data_3ONW
#
_model_server_result.job_id            P_fId9IZhlvQP4b51JiDcQ 
_model_server_result.datetime_utc      '2024-12-23 01:10:58' 
_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          3onw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":401}' 
#
_entry.id    3ONW 
#
_exptl.entry_id    3ONW 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            3ONW 
_cell.length_a            70.392 
_cell.length_b            83.679 
_cell.length_c            190.148 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3ONW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        17 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,F,J,L 1 1 
B,D,G,H,I,K,M 2 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 G N 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 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                     3ONW 
_atom_sites.fract_transf_matrix[1][1]    0.014206 
_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]    0.01195 
_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]    0.005259 
_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
E 3 GDP A 1 401 401 GDP GDP . 
F 4 SO4 A 1 3 3 SO4 SO4 . 
G 3 GDP B 1 401 401 GDP GDP . 
H 4 SO4 B 1 1 1 SO4 SO4 . 
I 4 SO4 B 1 2 2 SO4 SO4 . 
J 5 HOH A 1 2 2 HOH HOH . 
J 5 HOH A 2 4 4 HOH HOH . 
J 5 HOH A 3 5 5 HOH HOH . 
J 5 HOH A 4 7 7 HOH HOH . 
J 5 HOH A 5 9 9 HOH HOH . 
J 5 HOH A 6 10 10 HOH HOH . 
J 5 HOH A 7 14 14 HOH HOH . 
J 5 HOH A 8 18 18 HOH HOH . 
J 5 HOH A 9 22 22 HOH HOH . 
J 5 HOH A 10 25 25 HOH HOH . 
J 5 HOH A 11 26 26 HOH HOH . 
J 5 HOH A 12 355 3 HOH HOH . 
J 5 HOH A 13 356 29 HOH HOH . 
J 5 HOH A 14 357 30 HOH HOH . 
J 5 HOH A 15 358 33 HOH HOH . 
J 5 HOH A 16 359 34 HOH HOH . 
J 5 HOH A 17 360 36 HOH HOH . 
J 5 HOH A 18 361 37 HOH HOH . 
J 5 HOH A 19 362 39 HOH HOH . 
J 5 HOH A 20 363 43 HOH HOH . 
J 5 HOH A 21 364 52 HOH HOH . 
J 5 HOH A 22 365 53 HOH HOH . 
J 5 HOH A 23 366 55 HOH HOH . 
J 5 HOH A 24 367 56 HOH HOH . 
J 5 HOH A 25 368 57 HOH HOH . 
J 5 HOH A 26 369 58 HOH HOH . 
J 5 HOH A 27 370 60 HOH HOH . 
J 5 HOH A 28 371 66 HOH HOH . 
J 5 HOH A 29 372 67 HOH HOH . 
J 5 HOH A 30 373 68 HOH HOH . 
J 5 HOH A 31 374 70 HOH HOH . 
J 5 HOH A 32 375 72 HOH HOH . 
J 5 HOH A 33 376 75 HOH HOH . 
J 5 HOH A 34 377 79 HOH HOH . 
J 5 HOH A 35 378 80 HOH HOH . 
J 5 HOH A 36 379 83 HOH HOH . 
J 5 HOH A 37 380 86 HOH HOH . 
J 5 HOH A 38 381 87 HOH HOH . 
J 5 HOH A 39 382 93 HOH HOH . 
J 5 HOH A 40 383 94 HOH HOH . 
J 5 HOH A 41 384 95 HOH HOH . 
J 5 HOH A 42 385 96 HOH HOH . 
J 5 HOH A 43 386 98 HOH HOH . 
J 5 HOH A 44 387 99 HOH HOH . 
J 5 HOH A 45 388 102 HOH HOH . 
J 5 HOH A 46 389 103 HOH HOH . 
J 5 HOH A 47 390 104 HOH HOH . 
J 5 HOH A 48 391 106 HOH HOH . 
J 5 HOH A 49 392 112 HOH HOH . 
J 5 HOH A 50 393 127 HOH HOH . 
J 5 HOH A 51 394 128 HOH HOH . 
J 5 HOH A 52 395 129 HOH HOH . 
K 5 HOH B 1 6 6 HOH HOH . 
K 5 HOH B 2 8 8 HOH HOH . 
K 5 HOH B 3 11 11 HOH HOH . 
K 5 HOH B 4 13 13 HOH HOH . 
K 5 HOH B 5 16 16 HOH HOH . 
K 5 HOH B 6 17 17 HOH HOH . 
K 5 HOH B 7 19 19 HOH HOH . 
K 5 HOH B 8 20 20 HOH HOH . 
K 5 HOH B 9 21 21 HOH HOH . 
K 5 HOH B 10 23 23 HOH HOH . 
K 5 HOH B 11 24 24 HOH HOH . 
K 5 HOH B 12 355 1 HOH HOH . 
K 5 HOH B 13 356 27 HOH HOH . 
K 5 HOH B 14 357 28 HOH HOH . 
K 5 HOH B 15 358 31 HOH HOH . 
K 5 HOH B 16 359 35 HOH HOH . 
K 5 HOH B 17 360 40 HOH HOH . 
K 5 HOH B 18 361 42 HOH HOH . 
K 5 HOH B 19 362 45 HOH HOH . 
K 5 HOH B 20 363 46 HOH HOH . 
