data_6VIK
#
_model_server_result.job_id            U9kG4EOI-wi8MCxo1uDpjA 
_model_server_result.datetime_utc      '2025-03-09 03:53:21' 
_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          6vik 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    6VIK 
#
_exptl.entry_id    6VIK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_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         120 
_cell.entry_id            6VIK 
_cell.length_a            61.117 
_cell.length_b            61.117 
_cell.length_c            224.311 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VIK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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                      3 
_struct_asym.id                             C 
_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 OD2 ASP 91 B ASP 66 1_555 B MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc2 B MG MG . B MG 301 1_555 C O1B GSP . B GSP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc3 B MG MG . B MG 301 1_555 C O2G GSP . B GSP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3 S' 
_chem_comp.formula_weight    539.246 
_chem_comp.id                GSP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" 
_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
PG O3B GSP sing 129 n n 
PG S1G GSP doub 130 n n 
PG O2G GSP sing 131 n n 
PG O3G GSP sing 132 n n 
O3B PB GSP sing 133 n n 
O2G HOG2 GSP sing 134 n n 
O3G HOG3 GSP sing 135 n n 
PB O1B GSP doub 136 n n 
PB O2B GSP sing 137 n n 
PB O3A GSP sing 138 n n 
O2B HOB2 GSP sing 139 n n 
PA O1A GSP doub 140 n n 
PA O2A GSP sing 141 n n 
PA O3A GSP sing 142 n n 
PA O5' GSP sing 143 n n 
O2A HOA2 GSP sing 144 n n 
O5' C5' GSP sing 145 n n 
C5' C4' GSP sing 146 n n 
C5' "H5'1" GSP sing 147 n n 
C5' "H5'2" GSP sing 148 n n 
C4' O4' GSP sing 149 n n 
C4' C3' GSP sing 150 n n 
C4' H4' GSP sing 151 n n 
O4' C1' GSP sing 152 n n 
C3' O3' GSP sing 153 n n 
C3' C2' GSP sing 154 n n 
C3' H3' GSP sing 155 n n 
O3' HO3' GSP sing 156 n n 
C2' O2' GSP sing 157 n n 
C2' C1' GSP sing 158 n n 
C2' H2' GSP sing 159 n n 
O2' HO2' GSP sing 160 n n 
C1' N9 GSP sing 161 n n 
C1' H1' GSP sing 162 n n 
N9 C8 GSP sing 163 n y 
N9 C4 GSP sing 164 n y 
C8 N7 GSP doub 165 n y 
C8 H8 GSP sing 166 n n 
N7 C5 GSP sing 167 n y 
C5 C6 GSP sing 168 n n 
C5 C4 GSP doub 169 n y 
C6 O6 GSP doub 170 n n 
C6 N1 GSP sing 171 n n 
N1 C2 GSP sing 172 n n 
N1 HN1 GSP sing 173 n n 
C2 N2 GSP sing 174 n n 
C2 N3 GSP doub 175 n n 
N2 HN21 GSP sing 176 n n 
N2 HN22 GSP sing 177 n n 
N3 C4 GSP sing 178 n n 
#
_atom_sites.entry_id                     6VIK 
_atom_sites.fract_transf_matrix[1][1]    0.016362 
_atom_sites.fract_transf_matrix[1][2]    0.009447 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018893 
_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]    0.004458 
_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 MG B 1 301 301 MG MG . 
C 3 GSP B 1 302 401 GSP GSP . 
D 4 HOH B 1 401 75 HOH HOH . 
D 4 HOH B 2 402 81 HOH HOH . 
D 4 HOH B 3 403 95 HOH HOH . 
D 4 HOH B 4 404 74 HOH HOH . 
D 4 HOH B 5 405 42 HOH HOH . 
D 4 HOH B 6 406 76 HOH HOH . 
D 4 HOH B 7 407 36 HOH HOH . 
D 4 HOH B 8 408 25 HOH HOH . 
D 4 HOH B 9 409 40 HOH HOH . 
D 4 HOH B 10 410 44 HOH HOH . 
D 4 HOH B 11 411 33 HOH HOH . 
D 4 HOH B 12 412 64 HOH HOH . 
D 4 HOH B 13 413 41 HOH HOH . 
D 4 HOH B 14 414 59 HOH HOH . 
D 4 HOH B 15 415 78 HOH HOH . 
D 4 HOH B 16 416 34 HOH HOH . 
D 4 HOH B 17 417 47 HOH HOH . 
D 4 HOH B 18 418 93 HOH HOH . 
D 4 HOH B 19 419 6 HOH HOH . 
