data_8BWG
#
_model_server_result.job_id            jCWgLSxmINvvPV-uKd923Q 
_model_server_result.datetime_utc      '2024-11-26 17:14:09' 
_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          8bwg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    8BWG 
#
_exptl.entry_id    8BWG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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            8BWG 
_cell.length_a            92.662 
_cell.length_b            92.662 
_cell.length_c            119.323 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8BWG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 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 
_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
metalc ? metalc1 A OG SER 17 R SER 17 1_555 C MG MG . R MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc2 B O3B GDP . R GDP 201 1_555 C MG MG . R MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc3 C MG MG . R MG 202 1_555 E O HOH . R HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc4 C MG MG . R MG 202 1_555 E O HOH . R HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc5 C MG MG . R MG 202 1_555 E O HOH . R HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc6 C MG MG . R MG 202 1_555 E O HOH . R HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
#
_chem_comp.formula           'C10 H15 N5 O11 P2' 
_chem_comp.formula_weight    443.201 
_chem_comp.id                GDP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
PB O1B GDP doub 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     8BWG 
_atom_sites.fract_transf_matrix[1][1]    0.010792 
_atom_sites.fract_transf_matrix[1][2]    0.006231 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012461 
_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]    0.008381 
_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 GDP R 1 201 201 GDP GDP . 
C 3 MG R 1 202 1 MG MG . 
D 4 SO4 R 1 203 1 SO4 SO4 . 
E 5 HOH R 1 301 88 HOH HOH . 
E 5 HOH R 2 302 52 HOH HOH . 
E 5 HOH R 3 303 114 HOH HOH . 
E 5 HOH R 4 304 33 HOH HOH . 
E 5 HOH R 5 305 146 HOH HOH . 
E 5 HOH R 6 306 31 HOH HOH . 
E 5 HOH R 7 307 160 HOH HOH . 
E 5 HOH R 8 308 129 HOH HOH . 
E 5 HOH R 9 309 105 HOH HOH . 
E 5 HOH R 10 310 123 HOH HOH . 
E 5 HOH R 11 311 65 HOH HOH . 
E 5 HOH R 12 312 133 HOH HOH . 
E 5 HOH R 13 313 36 HOH HOH . 
E 5 HOH R 14 314 83 HOH HOH . 
E 5 HOH R 15 315 116 HOH HOH . 
E 5 HOH R 16 316 12 HOH HOH . 
E 5 HOH R 17 317 28 HOH HOH . 
E 5 HOH R 18 318 126 HOH HOH . 
E 5 HOH R 19 319 109 HOH HOH . 
E 5 HOH R 20 320 127 HOH HOH . 
E 5 HOH R 21 321 32 HOH HOH . 
E 5 HOH R 22 322 108 HOH HOH . 
E 5 HOH R 23 323 9 HOH HOH . 
E 5 HOH R 24 324 47 HOH HOH . 
E 5 HOH R 25 325 42 HOH HOH . 
E 5 HOH R 26 326 119 HOH HOH . 
E 5 HOH R 27 327 95 HOH HOH . 
E 5 HOH R 28 328 7 HOH HOH . 
E 5 HOH R 29 329 8 HOH HOH . 
E 5 HOH R 30 330 37 HOH HOH . 
E 5 HOH R 31 331 104 HOH HOH . 
E 5 HOH R 32 332 34 HOH HOH . 
E 5 HOH R 33 333 93 HOH HOH . 
E 5 HOH R 34 334 11 HOH HOH . 
E 5 HOH R 35 335 143 HOH HOH . 
E 5 HOH R 36 336 21 HOH HOH . 
E 5 HOH R 37 337 132 HOH HOH . 
E 5 HOH R 38 338 40 HOH HOH . 
E 5 HOH R 39 339 43 HOH HOH . 
E 5 HOH R 40 340 59 HOH HOH . 
E 5 HOH R 41 341 112 HOH HOH . 
E 5 HOH R 42 342 55 HOH HOH . 
E 5 HOH R 43 343 44 HOH HOH . 
E 5 HOH R 44 344 5 HOH HOH . 
E 5 HOH R 45 345 117 HOH HOH . 
E 5 HOH R 46 346 6 HOH HOH . 
E 5 HOH R 47 347 16 HOH HOH . 
E 5 HOH R 48 348 102 HOH HOH . 
E 5 HOH R 49 349 1 HOH HOH . 
