data_3NXS
#
_model_server_result.job_id            fyqdXOg5eOc1Y94YVdoc8Q 
_model_server_result.datetime_utc      '2024-11-17 09:45:30' 
_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          3nxs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":327}' 
#
_entry.id    3NXS 
#
_exptl.entry_id    3NXS 
_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         90 
_cell.entry_id            3NXS 
_cell.length_a            78.63 
_cell.length_b            91.46 
_cell.length_c            57.47 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NXS 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 78.63 0 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 
#
_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 70 n n 
PB O2B GDP sing 71 n n 
PB O3B GDP sing 72 n n 
PB O3A GDP sing 73 n n 
O2B HOB2 GDP sing 74 n n 
O3B HOB3 GDP sing 75 n n 
O3A PA GDP sing 76 n n 
PA O1A GDP doub 77 n n 
PA O2A GDP sing 78 n n 
PA O5' GDP sing 79 n n 
O2A HOA2 GDP sing 80 n n 
O5' C5' GDP sing 81 n n 
C5' C4' GDP sing 82 n n 
C5' H5' GDP sing 83 n n 
C5' "H5''" GDP sing 84 n n 
C4' O4' GDP sing 85 n n 
C4' C3' GDP sing 86 n n 
C4' H4' GDP sing 87 n n 
O4' C1' GDP sing 88 n n 
C3' O3' GDP sing 89 n n 
C3' C2' GDP sing 90 n n 
C3' H3' GDP sing 91 n n 
O3' HO3' GDP sing 92 n n 
C2' O2' GDP sing 93 n n 
C2' C1' GDP sing 94 n n 
C2' H2' GDP sing 95 n n 
O2' HO2' GDP sing 96 n n 
C1' N9 GDP sing 97 n n 
C1' H1' GDP sing 98 n n 
N9 C8 GDP sing 99 n y 
N9 C4 GDP sing 100 n y 
C8 N7 GDP doub 101 n y 
C8 H8 GDP sing 102 n n 
N7 C5 GDP sing 103 n y 
C5 C6 GDP sing 104 n n 
C5 C4 GDP doub 105 n y 
C6 O6 GDP doub 106 n n 
C6 N1 GDP sing 107 n n 
N1 C2 GDP sing 108 n n 
N1 HN1 GDP sing 109 n n 
C2 N2 GDP sing 110 n n 
C2 N3 GDP doub 111 n n 
N2 HN21 GDP sing 112 n n 
N2 HN22 GDP sing 113 n n 
N3 C4 GDP sing 114 n n 
#
_atom_sites.entry_id                     3NXS 
_atom_sites.fract_transf_matrix[1][1]    0.012718 
_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]    0.010934 
_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]    0.0174 
_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 A 1 327 327 GDP GDP . 
C 3 CL A 1 328 328 CL CL . 
D 4 HOH A 1 329 1 HOH HOH . 
D 4 HOH A 2 330 2 HOH HOH . 
D 4 HOH A 3 331 3 HOH HOH . 
D 4 HOH A 4 332 4 HOH HOH . 
D 4 HOH A 5 333 5 HOH HOH . 
D 4 HOH A 6 334 6 HOH HOH . 
D 4 HOH A 7 335 7 HOH HOH . 
D 4 HOH A 8 336 8 HOH HOH . 
D 4 HOH A 9 337 9 HOH HOH . 
D 4 HOH A 10 338 10 HOH HOH . 
D 4 HOH A 11 339 11 HOH HOH . 
D 4 HOH A 12 340 12 HOH HOH . 
D 4 HOH A 13 341 13 HOH HOH . 
D 4 HOH A 14 342 14 HOH HOH . 
D 4 HOH A 15 343 15 HOH HOH . 
D 4 HOH A 16 344 16 HOH HOH . 
D 4 HOH A 17 345 17 HOH HOH . 
D 4 HOH A 18 346 18 HOH HOH . 
D 4 HOH A 19 347 19 HOH HOH . 
D 4 HOH A 20 348 20 HOH HOH . 
