data_8ZNY
#
_model_server_result.job_id            -wnr60KzoL2soOFULkVIbw 
_model_server_result.datetime_utc      '2025-07-26 21:18:29' 
_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          8zny 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    8ZNY 
#
_exptl.entry_id    8ZNY 
_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            8ZNY 
_cell.length_a            32.14 
_cell.length_b            64.06 
_cell.length_c            82.37 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8ZNY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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 
#
_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 
#
_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 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OG1 THR 20 A THR 19 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc2 A O PRO 37 A PRO 36 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc3 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? 
metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
#
_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                     8ZNY 
_atom_sites.fract_transf_matrix[1][1]    0.031114 
_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]    0.01561 
_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]    0.01214 
_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 1 201 201 GDP GDP . 
C 3 MG A 1 202 1 MG MG . 
D 4 HOH A 1 301 83 HOH HOH . 
D 4 HOH A 2 302 189 HOH HOH . 
D 4 HOH A 3 303 48 HOH HOH . 
D 4 HOH A 4 304 53 HOH HOH . 
D 4 HOH A 5 305 84 HOH HOH . 
D 4 HOH A 6 306 8 HOH HOH . 
D 4 HOH A 7 307 56 HOH HOH . 
D 4 HOH A 8 308 217 HOH HOH . 
D 4 HOH A 9 309 7 HOH HOH . 
D 4 HOH A 10 310 137 HOH HOH . 
D 4 HOH A 11 311 131 HOH HOH . 
D 4 HOH A 12 312 68 HOH HOH . 
D 4 HOH A 13 313 73 HOH HOH . 
D 4 HOH A 14 314 29 HOH HOH . 
D 4 HOH A 15 315 2 HOH HOH . 
D 4 HOH A 16 316 248 HOH HOH . 
D 4 HOH A 17 317 5 HOH HOH . 
D 4 HOH A 18 318 62 HOH HOH . 
D 4 HOH A 19 319 21 HOH HOH . 
D 4 HOH A 20 320 9 HOH HOH . 
D 4 HOH A 21 321 30 HOH HOH . 
D 4 HOH A 22 322 112 HOH HOH . 
D 4 HOH A 23 323 244 HOH HOH . 
D 4 HOH A 24 324 10 HOH HOH . 
D 4 HOH A 25 325 19 HOH HOH . 
D 4 HOH A 26 326 11 HOH HOH . 
D 4 HOH A 27 327 3 HOH HOH . 
D 4 HOH A 28 328 36 HOH HOH . 
D 4 HOH A 29 329 12 HOH HOH . 
D 4 HOH A 30 330 14 HOH HOH . 
D 4 HOH A 31 331 32 HOH HOH . 
D 4 HOH A 32 332 20 HOH HOH . 
D 4 HOH A 33 333 18 HOH HOH . 
D 4 HOH A 34 334 1 HOH HOH . 
D 4 HOH A 35 335 6 HOH HOH . 
D 4 HOH A 36 336 113 HOH HOH . 
D 4 HOH A 37 337 15 HOH HOH . 
D 4 HOH A 38 338 42 HOH HOH . 
D 4 HOH A 39 339 41 HOH HOH . 
D 4 HOH A 40 340 158 HOH HOH . 
D 4 HOH A 41 341 142 HOH HOH . 
D 4 HOH A 42 342 9 HOH HOH . 
D 4 HOH A 43 343 87 HOH HOH . 
D 4 HOH A 44 344 196 HOH HOH . 
D 4 HOH A 45 345 45 HOH HOH . 
D 4 HOH A 46 346 28 HOH HOH . 
D 4 HOH A 47 347 210 HOH HOH . 
D 4 HOH A 48 348 149 HOH HOH . 
D 4 HOH A 49 349 44 HOH HOH . 
D 4 HOH A 50 350 6 HOH HOH . 
D 4 HOH A 51 351 33 HOH HOH . 
D 4 HOH A 52 352 13 HOH HOH . 
D 4 HOH A 53 353 5 HOH HOH . 
D 4 HOH A 54 354 16 HOH HOH . 
D 4 HOH A 55 355 7 HOH HOH . 
D 4 HOH A 56 356 203 HOH HOH . 
D 4 HOH A 57 357 74 HOH HOH . 
D 4 HOH A 58 358 24 HOH HOH . 
D 4 HOH A 59 359 67 HOH HOH . 
D 4 HOH A 60 360 37 HOH HOH . 
D 4 HOH A 61 361 8 HOH HOH . 
D 4 HOH A 62 362 145 HOH HOH . 
D 4 HOH A 63 363 10 HOH HOH . 
D 4 HOH A 64 364 114 HOH HOH . 
