data_1Z6Y
#
_model_server_result.job_id            8k_NaVpuT0lXWldbW2NkHg 
_model_server_result.datetime_utc      '2024-10-11 06:16:34' 
_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          1z6y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":180}' 
#
_entry.id    1Z6Y 
#
_exptl.entry_id    1Z6Y 
_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         112.96 
_cell.angle_beta          97.69 
_cell.angle_gamma         90 
_cell.entry_id            1Z6Y 
_cell.length_a            38.657 
_cell.length_b            48.775 
_cell.length_c            55.905 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Z6Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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,E 1 1 
B,D,F 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 D 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                     1Z6Y 
_atom_sites.fract_transf_matrix[1][1]    0.025869 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.0038 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020502 
_atom_sites.fract_transf_matrix[2][3]    0.008779 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.019635 
_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 1 180 1 GDP GDP . 
D 2 GDP B 1 180 2 GDP GDP . 
E 3 HOH A 1 201 201 HOH HOH . 
E 3 HOH A 2 206 206 HOH HOH . 
E 3 HOH A 3 207 207 HOH HOH . 
E 3 HOH A 4 209 209 HOH HOH . 
E 3 HOH A 5 212 212 HOH HOH . 
E 3 HOH A 6 213 213 HOH HOH . 
E 3 HOH A 7 216 216 HOH HOH . 
E 3 HOH A 8 217 217 HOH HOH . 
E 3 HOH A 9 220 220 HOH HOH . 
E 3 HOH A 10 221 221 HOH HOH . 
E 3 HOH A 11 222 222 HOH HOH . 
E 3 HOH A 12 223 223 HOH HOH . 
E 3 HOH A 13 224 224 HOH HOH . 
E 3 HOH A 14 226 226 HOH HOH . 
E 3 HOH A 15 228 228 HOH HOH . 
E 3 HOH A 16 229 229 HOH HOH . 
E 3 HOH A 17 232 232 HOH HOH . 
E 3 HOH A 18 234 234 HOH HOH . 
E 3 HOH A 19 239 239 HOH HOH . 
E 3 HOH A 20 243 243 HOH HOH . 
E 3 HOH A 21 245 245 HOH HOH . 
E 3 HOH A 22 246 246 HOH HOH . 
E 3 HOH A 23 248 248 HOH HOH . 
E 3 HOH A 24 249 249 HOH HOH . 
E 3 HOH A 25 252 252 HOH HOH . 
E 3 HOH A 26 253 253 HOH HOH . 
E 3 HOH A 27 257 257 HOH HOH . 
E 3 HOH A 28 258 258 HOH HOH . 
E 3 HOH A 29 259 259 HOH HOH . 
E 3 HOH A 30 262 262 HOH HOH . 
E 3 HOH A 31 263 263 HOH HOH . 
E 3 HOH A 32 264 264 HOH HOH . 
E 3 HOH A 33 265 265 HOH HOH . 
E 3 HOH A 34 266 266 HOH HOH . 
E 3 HOH A 35 267 267 HOH HOH . 
E 3 HOH A 36 271 271 HOH HOH . 
E 3 HOH A 37 272 272 HOH HOH . 
E 3 HOH A 38 273 273 HOH HOH . 
E 3 HOH A 39 277 277 HOH HOH . 
E 3 HOH A 40 279 279 HOH HOH . 
E 3 HOH A 41 280 280 HOH HOH . 
E 3 HOH A 42 281 281 HOH HOH . 
E 3 HOH A 43 282 282 HOH HOH . 
E 3 HOH A 44 285 285 HOH HOH . 
E 3 HOH A 45 287 287 HOH HOH . 
E 3 HOH A 46 288 288 HOH HOH . 
E 3 HOH A 47 290 290 HOH HOH . 
E 3 HOH A 48 291 291 HOH HOH . 
E 3 HOH A 49 293 293 HOH HOH . 
E 3 HOH A 50 294 294 HOH HOH . 
E 3 HOH A 51 295 295 HOH HOH . 
E 3 HOH A 52 296 296 HOH HOH . 
E 3 HOH A 53 299 299 HOH HOH . 
E 3 HOH A 54 300 300 HOH HOH . 
E 3 HOH A 55 301 301 HOH HOH . 
E 3 HOH A 56 303 303 HOH HOH . 
