data_6GD9
#
_model_server_result.job_id            1sgTIMQM5A1PzG0O3qaoWw 
_model_server_result.datetime_utc      '2024-11-13 08:14:18' 
_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          6gd9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    6GD9 
#
_exptl.entry_id    6GD9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              618.503 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'HEME C' 
_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            6GD9 
_cell.length_a            101.59 
_cell.length_b            101.59 
_cell.length_c            86.52 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GD9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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,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 
#
_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
covale ? covale1 A SG CYS 19 A CYS 14 1_555 B CAB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? 
covale ? covale2 A SG CYS 19 A CYS 14 1_555 B CBB HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? 
covale ? covale3 A SG CYS 22 A CYS 17 1_555 B CAC HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.655 ? 
metalc ? metalc1 A NE2 HIS 23 A HIS 18 1_555 B FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc2 A SD MET 85 A MET 80 1_555 B FE HEC . A HEC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
#
_chem_comp.formula           'C34 H34 Fe N4 O4' 
_chem_comp.formula_weight    618.503 
_chem_comp.id                HEC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'HEME C' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
FE NA HEC sing 314 n n 
FE NB HEC sing 315 n n 
FE NC HEC sing 316 n n 
FE ND HEC sing 317 n n 
CHA C1A HEC doub 318 n n 
CHA C4D HEC sing 319 n n 
CHA HHA HEC sing 320 n n 
CHB C4A HEC doub 321 n n 
CHB C1B HEC sing 322 n n 
CHB HHB HEC sing 323 n n 
CHC C4B HEC doub 324 n n 
CHC C1C HEC sing 325 n n 
CHC HHC HEC sing 326 n n 
CHD C4C HEC doub 327 n n 
CHD C1D HEC sing 328 n n 
CHD HHD HEC sing 329 n n 
NA C1A HEC sing 330 n y 
NA C4A HEC sing 331 n y 
C1A C2A HEC sing 332 n y 
C2A C3A HEC doub 333 n y 
C2A CAA HEC sing 334 n n 
C3A C4A HEC sing 335 n y 
C3A CMA HEC sing 336 n n 
CMA HMA1 HEC sing 337 n n 
CMA HMA2 HEC sing 338 n n 
CMA HMA3 HEC sing 339 n n 
CAA CBA HEC sing 340 n n 
CAA HAA1 HEC sing 341 n n 
CAA HAA2 HEC sing 342 n n 
CBA CGA HEC sing 343 n n 
CBA HBA1 HEC sing 344 n n 
CBA HBA2 HEC sing 345 n n 
CGA O1A HEC doub 346 n n 
CGA O2A HEC sing 347 n n 
O2A H2A HEC sing 348 n n 
NB C1B HEC sing 349 n y 
NB C4B HEC sing 350 n y 
C1B C2B HEC doub 351 n y 
C2B C3B HEC sing 352 n y 
C2B CMB HEC sing 353 n n 
C3B C4B HEC sing 354 n y 
C3B CAB HEC doub 355 e n 
CMB HMB1 HEC sing 356 n n 
CMB HMB2 HEC sing 357 n n 
CMB HMB3 HEC sing 358 n n 
CAB CBB HEC sing 359 n n 
CAB HAB HEC sing 360 n n 
CBB HBB1 HEC sing 361 n n 
CBB HBB2 HEC sing 362 n n 
CBB HBB3 HEC sing 363 n n 
NC C1C HEC sing 364 n y 
NC C4C HEC sing 365 n y 
C1C C2C HEC doub 366 n y 
C2C C3C HEC sing 367 n y 
C2C CMC HEC sing 368 n n 
C3C C4C HEC sing 369 n y 
C3C CAC HEC doub 370 e n 
CMC HMC1 HEC sing 371 n n 
CMC HMC2 HEC sing 372 n n 
CMC HMC3 HEC sing 373 n n 
CAC CBC HEC sing 374 n n 
CAC HAC HEC sing 375 n n 
CBC HBC1 HEC sing 376 n n 
CBC HBC2 HEC sing 377 n n 
CBC HBC3 HEC sing 378 n n 
ND C1D HEC sing 379 n y 
ND C4D HEC sing 380 n y 
C1D C2D HEC doub 381 n y 
C2D C3D HEC sing 382 n y 
C2D CMD HEC sing 383 n n 
C3D C4D HEC doub 384 n y 
C3D CAD HEC sing 385 n n 
CMD HMD1 HEC sing 386 n n 
CMD HMD2 HEC sing 387 n n 
CMD HMD3 HEC sing 388 n n 
CAD CBD HEC sing 389 n n 
CAD HAD1 HEC sing 390 n n 
CAD HAD2 HEC sing 391 n n 
CBD CGD HEC sing 392 n n 
CBD HBD1 HEC sing 393 n n 
CBD HBD2 HEC sing 394 n n 
CGD O1D HEC doub 395 n n 
CGD O2D HEC sing 396 n n 
O2D H2D HEC sing 397 n n 
#
_atom_sites.entry_id                     6GD9 
_atom_sites.fract_transf_matrix[1][1]    0.009843 
_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]    0.009843 
_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]    0.011558 
_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 HEC A 1 201 118 HEC HEM . 