K 5 HOH B 21 364 48 HOH HOH . 
K 5 HOH B 22 365 49 HOH HOH . 
K 5 HOH B 23 366 50 HOH HOH . 
K 5 HOH B 24 367 54 HOH HOH . 
K 5 HOH B 25 368 62 HOH HOH . 
K 5 HOH B 26 369 63 HOH HOH . 
K 5 HOH B 27 370 64 HOH HOH . 
K 5 HOH B 28 371 69 HOH HOH . 
K 5 HOH B 29 372 76 HOH HOH . 
K 5 HOH B 30 373 85 HOH HOH . 
K 5 HOH B 31 374 90 HOH HOH . 
K 5 HOH B 32 375 91 HOH HOH . 
K 5 HOH B 33 376 92 HOH HOH . 
K 5 HOH B 34 377 108 HOH HOH . 
K 5 HOH B 35 378 110 HOH HOH . 
K 5 HOH B 36 379 117 HOH HOH . 
K 5 HOH B 37 380 118 HOH HOH . 
K 5 HOH B 38 381 121 HOH HOH . 
K 5 HOH B 39 382 125 HOH HOH . 
K 5 HOH B 40 383 130 HOH HOH . 
L 5 HOH C 1 12 12 HOH HOH . 
L 5 HOH C 2 97 97 HOH HOH . 
M 5 HOH D 1 88 88 HOH HOH . 
M 5 HOH D 2 89 89 HOH HOH . 
M 5 HOH D 3 131 131 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 . . . E 3 16.326 32.795 20.904 1 45.31 ? PB GDP 401 A 1 
HETATM 2 O O1B GDP . . . E 3 15.325 31.694 21.08 1 44.87 ? O1B GDP 401 A 1 
HETATM 3 O O2B GDP . . . E 3 16.585 33.501 22.212 1 44.6 ? O2B GDP 401 A 1 
HETATM 4 O O3B GDP . . . E 3 17.634 32.239 20.384 1 44.38 ? O3B GDP 401 A 1 
HETATM 5 O O3A GDP . . . E 3 15.756 33.883 19.861 1 45.53 ? O3A GDP 401 A 1 
HETATM 6 P PA GDP . . . E 3 14.183 34.072 19.646 1 45.69 ? PA GDP 401 A 1 
HETATM 7 O O1A GDP . . . E 3 13.441 33.989 20.948 1 49.27 ? O1A GDP 401 A 1 
HETATM 8 O O2A GDP . . . E 3 13.632 33.05 18.697 1 49.78 ? O2A GDP 401 A 1 
HETATM 9 O O5' GDP . . . E 3 14.063 35.539 19.002 1 46.3 ? O5' GDP 401 A 1 
HETATM 10 C C5' GDP . . . E 3 14.431 36.714 19.716 1 45 ? C5' GDP 401 A 1 
HETATM 11 C C4' GDP . . . E 3 13.516 37.893 19.376 1 43.99 ? C4' GDP 401 A 1 
HETATM 12 O O4' GDP . . . E 3 13.851 38.381 18.088 1 44 ? O4' GDP 401 A 1 
HETATM 13 C C3' GDP . . . E 3 12.029 37.579 19.313 1 45.36 ? C3' GDP 401 A 1 
HETATM 14 O O3' GDP . . . E 3 11.342 38.759 19.778 1 44.96 ? O3' GDP 401 A 1 
HETATM 15 C C2' GDP . . . E 3 11.742 37.326 17.832 1 45.41 ? C2' GDP 401 A 1 
HETATM 16 O O2' GDP . . . E 3 10.43 37.745 17.427 1 46.88 ? O2' GDP 401 A 1 
HETATM 17 C C1' GDP . . . E 3 12.757 38.218 17.171 1 43.85 ? C1' GDP 401 A 1 
HETATM 18 N N9 GDP . . . E 3 13.351 37.716 15.914 1 44.24 ? N9 GDP 401 A 1 
HETATM 19 C C8 GDP . . . E 3 13.985 36.545 15.704 1 44.68 ? C8 GDP 401 A 1 
HETATM 20 N N7 GDP . . . E 3 14.454 36.476 14.426 1 45.71 ? N7 GDP 401 A 1 
HETATM 21 C C5 GDP . . . E 3 14.119 37.641 13.816 1 44.7 ? C5 GDP 401 A 1 
HETATM 22 C C6 GDP . . . E 3 14.296 38.238 12.476 1 45.55 ? C6 GDP 401 A 1 
HETATM 23 O O6 GDP . . . E 3 14.906 37.613 11.572 1 48.93 ? O6 GDP 401 A 1 
HETATM 24 N N1 GDP . . . E 3 13.819 39.475 12.268 1 45.02 ? N1 GDP 401 A 1 
HETATM 25 C C2 GDP . . . E 3 13.171 40.18 13.217 1 42.62 ? C2 GDP 401 A 1 
HETATM 26 N N2 GDP . . . E 3 12.702 41.407 12.904 1 41.93 ? N2 GDP 401 A 1 
HETATM 27 N N3 GDP . . . E 3 12.969 39.698 14.463 1 40.95 ? N3 GDP 401 A 1 
HETATM 28 C C4 GDP . . . E 3 13.42 38.462 14.808 1 43.26 ? C4 GDP 401 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           239 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           28 
#