 B 1 
HETATM 30 C C2D HEM . . . H 2 5.724 6.38 66.643 1 60.62 ? C2D HEM 501 B 1 
HETATM 31 C C3D HEM . . . H 2 5.081 6.301 65.263 1 64.93 ? C3D HEM 501 B 1 
HETATM 32 C C4D HEM . . . H 2 4.346 7.544 65.109 1 65.6 ? C4D HEM 501 B 1 
HETATM 33 C CMD HEM . . . H 2 6.608 5.335 67.341 1 61.67 ? CMD HEM 501 B 1 
HETATM 34 C CAD HEM . . . H 2 5.169 5.124 64.265 1 55.04 ? CAD HEM 501 B 1 
HETATM 35 C CBD HEM . . . H 2 3.757 4.533 64.25 1 54.99 ? CBD HEM 501 B 1 
HETATM 36 C CGD HEM . . . H 2 3.736 3.105 63.808 1 66.8 ? CGD HEM 501 B 1 
HETATM 37 O O1D HEM . . . H 2 4.69 2.657 63.115 1 82.77 ? O1D HEM 501 B 1 
HETATM 38 O O2D HEM . . . H 2 2.752 2.417 64.164 1 64 ? O2D HEM 501 B 1 
HETATM 39 N NA HEM . . . H 2 2.974 10.18 64.631 1 71.11 ? NA HEM 501 B 1 
HETATM 40 N NB HEM . . . H 2 2.805 11.964 66.808 1 66.51 ? NB HEM 501 B 1 
HETATM 41 N NC HEM . . . H 2 4.399 10.168 68.471 1 57.59 ? NC HEM 501 B 1 
HETATM 42 N ND HEM . . . H 2 4.516 8.309 66.242 1 60.49 ? ND HEM 501 B 1 
HETATM 43 FE FE HEM . . . H 2 3.89 10.262 66.42 1 63.46 ? FE HEM 501 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#