data_8DZN
#
_model_server_result.job_id            0gOD2bv1vdQ-9DDcitcGFg 
_model_server_result.datetime_utc      '2024-11-01 03:26:29' 
_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          8dzn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":202}' 
#
_entry.id    8DZN 
#
_exptl.entry_id    8DZN 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          105.95 
_cell.angle_gamma         90 
_cell.entry_id            8DZN 
_cell.length_a            57.172 
_cell.length_b            63.97 
_cell.length_c            62.233 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DZN 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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,F 1 1 
B,D,E,G 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
? 2 C N N 
? 2 E 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                     8DZN 
_atom_sites.fract_transf_matrix[1][1]    0.017491 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004998 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015632 
_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]    0.016712 
_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
C 2 GDP A 1 201 1 GDP GDP . 
D 3 SO4 B 1 201 1 SO4 SO4 . 
E 2 GDP B 1 202 2 GDP GDP . 
F 4 HOH A 1 301 32 HOH HOH . 
F 4 HOH A 2 302 77 HOH HOH . 
F 4 HOH A 3 303 58 HOH HOH . 
F 4 HOH A 4 304 54 HOH HOH . 
F 4 HOH A 5 305 114 HOH HOH . 
F 4 HOH A 6 306 2 HOH HOH . 
F 4 HOH A 7 307 19 HOH HOH . 
F 4 HOH A 8 308 13 HOH HOH . 
F 4 HOH A 9 309 5 HOH HOH . 
F 4 HOH A 10 310 55 HOH HOH . 
F 4 HOH A 11 311 10 HOH HOH . 
F 4 HOH A 12 312 28 HOH HOH . 
F 4 HOH A 13 313 1 HOH HOH . 
F 4 HOH A 14 314 11 HOH HOH . 
F 4 HOH A 15 315 78 HOH HOH . 
F 4 HOH A 16 316 67 HOH HOH . 
F 4 HOH A 17 317 56 HOH HOH . 
F 4 HOH A 18 318 62 HOH HOH . 
F 4 HOH A 19 319 104 HOH HOH . 
F 4 HOH A 20 320 24 HOH HOH . 
F 4 HOH A 21 321 6 HOH HOH . 
F 4 HOH A 22 322 35 HOH HOH . 
F 4 HOH A 23 323 102 HOH HOH . 
F 4 HOH A 24 324 86 HOH HOH . 
F 4 HOH A 25 325 61 HOH HOH . 
F 4 HOH A 26 326 82 HOH HOH . 
F 4 HOH A 27 327 16 HOH HOH . 
F 4 HOH A 28 328 63 HOH HOH . 
F 4 HOH A 29 329 27 HOH HOH . 
F 4 HOH A 30 330 107 HOH HOH . 
F 4 HOH A 31 331 15 HOH HOH . 
F 4 HOH A 32 332 69 HOH HOH . 
F 4 HOH A 33 333 80 HOH HOH . 
F 4 HOH A 34 334 31 HOH HOH . 
F 4 HOH A 35 335 17 HOH HOH . 
F 4 HOH A 36 336 22 HOH HOH . 
F 4 HOH A 37 337 23 HOH HOH . 
F 4 HOH A 38 338 64 HOH HOH . 
F 4 HOH A 39 339 93 HOH HOH . 
F 4 HOH A 40 340 70 HOH HOH . 
F 4 HOH A 41 341 45 HOH HOH . 
F 4 HOH A 42 342 92 HOH HOH . 
F 4 HOH A 43 343 88 HOH HOH . 
F 4 HOH A 44 344 21 HOH HOH . 
F 4 HOH A 45 345 14 HOH HOH . 
F 4 HOH A 46 346 84 HOH HOH . 
F 4 HOH A 47 347 4 HOH HOH . 
F 4 HOH A 48 348 42 HOH HOH . 
F 4 HOH A 49 349 57 HOH HOH . 
F 4 HOH A 50 350 68 HOH HOH . 
F 4 HOH A 51 351 117 HOH HOH . 
F 4 HOH A 52 352 118 HOH HOH . 