E 5 HOH R 50 350 66 HOH HOH . 
E 5 HOH R 51 351 97 HOH HOH . 
E 5 HOH R 52 352 2 HOH HOH . 
E 5 HOH R 53 353 111 HOH HOH . 
E 5 HOH R 54 354 73 HOH HOH . 
E 5 HOH R 55 355 77 HOH HOH . 
E 5 HOH R 56 356 103 HOH HOH . 
E 5 HOH R 57 357 4 HOH HOH . 
E 5 HOH R 58 358 164 HOH HOH . 
E 5 HOH R 59 359 76 HOH HOH . 
E 5 HOH R 60 360 64 HOH HOH . 
E 5 HOH R 61 361 130 HOH HOH . 
E 5 HOH R 62 362 24 HOH HOH . 
E 5 HOH R 63 363 122 HOH HOH . 
E 5 HOH R 64 364 92 HOH HOH . 
E 5 HOH R 65 365 22 HOH HOH . 
E 5 HOH R 66 366 54 HOH HOH . 
E 5 HOH R 67 367 138 HOH HOH . 
E 5 HOH R 68 368 128 HOH HOH . 
E 5 HOH R 69 369 120 HOH HOH . 
E 5 HOH R 70 370 17 HOH HOH . 
E 5 HOH R 71 371 158 HOH HOH . 
E 5 HOH R 72 372 151 HOH HOH . 
E 5 HOH R 73 373 110 HOH HOH . 
E 5 HOH R 74 374 30 HOH HOH . 
E 5 HOH R 75 375 23 HOH HOH . 
E 5 HOH R 76 376 14 HOH HOH . 
E 5 HOH R 77 377 48 HOH HOH . 
E 5 HOH R 78 378 162 HOH HOH . 
E 5 HOH R 79 379 51 HOH HOH . 
E 5 HOH R 80 380 90 HOH HOH . 
E 5 HOH R 81 381 39 HOH HOH . 
E 5 HOH R 82 382 135 HOH HOH . 
E 5 HOH R 83 383 82 HOH HOH . 
E 5 HOH R 84 384 62 HOH HOH . 
E 5 HOH R 85 385 147 HOH HOH . 
E 5 HOH R 86 386 63 HOH HOH . 
E 5 HOH R 87 387 29 HOH HOH . 
E 5 HOH R 88 388 141 HOH HOH . 
E 5 HOH R 89 389 18 HOH HOH . 
E 5 HOH R 90 390 89 HOH HOH . 
E 5 HOH R 91 391 99 HOH HOH . 
E 5 HOH R 92 392 13 HOH HOH . 
E 5 HOH R 93 393 149 HOH HOH . 
E 5 HOH R 94 394 85 HOH HOH . 
E 5 HOH R 95 395 46 HOH HOH . 
E 5 HOH R 96 396 35 HOH HOH . 
E 5 HOH R 97 397 15 HOH HOH . 
E 5 HOH R 98 398 131 HOH HOH . 
E 5 HOH R 99 399 67 HOH HOH . 
E 5 HOH R 100 400 69 HOH HOH . 
E 5 HOH R 101 401 80 HOH HOH . 
E 5 HOH R 102 402 45 HOH HOH . 
E 5 HOH R 103 403 79 HOH HOH . 
E 5 HOH R 104 404 101 HOH HOH . 
E 5 HOH R 105 405 159 HOH HOH . 
E 5 HOH R 106 406 38 HOH HOH . 
E 5 HOH R 107 407 75 HOH HOH . 
E 5 HOH R 108 408 163 HOH HOH . 
E 5 HOH R 109 409 96 HOH HOH . 
E 5 HOH R 110 410 145 HOH HOH . 
E 5 HOH R 111 411 148 HOH HOH . 
E 5 HOH R 112 412 121 HOH HOH . 
E 5 HOH R 113 413 26 HOH HOH . 
E 5 HOH R 114 414 86 HOH HOH . 
E 5 HOH R 115 415 107 HOH HOH . 
E 5 HOH R 116 416 165 HOH HOH . 
E 5 HOH R 117 417 10 HOH HOH . 
E 5 HOH R 118 418 78 HOH HOH . 
E 5 HOH R 119 419 166 HOH HOH . 
E 5 HOH R 120 420 74 HOH HOH . 
E 5 HOH R 121 421 57 HOH HOH . 
E 5 HOH R 122 422 56 HOH HOH . 
