data_1Y3A
#
_model_server_result.job_id            HXNZ83GpAfCSsDloAl5dHA 
_model_server_result.datetime_utc      '2024-10-11 00:26:49' 
_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          1y3a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":355}' 
#
_entry.id    1Y3A 
#
_exptl.entry_id    1Y3A 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          93.75 
_cell.angle_gamma         90 
_cell.entry_id            1Y3A 
_cell.length_a            72.943 
_cell.length_b            112.785 
_cell.length_c            109.49 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y3A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
PISA dimeric 2 software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I,M,Q 1 1 
B,F,J,N,R 2 1 
C,G,K,O,S 3 1 
D,H,L,P,T 4 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 I N N 
? 3 J N N 
? 3 K N N 
? 3 L 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                     1Y3A 
_atom_sites.fract_transf_matrix[1][1]    0.013709 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000899 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008866 
_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]    0.009153 
_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
I 3 GDP A 1 355 355 GDP GDP . 
J 3 GDP B 1 356 356 GDP GDP . 
K 3 GDP C 1 357 357 GDP GDP . 
L 3 GDP D 1 358 358 GDP GDP . 
M 4 HOH A 1 356 2 HOH HOH . 
M 4 HOH A 2 357 6 HOH HOH . 
M 4 HOH A 3 358 8 HOH HOH . 
M 4 HOH A 4 359 12 HOH HOH . 
M 4 HOH A 5 360 13 HOH HOH . 
M 4 HOH A 6 361 14 HOH HOH . 
M 4 HOH A 7 362 17 HOH HOH . 
M 4 HOH A 8 363 24 HOH HOH . 
M 4 HOH A 9 364 29 HOH HOH . 
M 4 HOH A 10 365 36 HOH HOH . 
M 4 HOH A 11 366 39 HOH HOH . 
M 4 HOH A 12 367 44 HOH HOH . 
M 4 HOH A 13 368 46 HOH HOH . 
M 4 HOH A 14 369 47 HOH HOH . 
M 4 HOH A 15 370 48 HOH HOH . 
M 4 HOH A 16 371 51 HOH HOH . 
M 4 HOH A 17 372 52 HOH HOH . 
M 4 HOH A 18 373 53 HOH HOH . 
M 4 HOH A 19 374 55 HOH HOH . 
M 4 HOH A 20 375 57 HOH HOH . 
M 4 HOH A 21 376 59 HOH HOH . 
M 4 HOH A 22 377 62 HOH HOH . 
M 4 HOH A 23 378 65 HOH HOH . 
M 4 HOH A 24 379 66 HOH HOH . 
M 4 HOH A 25 380 69 HOH HOH . 
M 4 HOH A 26 381 70 HOH HOH . 
M 4 HOH A 27 382 72 HOH HOH . 
M 4 HOH A 28 383 74 HOH HOH . 
M 4 HOH A 29 384 77 HOH HOH . 
M 4 HOH A 30 385 80 HOH HOH . 
M 4 HOH A 31 386 83 HOH HOH . 
M 4 HOH A 32 387 85 HOH HOH . 
M 4 HOH A 33 388 86 HOH HOH . 
M 4 HOH A 34 389 94 HOH HOH . 
M 4 HOH A 35 390 99 HOH HOH . 
M 4 HOH A 36 391 100 HOH HOH . 
M 4 HOH A 37 392 101 HOH HOH . 
M 4 HOH A 38 393 103 HOH HOH . 
M 4 HOH A 39 394 104 HOH HOH . 
M 4 HOH A 40 395 107 HOH HOH . 
M 4 HOH A 41 396 114 HOH HOH . 
M 4 HOH A 42 397 119 HOH HOH . 
M 4 HOH A 43 398 121 HOH HOH . 
M 4 HOH A 44 399 122 HOH HOH . 
M 4 HOH A 45 400 128 HOH HOH . 
M 4 HOH A 46 401 130 HOH HOH . 
N 4 HOH B 1 357 9 HOH HOH . 
N 4 HOH B 2 358 10 HOH HOH . 
N 4 HOH B 3 359 19 HOH HOH . 
N 4 HOH B 4 360 20 HOH HOH . 
N 4 HOH B 5 361 21 HOH HOH . 
N 4 HOH B 6 362 22 HOH HOH . 
N 4 HOH B 7 363 27 HOH HOH . 
N 4 HOH B 8 364 50 HOH HOH . 