E 3 HOH A 57 304 304 HOH HOH . 
E 3 HOH A 58 305 305 HOH HOH . 
E 3 HOH A 59 306 306 HOH HOH . 
E 3 HOH A 60 307 307 HOH HOH . 
E 3 HOH A 61 308 308 HOH HOH . 
E 3 HOH A 62 313 313 HOH HOH . 
E 3 HOH A 63 314 314 HOH HOH . 
E 3 HOH A 64 315 315 HOH HOH . 
E 3 HOH A 65 316 316 HOH HOH . 
E 3 HOH A 66 317 317 HOH HOH . 
E 3 HOH A 67 326 326 HOH HOH . 
E 3 HOH A 68 327 327 HOH HOH . 
E 3 HOH A 69 328 328 HOH HOH . 
E 3 HOH A 70 331 331 HOH HOH . 
E 3 HOH A 71 333 333 HOH HOH . 
E 3 HOH A 72 335 335 HOH HOH . 
E 3 HOH A 73 336 336 HOH HOH . 
F 3 HOH B 1 202 202 HOH HOH . 
F 3 HOH B 2 203 203 HOH HOH . 
F 3 HOH B 3 204 204 HOH HOH . 
F 3 HOH B 4 205 205 HOH HOH . 
F 3 HOH B 5 208 208 HOH HOH . 
F 3 HOH B 6 210 210 HOH HOH . 
F 3 HOH B 7 211 211 HOH HOH . 
F 3 HOH B 8 214 214 HOH HOH . 
F 3 HOH B 9 215 215 HOH HOH . 
F 3 HOH B 10 218 218 HOH HOH . 
F 3 HOH B 11 219 219 HOH HOH . 
F 3 HOH B 12 225 225 HOH HOH . 
F 3 HOH B 13 227 227 HOH HOH . 
F 3 HOH B 14 230 230 HOH HOH . 
F 3 HOH B 15 231 231 HOH HOH . 
F 3 HOH B 16 233 233 HOH HOH . 
F 3 HOH B 17 235 235 HOH HOH . 
F 3 HOH B 18 236 236 HOH HOH . 
F 3 HOH B 19 238 238 HOH HOH . 
F 3 HOH B 20 240 240 HOH HOH . 
F 3 HOH B 21 241 241 HOH HOH . 
F 3 HOH B 22 242 242 HOH HOH . 
F 3 HOH B 23 244 244 HOH HOH . 
F 3 HOH B 24 247 247 HOH HOH . 
F 3 HOH B 25 250 250 HOH HOH . 
F 3 HOH B 26 251 251 HOH HOH . 
F 3 HOH B 27 254 254 HOH HOH . 
F 3 HOH B 28 255 255 HOH HOH . 
F 3 HOH B 29 256 256 HOH HOH . 
F 3 HOH B 30 260 260 HOH HOH . 
F 3 HOH B 31 261 261 HOH HOH . 
F 3 HOH B 32 268 268 HOH HOH . 
F 3 HOH B 33 269 269 HOH HOH . 
F 3 HOH B 34 270 270 HOH HOH . 
F 3 HOH B 35 274 274 HOH HOH . 
F 3 HOH B 36 275 275 HOH HOH . 
F 3 HOH B 37 276 276 HOH HOH . 
F 3 HOH B 38 278 278 HOH HOH . 
F 3 HOH B 39 283 283 HOH HOH . 
F 3 HOH B 40 284 284 HOH HOH . 
F 3 HOH B 41 286 286 HOH HOH . 
F 3 HOH B 42 289 289 HOH HOH . 
F 3 HOH B 43 292 292 HOH HOH . 
F 3 HOH B 44 297 297 HOH HOH . 
F 3 HOH B 45 298 298 HOH HOH . 
F 3 HOH B 46 302 302 HOH HOH . 
F 3 HOH B 47 309 309 HOH HOH . 
F 3 HOH B 48 310 310 HOH HOH . 
F 3 HOH B 49 311 311 HOH HOH . 
F 3 HOH B 50 312 312 HOH HOH . 
F 3 HOH B 51 318 318 HOH HOH . 
F 3 HOH B 52 319 319 HOH HOH . 
F 3 HOH B 53 320 320 HOH HOH . 
F 3 HOH B 54 321 321 HOH HOH . 
F 3 HOH B 55 322 322 HOH HOH . 
