data_8GY3
#
_model_server_result.job_id            1-REZCdfjYdd13xiZ9bF9g 
_model_server_result.datetime_utc      '2025-07-05 15:15:05' 
_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          8gy3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":801}' 
#
_entry.id    8GY3 
#
_exptl.entry_id    8GY3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              844.471 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)' 
_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            8GY3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GY3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J 
_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    ? 
_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                      7 
_struct_asym.id                             J 
_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 57 A CYS 57 1_555 D CAB HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? 
covale ? covale2 A SG CYS 60 A CYS 60 1_555 D CAC HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
covale ? covale3 A SG CYS 207 A CYS 207 1_555 E CAB HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
covale ? covale4 A SG CYS 210 A CYS 210 1_555 E CAC HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
covale ? covale5 A SG CYS 341 A CYS 341 1_555 F CAB HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? 
covale ? covale6 A SG CYS 344 A CYS 344 1_555 F CAC HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? 
metalc ? metalc1 A NE2 HIS 61 A HIS 61 1_555 D FE HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc2 A NE2 HIS 211 A HIS 211 1_555 E FE HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc3 A NE2 HIS 345 A HIS 345 1_555 F FE HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc4 B SG CYS 39 B CYS 39 1_555 H FE1 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc5 B SG CYS 44 B CYS 44 1_555 H FE1 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc6 B SG CYS 47 B CYS 47 1_555 H FE2 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc7 B SG CYS 59 B CYS 59 1_555 H FE2 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc8 B SG CYS 97 B CYS 97 1_555 I FE1 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc9 B SG CYS 100 B CYS 100 1_555 I FE2 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc10 B SG CYS 132 B CYS 132 1_555 I FE2 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc11 B SG CYS 134 B CYS 134 1_555 I FE1 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
#
_chem_comp.formula           'C19 H26 Mo N8 O16 P2 S2' 
_chem_comp.formula_weight    844.471 
_chem_comp.id                PCD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'MOLYBDENUM COFACTOR;MOCO' 
#
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
N1 C2 PCD sing 323 n n 
N1 C6 PCD sing 324 n n 
N1 C1' PCD sing 325 n n 
C2 N3 PCD sing 326 n n 
C2 O2 PCD doub 327 n n 
N3 C4 PCD doub 328 n n 
C4 C5 PCD sing 329 n n 
C4 N4 PCD sing 330 n n 
C5 C6 PCD doub 331 n n 
C5 H5 PCD sing 332 n n 
C6 H6 PCD sing 333 n n 
N4 H42 PCD sing 334 n n 
N4 H41 PCD sing 335 n n 