C 3 EVB A 1 202 1 EVB SC8 . 
D 3 EVB A 1 203 2 EVB SC8 . 
E 3 EVB A 1 204 3 EVB SC8 . 
F 4 EPE A 1 205 1 EPE EPE . 
G 4 EPE A 1 206 2 EPE EPE . 
H 4 EPE A 1 207 3 EPE EPE . 
I 4 EPE A 1 208 4 EPE EPE . 
J 5 SO4 A 1 209 1 SO4 SO4 . 
K 5 SO4 A 1 210 3 SO4 SO4 . 
L 5 SO4 A 1 211 4 SO4 SO4 . 
M 6 HOH A 1 301 37 HOH HOH . 
M 6 HOH A 2 302 16 HOH HOH . 
M 6 HOH A 3 303 7 HOH HOH . 
M 6 HOH A 4 304 21 HOH HOH . 
M 6 HOH A 5 305 12 HOH HOH . 
M 6 HOH A 6 306 30 HOH HOH . 
M 6 HOH A 7 307 17 HOH HOH . 
M 6 HOH A 8 308 2 HOH HOH . 
M 6 HOH A 9 309 27 HOH HOH . 
M 6 HOH A 10 310 18 HOH HOH . 
M 6 HOH A 11 311 34 HOH HOH . 
M 6 HOH A 12 312 14 HOH HOH . 
M 6 HOH A 13 313 29 HOH HOH . 
M 6 HOH A 14 314 9 HOH HOH . 
M 6 HOH A 15 315 11 HOH HOH . 
M 6 HOH A 16 316 3 HOH HOH . 
M 6 HOH A 17 317 15 HOH HOH . 
M 6 HOH A 18 318 36 HOH HOH . 
M 6 HOH A 19 319 28 HOH HOH . 
M 6 HOH A 20 320 6 HOH HOH . 
M 6 HOH A 21 321 1 HOH HOH . 
M 6 HOH A 22 322 8 HOH HOH . 
M 6 HOH A 23 323 10 HOH HOH . 
M 6 HOH A 24 324 13 HOH HOH . 
M 6 HOH A 25 325 5 HOH HOH . 
M 6 HOH A 26 326 4 HOH HOH . 
M 6 HOH A 27 327 35 HOH HOH . 
M 6 HOH A 28 328 25 HOH HOH . 
M 6 HOH A 29 329 33 HOH HOH . 
M 6 HOH A 30 330 19 HOH HOH . 
M 6 HOH A 31 331 22 HOH HOH . 
M 6 HOH A 32 332 20 HOH HOH . 
M 6 HOH A 33 333 23 HOH HOH . 
M 6 HOH A 34 334 24 HOH HOH . 
M 6 HOH A 35 335 32 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 FE FE HEC . . . B 2 -34.569 -2.719 2.345 1 31.68 ? FE HEC 201 A 1 
HETATM 2 C CHA HEC . . . B 2 -35.77 -0.649 0.026 1 31.8 ? CHA HEC 201 A 1 
HETATM 3 C CHB HEC . . . B 2 -32.824 -4.499 -0.067 1 31.66 ? CHB HEC 201 A 1 
HETATM 4 C CHC HEC . . . B 2 -32.898 -4.596 4.802 1 32.32 ? CHC HEC 201 A 1 
HETATM 5 C CHD HEC . . . B 2 -36.573 -1.47 4.753 1 32.18 ? CHD HEC 201 A 1 
HETATM 6 N NA HEC . . . B 2 -34.363 -2.639 0.372 1 31.8 ? NA HEC 201 A 1 
HETATM 7 C C1A HEC . . . B 2 -34.913 -1.639 -0.397 1 31.57 ? C1A HEC 201 A 1 
HETATM 8 C C2A HEC . . . B 2 -34.496 -1.829 -1.732 1 31.27 ? C2A HEC 201 A 1 
HETATM 9 C C3A HEC . . . B 2 -33.68 -2.915 -1.759 1 31.3 ? C3A HEC 201 A 1 
HETATM 10 C C4A HEC . . . B 2 -33.588 -3.415 -0.448 1 31.5 ? C4A HEC 201 A 1 
HETATM 11 C CMA HEC . . . B 2 -32.991 -3.483 -2.974 1 31.41 ? CMA HEC 201 A 1 
HETATM 12 C CAA HEC . . . B 2 -34.873 -0.994 -2.93 1 31.02 ? CAA HEC 201 A 1 
HETATM 13 C CBA HEC . . . B 2 -36.069 -1.656 -3.618 1 30.99 ? CBA HEC 201 A 1 
