data_9E5D
#
_model_server_result.job_id            1i-yNouek4VcVXeMsTyG8w 
_model_server_result.datetime_utc      '2025-01-22 15:46:52' 
_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          9e5d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    9E5D 
#
_exptl.entry_id    9E5D 
_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            9E5D 
_cell.length_a            40.04 
_cell.length_b            53.71 
_cell.length_c            88.85 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9E5D 
_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,E 
_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 OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc2 B O1B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
#
_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 176 n n 
PB O2B GDP sing 177 n n 
PB O3B GDP sing 178 n n 
PB O3A GDP sing 179 n n 
O2B HOB2 GDP sing 180 n n 
O3B HOB3 GDP sing 181 n n 
O3A PA GDP sing 182 n n 
PA O1A GDP doub 183 n n 
PA O2A GDP sing 184 n n 
PA O5' GDP sing 185 n n 
O2A HOA2 GDP sing 186 n n 
O5' C5' GDP sing 187 n n 
C5' C4' GDP sing 188 n n 
C5' H5' GDP sing 189 n n 
C5' "H5''" GDP sing 190 n n 
C4' O4' GDP sing 191 n n 
C4' C3' GDP sing 192 n n 
C4' H4' GDP sing 193 n n 
O4' C1' GDP sing 194 n n 
C3' O3' GDP sing 195 n n 
C3' C2' GDP sing 196 n n 
C3' H3' GDP sing 197 n n 
O3' HO3' GDP sing 198 n n 
C2' O2' GDP sing 199 n n 
C2' C1' GDP sing 200 n n 
C2' H2' GDP sing 201 n n 
O2' HO2' GDP sing 202 n n 
C1' N9 GDP sing 203 n n 
C1' H1' GDP sing 204 n n 
N9 C8 GDP sing 205 n y 
N9 C4 GDP sing 206 n y 
C8 N7 GDP doub 207 n y 
C8 H8 GDP sing 208 n n 
N7 C5 GDP sing 209 n y 
C5 C6 GDP sing 210 n n 
C5 C4 GDP doub 211 n y 
C6 O6 GDP doub 212 n n 
C6 N1 GDP sing 213 n n 
N1 C2 GDP sing 214 n n 
N1 HN1 GDP sing 215 n n 
C2 N2 GDP sing 216 n n 
C2 N3 GDP doub 217 n n 
N2 HN21 GDP sing 218 n n 
N2 HN22 GDP sing 219 n n 
N3 C4 GDP sing 220 n n 
#
_atom_sites.entry_id                     9E5D 
_atom_sites.fract_transf_matrix[1][1]    0.024975 
_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]    0.018619 
_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]    0.011255 
_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 1 201 200 GDP GDP . 
C 3 MG A 1 202 1 MG MG . 
D 4 A1BEI A 1 203 1 A1BEI INC . 
E 5 HOH A 1 301 5 HOH HOH . 
E 5 HOH A 2 302 99 HOH HOH . 
E 5 HOH A 3 303 64 HOH HOH . 
E 5 HOH A 4 304 56 HOH HOH . 
E 5 HOH A 5 305 45 HOH HOH . 
E 5 HOH A 6 306 84 HOH HOH . 
E 5 HOH A 7 307 46 HOH HOH . 
E 5 HOH A 8 308 108 HOH HOH . 
E 5 HOH A 9 309 120 HOH HOH . 
E 5 HOH A 10 310 61 HOH HOH . 
E 5 HOH A 11 311 123 HOH HOH . 
E 5 HOH A 12 312 53 HOH HOH . 
E 5 HOH A 13 313 19 HOH HOH . 
E 5 HOH A 14 314 17 HOH HOH . 
E 5 HOH A 15 315 105 HOH HOH . 
E 5 HOH A 16 316 51 HOH HOH . 
E 5 HOH A 17 317 107 HOH HOH . 
E 5 HOH A 18 318 81 HOH HOH . 
E 5 HOH A 19 319 43 HOH HOH . 
E 5 HOH A 20 320 60 HOH HOH . 
E 5 HOH A 21 321 35 HOH HOH . 
E 5 HOH A 22 322 67 HOH HOH . 
E 5 HOH A 23 323 15 HOH HOH . 
E 5 HOH A 24 324 26 HOH HOH . 
E 5 HOH A 25 325 29 HOH HOH . 
E 5 HOH A 26 326 92 HOH HOH . 
E 5 HOH A 27 327 118 HOH HOH . 
E 5 HOH A 28 328 117 HOH HOH . 
E 5 HOH A 29 329 33 HOH HOH . 
E 5 HOH A 30 330 82 HOH HOH . 