F 4 HOH A 53 353 41 HOH HOH . 
F 4 HOH A 54 354 97 HOH HOH . 
F 4 HOH A 55 355 111 HOH HOH . 
F 4 HOH A 56 356 83 HOH HOH . 
F 4 HOH A 57 357 113 HOH HOH . 
F 4 HOH A 58 358 119 HOH HOH . 
F 4 HOH A 59 359 18 HOH HOH . 
F 4 HOH A 60 360 85 HOH HOH . 
F 4 HOH A 61 361 89 HOH HOH . 
F 4 HOH A 62 362 48 HOH HOH . 
F 4 HOH A 63 363 66 HOH HOH . 
G 4 HOH B 1 301 94 HOH HOH . 
G 4 HOH B 2 302 95 HOH HOH . 
G 4 HOH B 3 303 121 HOH HOH . 
G 4 HOH B 4 304 109 HOH HOH . 
G 4 HOH B 5 305 96 HOH HOH . 
G 4 HOH B 6 306 30 HOH HOH . 
G 4 HOH B 7 307 98 HOH HOH . 
G 4 HOH B 8 308 116 HOH HOH . 
G 4 HOH B 9 309 99 HOH HOH . 
G 4 HOH B 10 310 53 HOH HOH . 
G 4 HOH B 11 311 51 HOH HOH . 
G 4 HOH B 12 312 20 HOH HOH . 
G 4 HOH B 13 313 29 HOH HOH . 
G 4 HOH B 14 314 36 HOH HOH . 
G 4 HOH B 15 315 39 HOH HOH . 
G 4 HOH B 16 316 33 HOH HOH . 
G 4 HOH B 17 317 3 HOH HOH . 
G 4 HOH B 18 318 7 HOH HOH . 
G 4 HOH B 19 319 100 HOH HOH . 
G 4 HOH B 20 320 38 HOH HOH . 
G 4 HOH B 21 321 44 HOH HOH . 
G 4 HOH B 22 322 101 HOH HOH . 
G 4 HOH B 23 323 8 HOH HOH . 
G 4 HOH B 24 324 74 HOH HOH . 
G 4 HOH B 25 325 79 HOH HOH . 
G 4 HOH B 26 326 108 HOH HOH . 
G 4 HOH B 27 327 71 HOH HOH . 
G 4 HOH B 28 328 120 HOH HOH . 
G 4 HOH B 29 329 34 HOH HOH . 
G 4 HOH B 30 330 26 HOH HOH . 
G 4 HOH B 31 331 47 HOH HOH . 
G 4 HOH B 32 332 49 HOH HOH . 
G 4 HOH B 33 333 12 HOH HOH . 
G 4 HOH B 34 334 59 HOH HOH . 
G 4 HOH B 35 335 75 HOH HOH . 
G 4 HOH B 36 336 43 HOH HOH . 
G 4 HOH B 37 337 72 HOH HOH . 
G 4 HOH B 38 338 87 HOH HOH . 
G 4 HOH B 39 339 40 HOH HOH . 
G 4 HOH B 40 340 103 HOH HOH . 
G 4 HOH B 41 341 9 HOH HOH . 
G 4 HOH B 42 342 60 HOH HOH . 
G 4 HOH B 43 343 115 HOH HOH . 
G 4 HOH B 44 344 37 HOH HOH . 
G 4 HOH B 45 345 46 HOH HOH . 
G 4 HOH B 46 346 50 HOH HOH . 
G 4 HOH B 47 347 25 HOH HOH . 
G 4 HOH B 48 348 65 HOH HOH . 
G 4 HOH B 49 349 112 HOH HOH . 
G 4 HOH B 50 350 90 HOH HOH . 
G 4 HOH B 51 351 76 HOH HOH . 
G 4 HOH B 52 352 73 HOH HOH . 
G 4 HOH B 53 353 52 HOH HOH . 
G 4 HOH B 54 354 105 HOH HOH . 
G 4 HOH B 55 355 106 HOH HOH . 
G 4 HOH B 56 356 110 HOH HOH . 
G 4 HOH B 57 357 81 HOH HOH . 