HETATM 14 C CGA HEC . . . B 2 -36.493 -0.89 -4.845 1 30.86 ? CGA HEC 201 A 1 
HETATM 15 O O1A HEC . . . B 2 -37.476 -1.286 -5.514 1 30.35 ? O1A HEC 201 A 1 
HETATM 16 O O2A HEC . . . B 2 -35.87 0.136 -5.203 1 30.94 ? O2A HEC 201 A 1 
HETATM 17 N NB HEC . . . B 2 -33.13 -4.266 2.362 1 31.98 ? NB HEC 201 A 1 
HETATM 18 C C1B HEC . . . B 2 -32.585 -4.831 1.275 1 31.86 ? C1B HEC 201 A 1 
HETATM 19 C C2B HEC . . . B 2 -31.646 -5.835 1.662 1 31.95 ? C2B HEC 201 A 1 
HETATM 20 C C3B HEC . . . B 2 -31.643 -5.891 3.031 1 32.52 ? C3B HEC 201 A 1 
HETATM 21 C C4B HEC . . . B 2 -32.608 -4.843 3.458 1 32.37 ? C4B HEC 201 A 1 
HETATM 22 C CMB HEC . . . B 2 -30.826 -6.688 0.725 1 32.2 ? CMB HEC 201 A 1 
HETATM 23 C CAB HEC . . . B 2 -30.828 -6.722 3.964 1 33.51 ? CAB HEC 201 A 1 
HETATM 24 C CBB HEC . . . B 2 -29.751 -7.43 3.614 1 34.21 ? CBB HEC 201 A 1 
HETATM 25 N NC HEC . . . B 2 -34.707 -3 4.415 1 32.07 ? NC HEC 201 A 1 
HETATM 26 C C1C HEC . . . B 2 -33.923 -3.765 5.231 1 32.21 ? C1C HEC 201 A 1 
HETATM 27 C C2C HEC . . . B 2 -34.386 -3.666 6.556 1 32.24 ? C2C HEC 201 A 1 
HETATM 28 C C3C HEC . . . B 2 -35.454 -2.775 6.558 1 32.7 ? C3C HEC 201 A 1 
HETATM 29 C C4C HEC . . . B 2 -35.626 -2.354 5.195 1 32.05 ? C4C HEC 201 A 1 
HETATM 30 C CMC HEC . . . B 2 -33.806 -4.384 7.749 1 31.91 ? CMC HEC 201 A 1 
HETATM 31 C CAC HEC . . . B 2 -36.283 -2.316 7.711 1 33.75 ? CAC HEC 201 A 1 
HETATM 32 C CBC HEC . . . B 2 -36.047 -2.57 8.999 1 33.55 ? CBC HEC 201 A 1 
HETATM 33 N ND HEC . . . B 2 -35.873 -1.369 2.38 1 32.34 ? ND HEC 201 A 1 
HETATM 34 C C1D HEC . . . B 2 -36.609 -0.993 3.439 1 32.58 ? C1D HEC 201 A 1 
HETATM 35 C C2D HEC . . . B 2 -37.508 0.103 3.057 1 32.56 ? C2D HEC 201 A 1 
HETATM 36 C C3D HEC . . . B 2 -37.295 0.342 1.751 1 32.72 ? C3D HEC 201 A 1 
HETATM 37 C C4D HEC . . . B 2 -36.239 -0.596 1.335 1 32.32 ? C4D HEC 201 A 1 
HETATM 38 C CMD HEC . . . B 2 -38.489 0.801 3.964 1 32.7 ? CMD HEC 201 A 1 
HETATM 39 C CAD HEC . . . B 2 -37.983 1.391 0.912 1 33.42 ? CAD HEC 201 A 1 
HETATM 40 C CBD HEC . . . B 2 -37.184 2.687 1.094 1 34.26 ? CBD HEC 201 A 1 
HETATM 41 C CGD HEC . . . B 2 -37.754 3.856 0.324 1 34.93 ? CGD HEC 201 A 1 
HETATM 42 O O1D HEC . . . B 2 -38.894 3.809 -0.192 1 35.76 ? O1D HEC 201 A 1 
HETATM 43 O O2D HEC . . . B 2 -37.068 4.896 0.205 1 35.14 ? O2D HEC 201 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           43 
#