D 4 HOH A 21 349 21 HOH HOH . 
D 4 HOH A 22 350 22 HOH HOH . 
D 4 HOH A 23 351 23 HOH HOH . 
D 4 HOH A 24 352 24 HOH HOH . 
D 4 HOH A 25 353 25 HOH HOH . 
D 4 HOH A 26 354 26 HOH HOH . 
D 4 HOH A 27 355 27 HOH HOH . 
D 4 HOH A 28 356 28 HOH HOH . 
D 4 HOH A 29 357 29 HOH HOH . 
D 4 HOH A 30 358 30 HOH HOH . 
D 4 HOH A 31 359 31 HOH HOH . 
D 4 HOH A 32 360 32 HOH HOH . 
D 4 HOH A 33 361 33 HOH HOH . 
D 4 HOH A 34 362 34 HOH HOH . 
D 4 HOH A 35 363 35 HOH HOH . 
D 4 HOH A 36 364 36 HOH HOH . 
D 4 HOH A 37 365 37 HOH HOH . 
D 4 HOH A 38 366 38 HOH HOH . 
D 4 HOH A 39 367 39 HOH HOH . 
D 4 HOH A 40 368 40 HOH HOH . 
D 4 HOH A 41 369 41 HOH HOH . 
D 4 HOH A 42 370 42 HOH HOH . 
D 4 HOH A 43 371 43 HOH HOH . 
D 4 HOH A 44 372 44 HOH HOH . 
D 4 HOH A 45 373 45 HOH HOH . 
D 4 HOH A 46 374 46 HOH HOH . 
D 4 HOH A 47 375 47 HOH HOH . 
D 4 HOH A 48 376 48 HOH HOH . 
D 4 HOH A 49 377 49 HOH HOH . 
D 4 HOH A 50 378 50 HOH HOH . 
D 4 HOH A 51 379 51 HOH HOH . 
D 4 HOH A 52 380 52 HOH HOH . 
D 4 HOH A 53 381 53 HOH HOH . 
D 4 HOH A 54 382 54 HOH HOH . 
D 4 HOH A 55 383 55 HOH HOH . 
D 4 HOH A 56 384 56 HOH HOH . 
D 4 HOH A 57 385 57 HOH HOH . 
D 4 HOH A 58 386 58 HOH HOH . 
D 4 HOH A 59 387 59 HOH HOH . 
D 4 HOH A 60 388 60 HOH HOH . 
D 4 HOH A 61 389 61 HOH HOH . 
D 4 HOH A 62 390 62 HOH HOH . 
D 4 HOH A 63 391 63 HOH HOH . 
D 4 HOH A 64 392 64 HOH HOH . 
D 4 HOH A 65 393 65 HOH HOH . 
D 4 HOH A 66 394 66 HOH HOH . 
D 4 HOH A 67 395 67 HOH HOH . 
D 4 HOH A 68 396 68 HOH HOH . 
D 4 HOH A 69 397 69 HOH HOH . 
D 4 HOH A 70 398 70 HOH HOH . 
D 4 HOH A 71 399 71 HOH HOH . 
D 4 HOH A 72 400 72 HOH HOH . 
D 4 HOH A 73 401 73 HOH HOH . 
D 4 HOH A 74 402 74 HOH HOH . 
D 4 HOH A 75 403 75 HOH HOH . 
D 4 HOH A 76 404 76 HOH HOH . 
D 4 HOH A 77 405 77 HOH HOH . 
D 4 HOH A 78 406 78 HOH HOH . 
D 4 HOH A 79 407 79 HOH HOH . 
D 4 HOH A 80 408 80 HOH HOH . 
D 4 HOH A 81 409 81 HOH HOH . 
D 4 HOH A 82 410 82 HOH HOH . 
D 4 HOH A 83 411 83 HOH HOH . 
D 4 HOH A 84 412 84 HOH HOH . 
D 4 HOH A 85 413 85 HOH HOH . 
D 4 HOH A 86 414 86 HOH HOH . 
D 4 HOH A 87 415 87 HOH HOH . 