F 3 HOH B 56 323 323 HOH HOH . 
F 3 HOH B 57 324 324 HOH HOH . 
F 3 HOH B 58 325 325 HOH HOH . 
F 3 HOH B 59 329 329 HOH HOH . 
F 3 HOH B 60 330 330 HOH HOH . 
F 3 HOH B 61 332 332 HOH HOH . 
F 3 HOH B 62 334 334 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 . . . C 2 15.675 -28.288 8.796 1 11.28 ? PB GDP 180 A 1 
HETATM 2 O O1B GDP . . . C 2 16.406 -29.25 7.893 1 13.21 ? O1B GDP 180 A 1 
HETATM 3 O O2B GDP . . . C 2 16.493 -27.88 9.997 1 11.96 ? O2B GDP 180 A 1 
HETATM 4 O O3B GDP . . . C 2 15.379 -27.036 8.014 1 13.41 ? O3B GDP 180 A 1 
HETATM 5 O O3A GDP . . . C 2 14.251 -28.833 9.245 1 11.88 ? O3A GDP 180 A 1 
HETATM 6 P PA GDP . . . C 2 13.705 -30.314 9.382 1 11.02 ? PA GDP 180 A 1 
HETATM 7 O O1A GDP . . . C 2 13.417 -30.879 8.006 1 12.99 ? O1A GDP 180 A 1 
HETATM 8 O O2A GDP . . . C 2 14.469 -31.161 10.341 1 12.65 ? O2A GDP 180 A 1 
HETATM 9 O O5' GDP . . . C 2 12.263 -30.062 10.05 1 13.26 ? O5' GDP 180 A 1 
HETATM 10 C C5' GDP . . . C 2 12.274 -29.786 11.434 1 14.88 ? C5' GDP 180 A 1 
HETATM 11 C C4' GDP . . . C 2 11.068 -30.427 12.107 1 17.15 ? C4' GDP 180 A 1 
HETATM 12 O O4' GDP . . . C 2 9.813 -29.942 11.617 1 16.28 ? O4' GDP 180 A 1 
HETATM 13 C C3' GDP . . . C 2 11.091 -31.918 11.91 1 16.53 ? C3' GDP 180 A 1 
HETATM 14 O O3' GDP . . . C 2 10.768 -32.366 13.225 1 17.91 ? O3' GDP 180 A 1 
HETATM 15 C C2' GDP . . . C 2 9.941 -32.247 11.002 1 19.18 ? C2' GDP 180 A 1 
HETATM 16 O O2' GDP . . . C 2 9.351 -33.462 11.514 1 22.88 ? O2' GDP 180 A 1 
HETATM 17 C C1' GDP . . . C 2 9.023 -31.008 11.122 1 16.71 ? C1' GDP 180 A 1 
HETATM 18 N N9 GDP . . . C 2 8.443 -30.645 9.806 1 15.37 ? N9 GDP 180 A 1 
HETATM 19 C C8 GDP . . . C 2 9.028 -30.546 8.596 1 12.28 ? C8 GDP 180 A 1 
HETATM 20 N N7 GDP . . . C 2 8.109 -30.221 7.644 1 13.21 ? N7 GDP 180 A 1 
HETATM 21 C C5 GDP . . . C 2 6.891 -30.112 8.251 1 13.34 ? C5 GDP 180 A 1 
HETATM 22 C C6 GDP . . . C 2 5.483 -29.81 7.868 1 13.12 ? C6 GDP 180 A 1 
HETATM 23 O O6 GDP . . . C 2 5.145 -29.536 6.669 1 10.27 ? O6 GDP 180 A 1 
HETATM 24 N N1 GDP . . . C 2 4.566 -29.811 8.875 1 13.36 ? N1 GDP 180 A 1 
HETATM 25 C C2 GDP . . . C 2 4.877 -30.086 10.165 1 13.88 ? C2 GDP 180 A 1 
HETATM 26 N N2 GDP . . . C 2 3.94 -30.147 11.141 1 14.9 ? N2 GDP 180 A 1 
HETATM 27 N N3 GDP . . . C 2 6.136 -30.363 10.565 1 15.03 ? N3 GDP 180 A 1 
HETATM 28 C C4 GDP . . . C 2 7.145 -30.384 9.668 1 14.7 ? C4 GDP 180 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#