C1' C2D PCD sing 336 n n 
C1' O4D PCD sing 337 n n 
C1' H1' PCD sing 338 n n 
C2D O2' PCD sing 339 n n 
C2D C3' PCD sing 340 n n 
C2D H2' PCD sing 341 n n 
O2' H2O1 PCD sing 342 n n 
C3' C4D PCD sing 343 n n 
C3' O3' PCD sing 344 n n 
C3' H3' PCD sing 345 n n 
C4D O4D PCD sing 346 n n 
C4D C5' PCD sing 347 n n 
C4D H4D PCD sing 348 n n 
O3' H3O1 PCD sing 349 n n 
C5' O5' PCD sing 350 n n 
C5' "H5'2" PCD sing 351 n n 
C5' "H5'1" PCD sing 352 n n 
O5' PA PCD sing 353 n n 
PA O1A PCD doub 354 n n 
PA O2A PCD sing 355 n n 
PA O3A PCD sing 356 n n 
O2A HOA2 PCD sing 357 n n 
O3A PB PCD sing 358 n n 
PB O1B PCD doub 359 n n 
PB O2B PCD sing 360 n n 
PB O3B PCD sing 361 n n 
O2B HOB2 PCD sing 362 n n 
O3B C10 PCD sing 363 n n 
C10 C9' PCD sing 364 n n 
C10 H102 PCD sing 365 n n 
C10 H101 PCD sing 366 n n 
C9' C8' PCD sing 367 n n 
C9' O9' PCD sing 368 n n 
C9' H9' PCD sing 369 n n 
C8' S8' PCD sing 370 n n 
C8' C7' PCD doub 371 n n 
S8' MO PCD sing 372 n n 
C7' S7' PCD sing 373 n n 
C7' C6' PCD sing 374 n n 
S7' MO PCD sing 375 n n 
C6' C7 PCD sing 376 n n 
C6' N5' PCD sing 377 n n 
C6' H6' PCD sing 378 n n 
C7 O9' PCD sing 379 n n 
C7 N8' PCD sing 380 n n 
C7 H7 PCD sing 381 n n 
N5' C4A PCD sing 382 n n 
N5' H5' PCD sing 383 n n 
C4A C4B PCD doub 384 n y 
C4A C4' PCD sing 385 n y 
N8' C4B PCD sing 386 n n 
N8' H8' PCD sing 387 n n 
C4B N1' PCD sing 388 n y 
N1' C2' PCD doub 389 n y 
C2' N2' PCD sing 390 n n 
C2' N3' PCD sing 391 n y 
N2' "H2'2" PCD sing 392 n n 
N2' "H2'1" PCD sing 393 n n 
N3' C4' PCD doub 394 n y 
C4' O4' PCD sing 395 n n 
O4' H4' PCD sing 396 n n 
MO OR1 PCD sing 397 n n 
MO OM2 PCD doub 398 n n 
MO OM1 PCD doub 399 n n 
OR1 HR11 PCD sing 400 n n 
OR1 HR12 PCD sing 401 n n 
#
_atom_sites.entry_id                     8GY3 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 4 HEC A 1 501 501 HEC HEC . 
E 4 HEC A 1 502 502 HEC HEC . 
F 4 HEC A 1 503 503 HEC HEC . 
G 5 U10 A 1 504 504 U10 U10 . 
H 6 FES B 1 201 201 FES FES . 
I 6 FES B 1 202 202 FES FES . 
J 7 PCD C 1 801 801 PCD PCD . 
#
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 N N1 PCD . . . J 7 154.552 128.636 157.62 1 87.64 ? N1 PCD 801 C 1 
HETATM 2 C C2 PCD . . . J 7 155.904 128.508 157.988 1 89.41 ? C2 PCD 801 C 1 
HETATM 3 N N3 PCD . . . J 7 156.297 128.788 159.247 1 85.44 ? N3 PCD 801 C 1 
HETATM 4 C C4 PCD . . . J 7 155.398 129.193 160.165 1 86.01 ? C4 PCD 801 C 1 
HETATM 5 C C5 PCD . . . J 7 154.062 129.323 159.817 1 93.32 ? C5 PCD 801 C 1 
HETATM 6 C C6 PCD . . . J 7 153.654 129.033 158.523 1 94.58 ? C6 PCD 801 C 1 
HETATM 7 O O2 PCD . . . J 7 156.744 128.133 157.145 1 99.31 ? O2 PCD 801 C 1 
HETATM 8 N N4 PCD . . . J 7 155.798 129.475 161.427 1 85.48 ? N4 PCD 801 C 1 
HETATM 9 C C1' PCD . . . J 7 154.132 128.328 156.252 1 89.67 ? C1' PCD 801 C 1 
HETATM 10 C C2D PCD . . . J 7 153.827 126.848 156.125 1 95.15 ? C2D PCD 801 C 1 
HETATM 11 O O2' PCD . . . J 7 154.571 126.308 155.032 1 96.62 ? O2' PCD 801 C 1 
HETATM 12 C C3' PCD . . . J 7 152.349 126.748 155.822 1 96.04 ? C3' PCD 801 C 1 