D 4 HOH B 20 420 68 HOH HOH . 
D 4 HOH B 21 421 69 HOH HOH . 
D 4 HOH B 22 422 37 HOH HOH . 
D 4 HOH B 23 423 43 HOH HOH . 
D 4 HOH B 24 424 17 HOH HOH . 
D 4 HOH B 25 425 8 HOH HOH . 
D 4 HOH B 26 426 46 HOH HOH . 
D 4 HOH B 27 427 39 HOH HOH . 
D 4 HOH B 28 428 11 HOH HOH . 
D 4 HOH B 29 429 31 HOH HOH . 
D 4 HOH B 30 430 55 HOH HOH . 
D 4 HOH B 31 431 13 HOH HOH . 
D 4 HOH B 32 432 24 HOH HOH . 
D 4 HOH B 33 433 12 HOH HOH . 
D 4 HOH B 34 434 48 HOH HOH . 
D 4 HOH B 35 435 23 HOH HOH . 
D 4 HOH B 36 436 50 HOH HOH . 
D 4 HOH B 37 437 1 HOH HOH . 
D 4 HOH B 38 438 4 HOH HOH . 
D 4 HOH B 39 439 3 HOH HOH . 
D 4 HOH B 40 440 32 HOH HOH . 
D 4 HOH B 41 441 51 HOH HOH . 
D 4 HOH B 42 442 58 HOH HOH . 
D 4 HOH B 43 443 96 HOH HOH . 
D 4 HOH B 44 444 21 HOH HOH . 
D 4 HOH B 45 445 38 HOH HOH . 
D 4 HOH B 46 446 92 HOH HOH . 
D 4 HOH B 47 447 14 HOH HOH . 
D 4 HOH B 48 448 45 HOH HOH . 
D 4 HOH B 49 449 18 HOH HOH . 
D 4 HOH B 50 450 49 HOH HOH . 
D 4 HOH B 51 451 20 HOH HOH . 
D 4 HOH B 52 452 52 HOH HOH . 
D 4 HOH B 53 453 22 HOH HOH . 
D 4 HOH B 54 454 79 HOH HOH . 
D 4 HOH B 55 455 29 HOH HOH . 
D 4 HOH B 56 456 7 HOH HOH . 
D 4 HOH B 57 457 26 HOH HOH . 
D 4 HOH B 58 458 60 HOH HOH . 
D 4 HOH B 59 459 91 HOH HOH . 
D 4 HOH B 60 460 57 HOH HOH . 
D 4 HOH B 61 461 27 HOH HOH . 
D 4 HOH B 62 462 15 HOH HOH . 
D 4 HOH B 63 463 86 HOH HOH . 
D 4 HOH B 64 464 10 HOH HOH . 
D 4 HOH B 65 465 99 HOH HOH . 
D 4 HOH B 66 466 82 HOH HOH . 
D 4 HOH B 67 467 28 HOH HOH . 
D 4 HOH B 68 468 5 HOH HOH . 
D 4 HOH B 69 469 63 HOH HOH . 
D 4 HOH B 70 470 73 HOH HOH . 
D 4 HOH B 71 471 83 HOH HOH . 
D 4 HOH B 72 472 9 HOH HOH . 
D 4 HOH B 73 473 16 HOH HOH . 
D 4 HOH B 74 474 54 HOH HOH . 
D 4 HOH B 75 475 94 HOH HOH . 
D 4 HOH B 76 476 2 HOH HOH . 
D 4 HOH B 77 477 90 HOH HOH . 
D 4 HOH B 78 478 30 HOH HOH . 
D 4 HOH B 79 479 77 HOH HOH . 
D 4 HOH B 80 480 100 HOH HOH . 
D 4 HOH B 81 481 97 HOH HOH . 
D 4 HOH B 82 482 66 HOH HOH . 
D 4 HOH B 83 483 101 HOH HOH . 
D 4 HOH B 84 484 56 HOH HOH . 
D 4 HOH B 85 485 98 HOH HOH . 
D 4 HOH B 86 486 84 HOH HOH . 
D 4 HOH B 87 487 53 HOH HOH . 
D 4 HOH B 88 488 87 HOH HOH . 
D 4 HOH B 89 489 72 HOH HOH . 
D 4 HOH B 90 490 35 HOH HOH . 
D 4 HOH B 91 491 19 HOH HOH . 
D 4 HOH B 92 492 62 HOH HOH . 
D 4 HOH B 93 493 88 HOH HOH . 
D 4 HOH B 94 494 61 HOH HOH . 
D 4 HOH B 95 495 89 HOH HOH . 