E 5 HOH R 123 423 156 HOH HOH . 
E 5 HOH R 124 424 106 HOH HOH . 
E 5 HOH R 125 425 25 HOH HOH . 
E 5 HOH R 126 426 70 HOH HOH . 
E 5 HOH R 127 427 134 HOH HOH . 
E 5 HOH R 128 428 115 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 PB GDP . . . B 2 -7.397 -14.492 -20.892 1 18.07 0 PB GDP 201 R 1 
HETATM 2 O O1B GDP . . . B 2 -6.353 -14.584 -21.976 1 17.58 0 O1B GDP 201 R 1 
HETATM 3 O O2B GDP . . . B 2 -7.069 -13.51 -19.81 1 19.12 0 O2B GDP 201 R 1 
HETATM 4 O O3B GDP . . . B 2 -7.793 -15.865 -20.331 1 19.3 0 O3B GDP 201 R 1 
HETATM 5 O O3A GDP . . . B 2 -8.696 -13.89 -21.647 1 18.63 0 O3A GDP 201 R 1 
HETATM 6 P PA GDP . . . B 2 -10.241 -14.326 -21.578 1 19.49 0 PA GDP 201 R 1 
HETATM 7 O O1A GDP . . . B 2 -10.433 -15.641 -22.219 1 20.89 0 O1A GDP 201 R 1 
HETATM 8 O O2A GDP . . . B 2 -10.661 -14.103 -20.151 1 22.53 0 O2A GDP 201 R 1 
HETATM 9 O O5' GDP . . . B 2 -10.916 -13.213 -22.508 1 19.18 0 O5' GDP 201 R 1 
HETATM 10 C C5' GDP . . . B 2 -10.731 -11.801 -22.194 1 18.91 0 C5' GDP 201 R 1 
HETATM 11 C C4' GDP . . . B 2 -11.91 -11.027 -22.717 1 20.76 0 C4' GDP 201 R 1 
HETATM 12 O O4' GDP . . . B 2 -11.889 -11.115 -24.148 1 19.4 0 O4' GDP 201 R 1 
HETATM 13 C C3' GDP . . . B 2 -13.298 -11.521 -22.305 1 23.06 0 C3' GDP 201 R 1 
HETATM 14 O O3' GDP . . . B 2 -14.173 -10.421 -22.131 1 24.83 0 O3' GDP 201 R 1 
HETATM 15 C C2' GDP . . . B 2 -13.712 -12.416 -23.477 1 21.38 0 C2' GDP 201 R 1 
HETATM 16 O O2' GDP . . . B 2 -15.109 -12.555 -23.599 1 29.48 0 O2' GDP 201 R 1 
HETATM 17 C C1' GDP . . . B 2 -13.103 -11.643 -24.635 1 18.93 0 C1' GDP 201 R 1 
HETATM 18 N N9 GDP . . . B 2 -12.781 -12.476 -25.785 1 18.08 0 N9 GDP 201 R 1 
HETATM 19 C C8 GDP . . . B 2 -11.947 -13.575 -25.775 1 18.72 0 C8 GDP 201 R 1 
HETATM 20 N N7 GDP . . . B 2 -11.82 -14.137 -26.956 1 17.37 0 N7 GDP 201 R 1 
HETATM 21 C C5 GDP . . . B 2 -12.581 -13.332 -27.801 1 16.84 0 C5 GDP 201 R 1 
HETATM 22 C C6 GDP . . . B 2 -12.787 -13.422 -29.209 1 18.86 0 C6 GDP 201 R 1 
HETATM 23 O O6 GDP . . . B 2 -12.323 -14.251 -30.009 1 17.61 0 O6 GDP 201 R 1 
HETATM 24 N N1 GDP . . . B 2 -13.63 -12.412 -29.67 1 18.56 0 N1 GDP 201 R 1 
HETATM 25 C C2 GDP . . . B 2 -14.17 -11.406 -28.889 1 17.33 0 C2 GDP 201 R 1 
HETATM 26 N N2 GDP . . . B 2 -14.99 -10.54 -29.499 1 20.84 0 N2 GDP 201 R 1 
HETATM 27 N N3 GDP . . . B 2 -13.982 -11.324 -27.571 1 17.44 0 N3 GDP 201 R 1 
HETATM 28 C C4 GDP . . . B 2 -13.158 -12.295 -27.097 1 17.52 0 C4 GDP 201 R 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#