data_2GVZ
#
_model_server_result.job_id            TMaQ34CHYkh4F7lGqFolPQ 
_model_server_result.datetime_utc      '2024-10-27 00:33:30' 
_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          2gvz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":395}' 
#
_entry.id    2GVZ 
#
_exptl.entry_id    2GVZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          8 
_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         90 
_cell.entry_id            2GVZ 
_cell.length_a            116.8 
_cell.length_b            132.1 
_cell.length_c            69.6 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2GVZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_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    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                      8 
_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
metalc ? metalc1 G O2A ONA . A ONA 100 1_555 D MN MN . A MN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? 
metalc ? metalc2 G O1B ONA . A ONA 100 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? 
metalc ? metalc3 A OD2 ASP 41 A ASP 396 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc4 A O ILE 42 A ILE 397 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc5 A OD2 ASP 85 A ASP 440 1_555 E MN MN . A MN 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
metalc ? metalc6 C OG SER 54 C SER 54 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc7 C OG1 THR 204 C THR 204 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc8 J O3G GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc9 J O2G GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? 
metalc ? metalc10 J O2B GSP . C GSP 395 1_555 H MN MN . C MN 396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
#
_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 221 n n 
PG S1G GSP doub 222 n n 
PG O2G GSP sing 223 n n 
PG O3G GSP sing 224 n n 
O3B PB GSP sing 225 n n 
O2G HOG2 GSP sing 226 n n 
O3G HOG3 GSP sing 227 n n 
PB O1B GSP doub 228 n n 
PB O2B GSP sing 229 n n 
PB O3A GSP sing 230 n n 
O2B HOB2 GSP sing 231 n n 
PA O1A GSP doub 232 n n 
PA O2A GSP sing 233 n n 
PA O3A GSP sing 234 n n 
PA O5' GSP sing 235 n n 
O2A HOA2 GSP sing 236 n n 
O5' C5' GSP sing 237 n n 
C5' C4' GSP sing 238 n n 
C5' "H5'1" GSP sing 239 n n 
C5' "H5'2" GSP sing 240 n n 
C4' O4' GSP sing 241 n n 
C4' C3' GSP sing 242 n n 
C4' H4' GSP sing 243 n n 
O4' C1' GSP sing 244 n n 
C3' O3' GSP sing 245 n n 
C3' C2' GSP sing 246 n n 
C3' H3' GSP sing 247 n n 
O3' HO3' GSP sing 248 n n 
C2' O2' GSP sing 249 n n 
C2' C1' GSP sing 250 n n 
C2' H2' GSP sing 251 n n 
O2' HO2' GSP sing 252 n n 
C1' N9 GSP sing 253 n n 
C1' H1' GSP sing 254 n n 
N9 C8 GSP sing 255 n y 
N9 C4 GSP sing 256 n y 
C8 N7 GSP doub 257 n y 
C8 H8 GSP sing 258 n n 
N7 C5 GSP sing 259 n y 
C5 C6 GSP sing 260 n n 
C5 C4 GSP doub 261 n y 
C6 O6 GSP doub 262 n n 
C6 N1 GSP sing 263 n n 
N1 C2 GSP sing 264 n n 
N1 HN1 GSP sing 265 n n 
C2 N2 GSP sing 266 n n 
C2 N3 GSP doub 267 n n 
N2 HN21 GSP sing 268 n n 
N2 HN22 GSP sing 269 n n 
N3 C4 GSP sing 270 n n 
#
_atom_sites.entry_id                     2GVZ 
_atom_sites.fract_transf_matrix[1][1]    0.008562 
_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]    0.00757 
_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]    0.014368 
_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 MN A 1 581 502 MN MN . 
E 4 MN A 1 582 503 MN MN . 
F 5 FKP A 1 1 1 FKP FKP . 
G 6 ONA A 1 100 100 ONA ONA . 
H 4 MN C 1 396 396 MN MN . 
I 7 CL C 1 397 397 CL CL . 
J 8 GSP C 1 395 395 GSP GSP . 
