data_1CJV
#
_model_server_result.job_id            SM6Tr8Si_qEcBU8OKqfUBA 
_model_server_result.datetime_utc      '2024-10-26 16:29:48' 
_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          1cjv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":406}' 
#
_entry.id    1CJV 
#
_exptl.entry_id    1CJV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              539.246 
_entity.id                          10 
_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            1CJV 
_cell.length_a            118.4 
_cell.length_b            134.2 
_cell.length_c            71.6 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1CJV 
_symmetry.cell_setting             orthorhombic 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,N,O 
_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                      10 
_struct_asym.id                             L 
_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 DAD . A DAD 102 1_555 D ZN ZN . A ZN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc2 G O2G DAD . A DAD 102 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc3 G O1B DAD . A DAD 102 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc4 G O2A DAD . A DAD 102 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc5 A OD1 ASP 33 A ASP 396 1_555 D ZN ZN . A ZN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc6 A OD2 ASP 33 A ASP 396 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc7 A O ILE 34 A ILE 397 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc8 A OD1 ASP 77 A ASP 440 1_555 D ZN ZN . A ZN 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? 
metalc ? metalc9 A OD2 ASP 77 A ASP 440 1_555 E MG MG . A MG 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc10 C NH2 ARG 42 C ARG 42 1_555 K ZN ZN . C ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc11 C OG SER 54 C SER 54 1_555 I MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc12 C OG1 THR 204 C THR 204 1_555 I MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc13 C OE2 GLU 209 C GLU 209 1_555 K ZN ZN . C ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? 
metalc ? metalc14 C ND1 HIS 220 C HIS 220 1_555 K ZN ZN . C ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc15 I MG MG . C MG 403 1_555 L O2B GSP . C GSP 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? 
metalc ? metalc16 I MG MG . C MG 403 1_555 L O2G GSP . C GSP 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.855 ? 
metalc ? metalc17 I MG MG . C MG 403 1_555 L O3B GSP . C GSP 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? 
metalc ? metalc18 I MG MG . C MG 403 1_555 O O HOH . C HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? 
metalc ? metalc19 I MG MG . C MG 403 1_555 O O HOH . C HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? 
#
_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 241 n n 
PG S1G GSP doub 242 n n 
PG O2G GSP sing 243 n n 
PG O3G GSP sing 244 n n 
O3B PB GSP sing 245 n n 
O2G HOG2 GSP sing 246 n n 
O3G HOG3 GSP sing 247 n n 
PB O1B GSP doub 248 n n 
PB O2B GSP sing 249 n n 
PB O3A GSP sing 250 n n 
O2B HOB2 GSP sing 251 n n 
PA O1A GSP doub 252 n n 
PA O2A GSP sing 253 n n 
PA O3A GSP sing 254 n n 
PA O5' GSP sing 255 n n 
O2A HOA2 GSP sing 256 n n 
O5' C5' GSP sing 257 n n 
C5' C4' GSP sing 258 n n 
C5' "H5'1" GSP sing 259 n n 
C5' "H5'2" GSP sing 260 n n 
C4' O4' GSP sing 261 n n 
C4' C3' GSP sing 262 n n 
C4' H4' GSP sing 263 n n 
O4' C1' GSP sing 264 n n 
C3' O3' GSP sing 265 n n 
C3' C2' GSP sing 266 n n 
C3' H3' GSP sing 267 n n 
O3' HO3' GSP sing 268 n n 
C2' O2' GSP sing 269 n n 
C2' C1' GSP sing 270 n n 
C2' H2' GSP sing 271 n n 
O2' HO2' GSP sing 272 n n 
C1' N9 GSP sing 273 n n 
C1' H1' GSP sing 274 n n 
N9 C8 GSP sing 275 n y 
N9 C4 GSP sing 276 n y 
C8 N7 GSP doub 277 n y 
C8 H8 GSP sing 278 n n 
N7 C5 GSP sing 279 n y 
C5 C6 GSP sing 280 n n 
C5 C4 GSP doub 281 n y 
C6 O6 GSP doub 282 n n 
C6 N1 GSP sing 283 n n 
N1 C2 GSP sing 284 n n 
N1 HN1 GSP sing 285 n n 
C2 N2 GSP sing 286 n n 
C2 N3 GSP doub 287 n n 
N2 HN21 GSP sing 288 n n 
N2 HN22 GSP sing 289 n n 
N3 C4 GSP sing 290 n n 
#
_atom_sites.entry_id                     1CJV 
_atom_sites.fract_transf_matrix[1][1]    0.008446 
_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]    0.007451 
_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]    0.013966 
_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 ZN A 1 581 502 ZN ZN . 