D 4 HOH B 96 496 67 HOH HOH . 
D 4 HOH B 97 497 85 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 P PG GSP . . . C 3 19.228 -31.147 18.365 1 93.62 ? PG GSP 302 B 1 
HETATM 2 O O3B GSP . . . C 3 19.692 -31.929 17.028 1 47.79 ? O3B GSP 302 B 1 
HETATM 3 S S1G GSP . . . C 3 18.047 -29.964 18.024 1 103.26 ? S1G GSP 302 B 1 
HETATM 4 O O2G GSP . . . C 3 20.458 -30.499 19.032 1 103.73 ? O2G GSP 302 B 1 
HETATM 5 O O3G GSP . . . C 3 18.624 -32.173 19.344 1 111.03 ? O3G GSP 302 B 1 
HETATM 6 P PB GSP . . . C 3 20.289 -31.237 15.696 1 18.68 ? PB GSP 302 B 1 
HETATM 7 O O1B GSP . . . C 3 21.188 -30.078 15.985 1 17.29 ? O1B GSP 302 B 1 
HETATM 8 O O2B GSP . . . C 3 19.234 -30.87 14.718 1 14.91 ? O2B GSP 302 B 1 
HETATM 9 P PA GSP . . . C 3 22.708 -32.721 15.07 1 18.27 ? PA GSP 302 B 1 
HETATM 10 O O1A GSP . . . C 3 23.171 -32.878 16.469 1 18.99 ? O1A GSP 302 B 1 
HETATM 11 O O2A GSP . . . C 3 23.489 -31.76 14.251 1 15.74 ? O2A GSP 302 B 1 
HETATM 12 O O3A GSP . . . C 3 21.13 -32.423 15.027 1 15.53 ? O3A GSP 302 B 1 
HETATM 13 O O5' GSP . . . C 3 22.724 -34.146 14.313 1 23.86 ? O5' GSP 302 B 1 
HETATM 14 C C5' GSP . . . C 3 22.135 -35.287 14.911 1 19.36 ? C5' GSP 302 B 1 
HETATM 15 C C4' GSP . . . C 3 22.962 -36.517 14.542 1 21.36 ? C4' GSP 302 B 1 
HETATM 16 O O4' GSP . . . C 3 22.866 -36.755 13.152 1 22.78 ? O4' GSP 302 B 1 
HETATM 17 C C3' GSP . . . C 3 24.437 -36.328 14.845 1 26.74 ? C3' GSP 302 B 1 
HETATM 18 O O3' GSP . . . C 3 24.974 -37.55 15.308 1 30.65 ? O3' GSP 302 B 1 
HETATM 19 C C2' GSP . . . C 3 25.047 -35.973 13.507 1 23.64 ? C2' GSP 302 B 1 
HETATM 20 O O2' GSP . . . C 3 26.384 -36.388 13.398 1 24.14 ? O2' GSP 302 B 1 
HETATM 21 C C1' GSP . . . C 3 24.148 -36.724 12.55 1 21.14 ? C1' GSP 302 B 1 
HETATM 22 N N9 GSP . . . C 3 24.012 -36.051 11.259 1 22.66 ? N9 GSP 302 B 1 
HETATM 23 C C8 GSP . . . C 3 23.585 -34.771 11.017 1 21.05 ? C8 GSP 302 B 1 
HETATM 24 N N7 GSP . . . C 3 23.583 -34.572 9.684 1 18.96 ? N7 GSP 302 B 1 
HETATM 25 C C5 GSP . . . C 3 23.987 -35.721 9.07 1 19.35 ? C5 GSP 302 B 1 
HETATM 26 C C6 GSP . . . C 3 24.171 -36.098 7.739 1 14.7 ? C6 GSP 302 B 1 
HETATM 27 O O6 GSP . . . C 3 23.955 -35.338 6.795 1 15.9 ? O6 GSP 302 B 1 
HETATM 28 N N1 GSP . . . C 3 24.613 -37.373 7.45 1 22.14 ? N1 GSP 302 B 1 
HETATM 29 C C2 GSP . . . C 3 24.864 -38.277 8.46 1 22.38 ? C2 GSP 302 B 1 
HETATM 30 N N2 GSP . . . C 3 25.29 -39.506 8.175 1 26.67 ? N2 GSP 302 B 1 
HETATM 31 N N3 GSP . . . C 3 24.683 -37.905 9.771 1 25.56 ? N3 GSP 302 B 1 
HETATM 32 C C4 GSP . . . C 3 24.255 -36.652 10.063 1 22.45 ? C4 GSP 302 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#