HETATM 13 C C4D PCD . . . J 7 151.882 128.163 155.54 1 90.23 ? C4D PCD 801 C 1 
HETATM 14 O O4D PCD . . . J 7 152.937 129.044 155.933 1 92.7 ? O4D PCD 801 C 1 
HETATM 15 O O3' PCD . . . J 7 152.146 125.927 154.672 1 107.01 ? O3' PCD 801 C 1 
HETATM 16 C C5' PCD . . . J 7 150.616 128.496 156.318 1 90.74 ? C5' PCD 801 C 1 
HETATM 17 O O5' PCD . . . J 7 150.673 127.885 157.602 1 91.82 ? O5' PCD 801 C 1 
HETATM 18 P PA PCD . . . J 7 149.641 128.318 158.754 1 89.33 ? PA PCD 801 C 1 
HETATM 19 O O1A PCD . . . J 7 149.536 127.186 159.742 1 98.5 ? O1A PCD 801 C 1 
HETATM 20 O O2A PCD . . . J 7 150.047 129.69 159.221 1 99.36 ? O2A PCD 801 C 1 
HETATM 21 O O3A PCD . . . J 7 148.236 128.47 157.988 1 101.22 ? O3A PCD 801 C 1 
HETATM 22 P PB PCD . . . J 7 147.252 127.223 157.738 1 90.26 ? PB PCD 801 C 1 
HETATM 23 O O1B PCD . . . J 7 146.416 127.009 158.974 1 94.78 ? O1B PCD 801 C 1 
HETATM 24 O O2B PCD . . . J 7 148.055 126.087 157.162 1 96.68 ? O2B PCD 801 C 1 
HETATM 25 O O3B PCD . . . J 7 146.284 127.785 156.587 1 96.76 ? O3B PCD 801 C 1 
HETATM 26 C C10 PCD . . . J 7 145.089 128.475 156.936 1 88.87 ? C10 PCD 801 C 1 
HETATM 27 C C9' PCD . . . J 7 145.202 129.916 156.46 1 95.17 ? C9' PCD 801 C 1 
HETATM 28 C C8' PCD . . . J 7 143.881 130.61 156.624 1 100.14 ? C8' PCD 801 C 1 
HETATM 29 S S8' PCD . . . J 7 143.078 130.495 158.075 1 112.24 ? S8' PCD 801 C 1 
HETATM 30 C C7' PCD . . . J 7 143.345 131.324 155.648 1 96.55 ? C7' PCD 801 C 1 
HETATM 31 S S7' PCD . . . J 7 141.813 131.909 155.872 1 106.33 ? S7' PCD 801 C 1 
HETATM 32 C C6' PCD . . . J 7 144.085 131.605 154.375 1 91.28 ? C6' PCD 801 C 1 
HETATM 33 C C7 PCD . . . J 7 145.556 131.269 154.58 1 96.36 ? C7 PCD 801 C 1 
HETATM 34 O O9' PCD . . . J 7 145.627 129.947 155.099 1 100.79 ? O9' PCD 801 C 1 
HETATM 35 N N5' PCD . . . J 7 143.527 130.858 153.264 1 94.34 ? N5' PCD 801 C 1 
HETATM 36 C C4A PCD . . . J 7 144.282 130.642 152.169 1 93.38 ? C4A PCD 801 C 1 
HETATM 37 N N8' PCD . . . J 7 146.288 131.372 153.332 1 98.11 ? N8' PCD 801 C 1 
HETATM 38 C C4B PCD . . . J 7 145.728 130.91 152.199 1 93.54 ? C4B PCD 801 C 1 
HETATM 39 N N1' PCD . . . J 7 146.454 130.684 151.086 1 94.43 ? N1' PCD 801 C 1 
HETATM 40 C C2' PCD . . . J 7 145.881 130.22 149.949 1 91.12 ? C2' PCD 801 C 1 
HETATM 41 N N2' PCD . . . J 7 146.661 130.014 148.864 1 97.24 ? N2' PCD 801 C 1 
HETATM 42 N N3' PCD . . . J 7 144.556 129.953 149.857 1 85.8 ? N3' PCD 801 C 1 
HETATM 43 C C4' PCD . . . J 7 143.721 130.137 150.9 1 90.88 ? C4' PCD 801 C 1 
HETATM 44 O O4' PCD . . . J 7 142.394 129.864 150.788 1 99.71 ? O4' PCD 801 C 1 
HETATM 45 MO MO PCD . . . J 7 140.961 131.468 157.989 1 153.46 ? MO PCD 801 C 1 
HETATM 46 O OR1 PCD . . . J 7 139.437 131.739 159.024 1 97.16 ? OR1 PCD 801 C 1 
HETATM 47 O OM2 PCD . . . J 7 139.73 132.424 156.972 1 92.21 ? OM2 PCD 801 C 1 
HETATM 48 O OM1 PCD . . . J 7 140.246 129.876 157.344 1 100.48 ? OM1 PCD 801 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           50 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           536 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           48 
#