E 5 MG A 1 582 503 MG MG . 
F 6 FOK A 1 101 101 FOK FOK . 
G 7 DAD A 1 102 102 DAD DAD . 
H 8 MES A 1 103 103 MES MES . 
I 5 MG C 1 403 396 MG MG . 
J 9 CL C 1 404 397 CL CL . 
K 4 ZN C 1 405 398 ZN ZN . 
L 10 GSP C 1 406 395 GSP GSP . 
M 11 HOH A 1 23 23 HOH HOH . 
M 11 HOH A 2 24 24 HOH HOH . 
M 11 HOH A 3 30 30 HOH HOH . 
M 11 HOH A 4 31 31 HOH HOH . 
M 11 HOH A 5 33 33 HOH HOH . 
M 11 HOH A 6 57 57 HOH HOH . 
N 11 HOH B 1 8 8 HOH HOH . 
N 11 HOH B 2 9 9 HOH HOH . 
N 11 HOH B 3 12 12 HOH HOH . 
N 11 HOH B 4 13 13 HOH HOH . 
N 11 HOH B 5 14 14 HOH HOH . 
N 11 HOH B 6 15 15 HOH HOH . 
N 11 HOH B 7 17 17 HOH HOH . 
N 11 HOH B 8 18 18 HOH HOH . 
N 11 HOH B 9 19 19 HOH HOH . 
N 11 HOH B 10 21 21 HOH HOH . 
N 11 HOH B 11 22 22 HOH HOH . 
N 11 HOH B 12 25 25 HOH HOH . 
N 11 HOH B 13 26 26 HOH HOH . 
N 11 HOH B 14 28 28 HOH HOH . 
N 11 HOH B 15 32 32 HOH HOH . 
N 11 HOH B 16 34 34 HOH HOH . 
N 11 HOH B 17 35 35 HOH HOH . 
N 11 HOH B 18 36 36 HOH HOH . 
N 11 HOH B 19 37 37 HOH HOH . 
N 11 HOH B 20 38 38 HOH HOH . 
N 11 HOH B 21 54 54 HOH HOH . 
O 11 HOH C 1 407 1 HOH HOH . 
O 11 HOH C 2 408 2 HOH HOH . 
O 11 HOH C 3 409 3 HOH HOH . 
O 11 HOH C 4 410 5 HOH HOH . 
O 11 HOH C 5 411 7 HOH HOH . 
O 11 HOH C 6 412 10 HOH HOH . 
O 11 HOH C 7 413 39 HOH HOH . 
O 11 HOH C 8 414 40 HOH HOH . 
O 11 HOH C 9 415 41 HOH HOH . 
O 11 HOH C 10 416 42 HOH HOH . 
O 11 HOH C 11 417 44 HOH HOH . 
O 11 HOH C 12 418 45 HOH HOH . 
O 11 HOH C 13 419 46 HOH HOH . 
O 11 HOH C 14 420 47 HOH HOH . 
O 11 HOH C 15 421 49 HOH HOH . 
O 11 HOH C 16 422 50 HOH HOH . 
O 11 HOH C 17 423 51 HOH HOH . 
O 11 HOH C 18 424 52 HOH HOH . 