G 4 HOH B 58 358 91 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 2 -106.134 -3.656 -74.678 1 32.54 ? PB GDP 202 B 1 
HETATM 2 O O1B GDP . . . E 2 -105.508 -4.808 -75.46 1 31.37 ? O1B GDP 202 B 1 
HETATM 3 O O2B GDP . . . E 2 -107.384 -4.072 -74.007 1 25 ? O2B GDP 202 B 1 
HETATM 4 O O3B GDP . . . E 2 -105.169 -3.061 -73.652 1 35.06 ? O3B GDP 202 B 1 
HETATM 5 O O3A GDP . . . E 2 -106.482 -2.503 -75.612 1 33.7 ? O3A GDP 202 B 1 
HETATM 6 P PA GDP . . . E 2 -106.749 -2.522 -77.136 1 30.74 ? PA GDP 202 B 1 
HETATM 7 O O1A GDP . . . E 2 -105.473 -2.7 -77.958 1 25.77 ? O1A GDP 202 B 1 
HETATM 8 O O2A GDP . . . E 2 -107.808 -3.54 -77.45 1 30.3 ? O2A GDP 202 B 1 
HETATM 9 O O5' GDP . . . E 2 -107.285 -1.074 -77.508 1 35.07 ? O5' GDP 202 B 1 
HETATM 10 C C5' GDP . . . E 2 -108.529 -0.643 -77.033 1 34.28 ? C5' GDP 202 B 1 
HETATM 11 C C4' GDP . . . E 2 -108.945 0.48 -77.928 1 42.66 ? C4' GDP 202 B 1 
HETATM 12 O O4' GDP . . . E 2 -108.175 1.528 -77.756 1 43.75 ? O4' GDP 202 B 1 
HETATM 13 C C3' GDP . . . E 2 -108.789 -0.013 -79.5 1 43.82 ? C3' GDP 202 B 1 
HETATM 14 O O3' GDP . . . E 2 -110.032 0.377 -80.23 1 39.62 ? O3' GDP 202 B 1 
HETATM 15 C C2' GDP . . . E 2 -107.797 0.575 -79.987 1 46.46 ? C2' GDP 202 B 1 
HETATM 16 O O2' GDP . . . E 2 -108.005 0.806 -81.434 1 46.11 ? O2' GDP 202 B 1 
HETATM 17 C C1' GDP . . . E 2 -107.81 1.95 -79.167 1 44.64 ? C1' GDP 202 B 1 
HETATM 18 N N9 GDP . . . E 2 -106.734 2.695 -79.239 1 39.96 ? N9 GDP 202 B 1 
HETATM 19 C C8 GDP . . . E 2 -105.696 1.893 -78.883 1 37.94 ? C8 GDP 202 B 1 
HETATM 20 N N7 GDP . . . E 2 -104.546 2.63 -78.945 1 35.1 ? N7 GDP 202 B 1 
HETATM 21 C C5 GDP . . . E 2 -104.865 3.89 -79.334 1 40.16 ? C5 GDP 202 B 1 
HETATM 22 C C6 GDP . . . E 2 -104.087 5.189 -79.583 1 39.16 ? C6 GDP 202 B 1 
HETATM 23 O O6 GDP . . . E 2 -102.884 5.299 -79.461 1 39.47 ? O6 GDP 202 B 1 
HETATM 24 N N1 GDP . . . E 2 -104.802 6.317 -79.997 1 36.67 ? N1 GDP 202 B 1 
HETATM 25 C C2 GDP . . . E 2 -106.202 6.267 -80.165 1 36.9 ? C2 GDP 202 B 1 
HETATM 26 N N2 GDP . . . E 2 -106.943 7.386 -80.579 1 44.5 ? N2 GDP 202 B 1 
HETATM 27 N N3 GDP . . . E 2 -106.923 5.059 -79.917 1 36 ? N3 GDP 202 B 1 
HETATM 28 C C4 GDP . . . E 2 -106.212 3.889 -79.504 1 39.57 ? C4 GDP 202 B 1 
#
_model_server_stats.io_time_ms              75 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#