#
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 . . . J 8 22.969 3.21 28.679 1 73.66 ? PG GSP 395 C 1 
HETATM 2 O O3B GSP . . . J 8 22.423 2.829 27.189 1 64.04 ? O3B GSP 395 C 1 
HETATM 3 S S1G GSP . . . J 8 24.778 3.696 28.366 1 76.13 ? S1G GSP 395 C 1 
HETATM 4 O O2G GSP . . . J 8 21.956 4.219 29.024 1 74.68 ? O2G GSP 395 C 1 
HETATM 5 O O3G GSP . . . J 8 23.139 1.995 29.513 1 72.35 ? O3G GSP 395 C 1 
HETATM 6 P PB GSP . . . J 8 20.872 2.275 27.027 1 51.47 ? PB GSP 395 C 1 
HETATM 7 O O1B GSP . . . J 8 21.123 1.116 26.168 1 56.74 ? O1B GSP 395 C 1 
HETATM 8 O O2B GSP . . . J 8 20.13 1.925 28.25 1 54.47 ? O2B GSP 395 C 1 
HETATM 9 P PA GSP . . . J 8 18.794 4.129 27.02 1 38.86 ? PA GSP 395 C 1 
HETATM 10 O O1A GSP . . . J 8 17.778 3.177 27.524 1 41.64 ? O1A GSP 395 C 1 
HETATM 11 O O2A GSP . . . J 8 19.45 5.104 27.915 1 37.76 ? O2A GSP 395 C 1 
HETATM 12 O O3A GSP . . . J 8 19.926 3.341 26.296 1 45.45 ? O3A GSP 395 C 1 
HETATM 13 O O5' GSP . . . J 8 18.09 5 25.813 1 33.3 ? O5' GSP 395 C 1 
HETATM 14 C C5' GSP . . . J 8 18.759 6.033 25.068 1 34.63 ? C5' GSP 395 C 1 
HETATM 15 C C4' GSP . . . J 8 17.697 6.808 24.326 1 38.41 ? C4' GSP 395 C 1 
HETATM 16 O O4' GSP . . . J 8 17.025 5.935 23.365 1 37.07 ? O4' GSP 395 C 1 
HETATM 17 C C3' GSP . . . J 8 16.504 7.313 25.246 1 42.78 ? C3' GSP 395 C 1 
HETATM 18 O O3' GSP . . . J 8 16.375 8.773 25.066 1 48.52 ? O3' GSP 395 C 1 
HETATM 19 C C2' GSP . . . J 8 15.227 6.577 24.663 1 40.45 ? C2' GSP 395 C 1 
HETATM 20 O O2' GSP . . . J 8 14.007 7.323 24.741 1 46.8 ? O2' GSP 395 C 1 
HETATM 21 C C1' GSP . . . J 8 15.64 6.332 23.208 1 36.5 ? C1' GSP 395 C 1 
HETATM 22 N N9 GSP . . . J 8 14.933 5.21 22.585 1 31.32 ? N9 GSP 395 C 1 
HETATM 23 C C8 GSP . . . J 8 14.786 3.887 22.921 1 31.02 ? C8 GSP 395 C 1 
HETATM 24 N N7 GSP . . . J 8 14.067 3.177 22.113 1 31.16 ? N7 GSP 395 C 1 
HETATM 25 C C5 GSP . . . J 8 13.705 4.118 21.157 1 35.29 ? C5 GSP 395 C 1 
HETATM 26 C C6 GSP . . . J 8 12.882 3.919 19.987 1 41.41 ? C6 GSP 395 C 1 
HETATM 27 O O6 GSP . . . J 8 12.378 2.826 19.697 1 47.66 ? O6 GSP 395 C 1 
HETATM 28 N N1 GSP . . . J 8 12.757 5.124 19.279 1 41.75 ? N1 GSP 395 C 1 
HETATM 29 C C2 GSP . . . J 8 13.326 6.359 19.616 1 39.35 ? C2 GSP 395 C 1 
HETATM 30 N N2 GSP . . . J 8 13.122 7.415 18.847 1 42.09 ? N2 GSP 395 C 1 
HETATM 31 N N3 GSP . . . J 8 14.1 6.52 20.734 1 34.98 ? N3 GSP 395 C 1 
HETATM 32 C C4 GSP . . . J 8 14.238 5.358 21.446 1 31.99 ? C4 GSP 395 C 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          18 
_model_server_stats.element_count           32 
#