O 11 HOH C 19 425 58 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 . . . L 10 23.517 3.14 28.959 1 28.99 ? PG GSP 406 C 1 
HETATM 2 O O3B GSP . . . L 10 22.357 3.367 28.016 1 23.64 ? O3B GSP 406 C 1 
HETATM 3 S S1G GSP . . . L 10 24.944 4.379 28.793 1 32.16 ? S1G GSP 406 C 1 
HETATM 4 O O2G GSP . . . L 10 23.03 3.359 30.347 1 26.56 ? O2G GSP 406 C 1 
HETATM 5 O O3G GSP . . . L 10 24.151 1.841 28.607 1 26.74 ? O3G GSP 406 C 1 
HETATM 6 P PB GSP . . . L 10 21.046 2.698 27.725 1 17.25 ? PB GSP 406 C 1 
HETATM 7 O O1B GSP . . . L 10 21.29 1.564 26.809 1 14.41 ? O1B GSP 406 C 1 
HETATM 8 O O2B GSP . . . L 10 20.36 2.451 29.01 1 18.38 ? O2B GSP 406 C 1 
HETATM 9 P PA GSP . . . L 10 19.045 4.486 27.37 1 16.82 ? PA GSP 406 C 1 
HETATM 10 O O1A GSP . . . L 10 18.018 3.494 27.772 1 16.28 ? O1A GSP 406 C 1 
HETATM 11 O O2A GSP . . . L 10 19.419 5.577 28.296 1 15.86 ? O2A GSP 406 C 1 
HETATM 12 O O3A GSP . . . L 10 20.289 3.749 26.984 1 17.02 ? O3A GSP 406 C 1 
HETATM 13 O O5' GSP . . . L 10 18.559 5.168 26.017 1 15.28 ? O5' GSP 406 C 1 
HETATM 14 C C5' GSP . . . L 10 19.285 6.263 25.468 1 15.5 ? C5' GSP 406 C 1 
HETATM 15 C C4' GSP . . . L 10 18.342 7.297 24.902 1 14.98 ? C4' GSP 406 C 1 
HETATM 16 O O4' GSP . . . L 10 17.69 6.814 23.702 1 16.26 ? O4' GSP 406 C 1 
HETATM 17 C C3' GSP . . . L 10 17.222 7.726 25.841 1 13.66 ? C3' GSP 406 C 1 
HETATM 18 O O3' GSP . . . L 10 16.992 9.114 25.64 1 16.25 ? O3' GSP 406 C 1 
HETATM 19 C C2' GSP . . . L 10 16.033 6.94 25.328 1 15.45 ? C2' GSP 406 C 1 
HETATM 20 O O2' GSP . . . L 10 14.793 7.546 25.607 1 18.34 ? O2' GSP 406 C 1 
HETATM 21 C C1' GSP . . . L 10 16.286 6.931 23.837 1 14.11 ? C1' GSP 406 C 1 
HETATM 22 N N9 GSP . . . L 10 15.676 5.786 23.169 1 12.59 ? N9 GSP 406 C 1 
HETATM 23 C C8 GSP . . . L 10 15.719 4.484 23.58 1 11.44 ? C8 GSP 406 C 1 
HETATM 24 N N7 GSP . . . L 10 15.058 3.68 22.797 1 13.2 ? N7 GSP 406 C 1 
HETATM 25 C C5 GSP . . . L 10 14.551 4.504 21.805 1 12.21 ? C5 GSP 406 C 1 
HETATM 26 C C6 GSP . . . L 10 13.744 4.196 20.687 1 13.42 ? C6 GSP 406 C 1 
HETATM 27 O O6 GSP . . . L 10 13.301 3.102 20.339 1 17.72 ? O6 GSP 406 C 1 
HETATM 28 N N1 GSP . . . L 10 13.459 5.324 19.938 1 11.61 ? N1 GSP 406 C 1 
HETATM 29 C C2 GSP . . . L 10 13.893 6.585 20.223 1 12.75 ? C2 GSP 406 C 1 
HETATM 30 N N2 GSP . . . L 10 13.522 7.549 19.361 1 12.64 ? N2 GSP 406 C 1 
HETATM 31 N N3 GSP . . . L 10 14.641 6.887 21.272 1 14.06 ? N3 GSP 406 C 1 
HETATM 32 C C4 GSP . . . L 10 14.931 5.804 22.014 1 11.85 ? C4 GSP 406 C 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           32 
#