D 4 HOH A 65 365 39 HOH HOH . 
D 4 HOH A 66 366 35 HOH HOH . 
D 4 HOH A 67 367 228 HOH HOH . 
D 4 HOH A 68 368 193 HOH HOH . 
D 4 HOH A 69 369 4 HOH HOH . 
D 4 HOH A 70 370 27 HOH HOH . 
D 4 HOH A 71 371 236 HOH HOH . 
D 4 HOH A 72 372 55 HOH HOH . 
D 4 HOH A 73 373 71 HOH HOH . 
D 4 HOH A 74 374 17 HOH HOH . 
D 4 HOH A 75 375 50 HOH HOH . 
D 4 HOH A 76 376 76 HOH HOH . 
D 4 HOH A 77 377 60 HOH HOH . 
D 4 HOH A 78 378 162 HOH HOH . 
D 4 HOH A 79 379 52 HOH HOH . 
D 4 HOH A 80 380 22 HOH HOH . 
D 4 HOH A 81 381 38 HOH HOH . 
D 4 HOH A 82 382 101 HOH HOH . 
D 4 HOH A 83 383 26 HOH HOH . 
D 4 HOH A 84 384 58 HOH HOH . 
D 4 HOH A 85 385 69 HOH HOH . 
D 4 HOH A 86 386 151 HOH HOH . 
D 4 HOH A 87 387 23 HOH HOH . 
D 4 HOH A 88 388 47 HOH HOH . 
D 4 HOH A 89 389 12 HOH HOH . 
D 4 HOH A 90 390 11 HOH HOH . 
D 4 HOH A 91 391 132 HOH HOH . 
D 4 HOH A 92 392 64 HOH HOH . 
D 4 HOH A 93 393 130 HOH HOH . 
D 4 HOH A 94 394 173 HOH HOH . 
D 4 HOH A 95 395 134 HOH HOH . 
D 4 HOH A 96 396 154 HOH HOH . 
D 4 HOH A 97 397 177 HOH HOH . 
D 4 HOH A 98 398 4 HOH HOH . 
D 4 HOH A 99 399 94 HOH HOH . 
D 4 HOH A 100 400 197 HOH HOH . 
D 4 HOH A 101 401 165 HOH HOH . 
D 4 HOH A 102 402 100 HOH HOH . 
D 4 HOH A 103 403 152 HOH HOH . 
D 4 HOH A 104 404 143 HOH HOH . 
D 4 HOH A 105 405 180 HOH HOH . 
D 4 HOH A 106 406 207 HOH HOH . 
D 4 HOH A 107 407 70 HOH HOH . 
D 4 HOH A 108 408 226 HOH HOH . 
D 4 HOH A 109 409 264 HOH HOH . 
D 4 HOH A 110 410 43 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 -3.116 -1.932 12.252 1 17.99 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . B 2 -4.567 -1.545 12.536 1 18.74 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . B 2 -2.177 -1.155 13.15 1 21.22 -1 O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . B 2 -2.726 -1.832 10.798 1 15.56 -1 O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . B 2 -3.035 -3.487 12.748 1 17.19 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . B 2 -2.28 -4.722 12.004 1 18.98 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . B 2 -0.821 -4.352 11.773 1 18.6 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . B 2 -2.986 -5.175 10.766 1 19.42 -1 O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . B 2 -2.368 -5.921 13.125 1 18.96 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . B 2 -1.93 -5.619 14.428 1 19.82 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . B 2 -1.583 -6.922 15.147 1 21.81 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . B 2 -2.913 -7.828 15.236 1 20.69 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . B 2 -0.69 -7.662 14.53 1 24.28 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . B 2 0.129 -8.364 15.546 1 24.48 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . B 2 -1.479 -8.739 13.735 1 21.91 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . B 2 -0.799 -9.913 13.608 1 22.68 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . B 2 -2.74 -8.954 14.581 1 21.33 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . B 2 -3.898 -9.109 13.671 1 21.7 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . B 2 -4.387 -8.555 12.545 1 17.09 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . B 2 -5.541 -9.18 12.229 1 19.43 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . B 2 -5.768 -10.112 13.153 1 19.78 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . B 2 -6.918 -11.12 13.292 1 20.34 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . B 2 -7.806 -11.148 12.493 1 20.51 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . B 2 -6.911 -12.019 14.393 1 20.57 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . B 2 -5.838 -11.982 15.357 1 23.3 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . B 2 -5.848 -12.905 16.462 1 23.04 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . B 2 -4.743 -11.026 15.214 1 19.24 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . B 2 -4.739 -10.08 14.062 1 20.07 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           475 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#