N 4 HOH B 9 365 56 HOH HOH . 
N 4 HOH B 10 366 61 HOH HOH . 
N 4 HOH B 11 367 64 HOH HOH . 
N 4 HOH B 12 368 76 HOH HOH . 
N 4 HOH B 13 369 78 HOH HOH . 
N 4 HOH B 14 370 82 HOH HOH . 
N 4 HOH B 15 371 90 HOH HOH . 
N 4 HOH B 16 372 92 HOH HOH . 
N 4 HOH B 17 373 105 HOH HOH . 
N 4 HOH B 18 374 108 HOH HOH . 
N 4 HOH B 19 375 109 HOH HOH . 
N 4 HOH B 20 376 111 HOH HOH . 
N 4 HOH B 21 377 113 HOH HOH . 
N 4 HOH B 22 378 115 HOH HOH . 
N 4 HOH B 23 379 116 HOH HOH . 
N 4 HOH B 24 380 120 HOH HOH . 
N 4 HOH B 25 381 123 HOH HOH . 
N 4 HOH B 26 382 126 HOH HOH . 
N 4 HOH B 27 383 132 HOH HOH . 
N 4 HOH B 28 384 134 HOH HOH . 
N 4 HOH B 29 385 136 HOH HOH . 
O 4 HOH C 1 358 5 HOH HOH . 
O 4 HOH C 2 359 7 HOH HOH . 
O 4 HOH C 3 360 16 HOH HOH . 
O 4 HOH C 4 361 25 HOH HOH . 
O 4 HOH C 5 362 26 HOH HOH . 
O 4 HOH C 6 363 28 HOH HOH . 
O 4 HOH C 7 364 31 HOH HOH . 
O 4 HOH C 8 365 34 HOH HOH . 
O 4 HOH C 9 366 35 HOH HOH . 
O 4 HOH C 10 367 37 HOH HOH . 
O 4 HOH C 11 368 38 HOH HOH . 
O 4 HOH C 12 369 43 HOH HOH . 
O 4 HOH C 13 370 54 HOH HOH . 
O 4 HOH C 14 371 58 HOH HOH . 
O 4 HOH C 15 372 67 HOH HOH . 
O 4 HOH C 16 373 68 HOH HOH . 
O 4 HOH C 17 374 71 HOH HOH . 
O 4 HOH C 18 375 75 HOH HOH . 
O 4 HOH C 19 376 79 HOH HOH . 
O 4 HOH C 20 377 87 HOH HOH . 
O 4 HOH C 21 378 88 HOH HOH . 
O 4 HOH C 22 379 91 HOH HOH . 
O 4 HOH C 23 380 96 HOH HOH . 
O 4 HOH C 24 381 102 HOH HOH . 
O 4 HOH C 25 382 117 HOH HOH . 
O 4 HOH C 26 383 118 HOH HOH . 
O 4 HOH C 27 384 124 HOH HOH . 
O 4 HOH C 28 385 129 HOH HOH . 
O 4 HOH C 29 386 131 HOH HOH . 
O 4 HOH C 30 387 135 HOH HOH . 
P 4 HOH D 1 359 1 HOH HOH . 
P 4 HOH D 2 360 3 HOH HOH . 
P 4 HOH D 3 361 4 HOH HOH . 
P 4 HOH D 4 362 11 HOH HOH . 
P 4 HOH D 5 363 15 HOH HOH . 
P 4 HOH D 6 364 18 HOH HOH . 
P 4 HOH D 7 365 23 HOH HOH . 
P 4 HOH D 8 366 30 HOH HOH . 
P 4 HOH D 9 367 32 HOH HOH . 
P 4 HOH D 10 368 33 HOH HOH . 
P 4 HOH D 11 369 41 HOH HOH . 
P 4 HOH D 12 370 42 HOH HOH . 
P 4 HOH D 13 371 45 HOH HOH . 
P 4 HOH D 14 372 49 HOH HOH . 
P 4 HOH D 15 373 84 HOH HOH . 
P 4 HOH D 16 374 89 HOH HOH . 
P 4 HOH D 17 375 93 HOH HOH . 
P 4 HOH D 18 376 95 HOH HOH . 
P 4 HOH D 19 377 97 HOH HOH . 
P 4 HOH D 20 378 98 HOH HOH . 
P 4 HOH D 21 379 106 HOH HOH . 
P 4 HOH D 22 380 110 HOH HOH . 