D 4 HOH A 88 416 88 HOH HOH . 
D 4 HOH A 89 417 89 HOH HOH . 
D 4 HOH A 90 418 90 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 16.665 4.809 11.011 1 61.68 ? PB GDP 327 A 1 
HETATM 2 O O1B GDP . . . B 2 16.185 5.898 10.088 1 61.11 ? O1B GDP 327 A 1 
HETATM 3 O O2B GDP . . . B 2 16.265 3.442 10.524 1 62.56 ? O2B GDP 327 A 1 
HETATM 4 O O3B GDP . . . B 2 18.191 4.795 11.203 1 62.49 ? O3B GDP 327 A 1 
HETATM 5 O O3A GDP . . . B 2 15.998 5.061 12.423 1 61.76 ? O3A GDP 327 A 1 
HETATM 6 P PA GDP . . . B 2 14.667 5.9 12.618 1 59.76 ? PA GDP 327 A 1 
HETATM 7 O O1A GDP . . . B 2 13.629 5.609 11.561 1 62.63 ? O1A GDP 327 A 1 
HETATM 8 O O2A GDP . . . B 2 14.984 7.362 12.788 1 64.8 ? O2A GDP 327 A 1 
HETATM 9 O O5' GDP . . . B 2 14.212 5.35 14.051 1 64.35 ? O5' GDP 327 A 1 
HETATM 10 C C5' GDP . . . B 2 14.059 3.936 14.254 1 64.67 ? C5' GDP 327 A 1 
HETATM 11 C C4' GDP . . . B 2 13.381 3.675 15.591 1 65.31 ? C4' GDP 327 A 1 
HETATM 12 O O4' GDP . . . B 2 14.245 4.08 16.652 1 62.82 ? O4' GDP 327 A 1 
HETATM 13 C C3' GDP . . . B 2 12.076 4.486 15.711 1 67.28 ? C3' GDP 327 A 1 
HETATM 14 O O3' GDP . . . B 2 11.094 3.69 16.377 1 67.85 ? O3' GDP 327 A 1 
HETATM 15 C C2' GDP . . . B 2 12.451 5.667 16.567 1 67.24 ? C2' GDP 327 A 1 
HETATM 16 O O2' GDP . . . B 2 11.369 6.185 17.356 1 71.79 ? O2' GDP 327 A 1 
HETATM 17 C C1' GDP . . . B 2 13.547 5.068 17.437 1 66.37 ? C1' GDP 327 A 1 
HETATM 18 N N9 GDP . . . B 2 14.468 6.137 17.898 1 67.27 ? N9 GDP 327 A 1 
HETATM 19 C C8 GDP . . . B 2 15.058 7.09 17.141 1 65.43 ? C8 GDP 327 A 1 
HETATM 20 N N7 GDP . . . B 2 15.843 7.896 17.898 1 65.27 ? N7 GDP 327 A 1 
HETATM 21 C C5 GDP . . . B 2 15.748 7.45 19.165 1 66.4 ? C5 GDP 327 A 1 
HETATM 22 C C6 GDP . . . B 2 16.318 7.834 20.468 1 67.5 ? C6 GDP 327 A 1 
HETATM 23 O O6 GDP . . . B 2 17.099 8.81 20.536 1 66.97 ? O6 GDP 327 A 1 
HETATM 24 N N1 GDP . . . B 2 15.965 7.109 21.554 1 67.66 ? N1 GDP 327 A 1 
HETATM 25 C C2 GDP . . . B 2 15.121 6.05 21.5 1 69.07 ? C2 GDP 327 A 1 
HETATM 26 N N2 GDP . . . B 2 14.833 5.369 22.648 1 68.33 ? N2 GDP 327 A 1 
HETATM 27 N N3 GDP . . . B 2 14.568 5.635 20.324 1 68.6 ? N3 GDP 327 A 1 
HETATM 28 C C4 GDP . . . B 2 14.846 6.288 19.165 1 67.3 ? C4 GDP 327 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           353 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           28 
#