P 4 HOH D 23 381 112 HOH HOH . 
P 4 HOH D 24 382 125 HOH HOH . 
P 4 HOH D 25 383 127 HOH HOH . 
Q 4 HOH E 1 40 40 HOH HOH . 
Q 4 HOH E 2 133 133 HOH HOH . 
R 4 HOH F 1 81 81 HOH HOH . 
S 4 HOH G 1 60 60 HOH HOH . 
S 4 HOH G 2 63 63 HOH HOH . 
T 4 HOH H 1 73 73 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 . . . I 3 15.293 -1.711 3.828 1 40.37 ? PB GDP 355 A 1 
HETATM 2 O O1B GDP . . . I 3 15.355 -2.593 4.964 1 39.03 ? O1B GDP 355 A 1 
HETATM 3 O O2B GDP . . . I 3 16.554 -1.577 3.037 1 41.34 ? O2B GDP 355 A 1 
HETATM 4 O O3B GDP . . . I 3 14.343 -2.09 2.713 1 47.28 ? O3B GDP 355 A 1 
HETATM 5 O O3A GDP . . . I 3 15.197 -0.174 4.513 1 48.23 ? O3A GDP 355 A 1 
HETATM 6 P PA GDP . . . I 3 13.959 0.302 5.48 1 49.71 ? PA GDP 355 A 1 
HETATM 7 O O1A GDP . . . I 3 14.555 1.59 6.006 1 50.51 ? O1A GDP 355 A 1 
HETATM 8 O O2A GDP . . . I 3 12.677 -0.319 5.801 1 50.05 ? O2A GDP 355 A 1 
HETATM 9 O O5' GDP . . . I 3 13.452 1.315 4.367 1 43.69 ? O5' GDP 355 A 1 
HETATM 10 C C5' GDP . . . I 3 12.642 1.311 3.212 1 38.02 ? C5' GDP 355 A 1 
HETATM 11 C C4' GDP . . . I 3 12.187 2.836 3.141 1 32.7 ? C4' GDP 355 A 1 
HETATM 12 O O4' GDP . . . I 3 10.788 3.057 2.733 1 31.36 ? O4' GDP 355 A 1 
HETATM 13 C C3' GDP . . . I 3 12.166 3.614 4.526 1 31.59 ? C3' GDP 355 A 1 
HETATM 14 O O3' GDP . . . I 3 12.346 5.023 4.22 1 31.28 ? O3' GDP 355 A 1 
HETATM 15 C C2' GDP . . . I 3 10.752 3.353 5.089 1 29.53 ? C2' GDP 355 A 1 
HETATM 16 O O2' GDP . . . I 3 10.336 4.332 6.027 1 24.81 ? O2' GDP 355 A 1 
HETATM 17 C C1' GDP . . . I 3 9.902 3.365 3.833 1 30.05 ? C1' GDP 355 A 1 
HETATM 18 N N9 GDP . . . I 3 8.861 2.273 3.81 1 30.8 ? N9 GDP 355 A 1 
HETATM 19 C C8 GDP . . . I 3 8.957 0.926 4.069 1 32.36 ? C8 GDP 355 A 1 
HETATM 20 N N7 GDP . . . I 3 7.842 0.281 3.933 1 32.35 ? N7 GDP 355 A 1 
HETATM 21 C C5 GDP . . . I 3 6.926 1.235 3.554 1 29.88 ? C5 GDP 355 A 1 
HETATM 22 C C6 GDP . . . I 3 5.526 1.143 3.248 1 29.19 ? C6 GDP 355 A 1 
HETATM 23 O O6 GDP . . . I 3 4.811 0.116 3.249 1 29.26 ? O6 GDP 355 A 1 
HETATM 24 N N1 GDP . . . I 3 4.977 2.406 2.901 1 27.29 ? N1 GDP 355 A 1 
HETATM 25 C C2 GDP . . . I 3 5.689 3.608 2.864 1 27.9 ? C2 GDP 355 A 1 
HETATM 26 N N2 GDP . . . I 3 4.998 4.681 2.519 1 23.95 ? N2 GDP 355 A 1 
HETATM 27 N N3 GDP . . . I 3 7.016 3.705 3.151 1 26.56 ? N3 GDP 355 A 1 
HETATM 28 C C4 GDP . . . I 3 7.537 2.503 3.482 1 27.92 ? C4 GDP 355 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#