E 5 HOH A 31 331 30 HOH HOH . 
E 5 HOH A 32 332 74 HOH HOH . 
E 5 HOH A 33 333 58 HOH HOH . 
E 5 HOH A 34 334 18 HOH HOH . 
E 5 HOH A 35 335 21 HOH HOH . 
E 5 HOH A 36 336 24 HOH HOH . 
E 5 HOH A 37 337 2 HOH HOH . 
E 5 HOH A 38 338 102 HOH HOH . 
E 5 HOH A 39 339 10 HOH HOH . 
E 5 HOH A 40 340 93 HOH HOH . 
E 5 HOH A 41 341 110 HOH HOH . 
E 5 HOH A 42 342 80 HOH HOH . 
E 5 HOH A 43 343 66 HOH HOH . 
E 5 HOH A 44 344 77 HOH HOH . 
E 5 HOH A 45 345 68 HOH HOH . 
E 5 HOH A 46 346 4 HOH HOH . 
E 5 HOH A 47 347 106 HOH HOH . 
E 5 HOH A 48 348 71 HOH HOH . 
E 5 HOH A 49 349 52 HOH HOH . 
E 5 HOH A 50 350 16 HOH HOH . 
E 5 HOH A 51 351 32 HOH HOH . 
E 5 HOH A 52 352 3 HOH HOH . 
E 5 HOH A 53 353 36 HOH HOH . 
E 5 HOH A 54 354 6 HOH HOH . 
E 5 HOH A 55 355 83 HOH HOH . 
E 5 HOH A 56 356 40 HOH HOH . 
E 5 HOH A 57 357 57 HOH HOH . 
E 5 HOH A 58 358 7 HOH HOH . 
E 5 HOH A 59 359 1 HOH HOH . 
E 5 HOH A 60 360 91 HOH HOH . 
E 5 HOH A 61 361 22 HOH HOH . 
E 5 HOH A 62 362 14 HOH HOH . 
E 5 HOH A 63 363 27 HOH HOH . 
E 5 HOH A 64 364 50 HOH HOH . 
E 5 HOH A 65 365 116 HOH HOH . 
E 5 HOH A 66 366 121 HOH HOH . 
E 5 HOH A 67 367 115 HOH HOH . 
E 5 HOH A 68 368 63 HOH HOH . 
E 5 HOH A 69 369 47 HOH HOH . 
E 5 HOH A 70 370 79 HOH HOH . 
E 5 HOH A 71 371 62 HOH HOH . 
E 5 HOH A 72 372 100 HOH HOH . 
E 5 HOH A 73 373 38 HOH HOH . 
E 5 HOH A 74 374 39 HOH HOH . 
E 5 HOH A 75 375 12 HOH HOH . 
E 5 HOH A 76 376 96 HOH HOH . 
E 5 HOH A 77 377 48 HOH HOH . 
E 5 HOH A 78 378 37 HOH HOH . 
E 5 HOH A 79 379 101 HOH HOH . 
E 5 HOH A 80 380 59 HOH HOH . 
E 5 HOH A 81 381 111 HOH HOH . 
E 5 HOH A 82 382 9 HOH HOH . 
E 5 HOH A 83 383 119 HOH HOH . 
E 5 HOH A 84 384 28 HOH HOH . 
E 5 HOH A 85 385 11 HOH HOH . 
E 5 HOH A 86 386 78 HOH HOH . 
E 5 HOH A 87 387 90 HOH HOH . 
E 5 HOH A 88 388 25 HOH HOH . 
E 5 HOH A 89 389 49 HOH HOH . 
E 5 HOH A 90 390 122 HOH HOH . 
E 5 HOH A 91 391 109 HOH HOH . 
E 5 HOH A 92 392 41 HOH HOH . 
E 5 HOH A 93 393 34 HOH HOH . 
E 5 HOH A 94 394 20 HOH HOH . 
E 5 HOH A 95 395 42 HOH HOH . 
E 5 HOH A 96 396 103 HOH HOH . 
E 5 HOH A 97 397 85 HOH HOH . 
E 5 HOH A 98 398 23 HOH HOH . 
E 5 HOH A 99 399 88 HOH HOH . 
E 5 HOH A 100 400 124 HOH HOH . 
E 5 HOH A 101 401 125 HOH HOH . 
E 5 HOH A 102 402 54 HOH HOH . 
E 5 HOH A 103 403 76 HOH HOH . 
E 5 HOH A 104 404 8 HOH HOH . 
E 5 HOH A 105 405 113 HOH HOH . 
E 5 HOH A 106 406 69 HOH HOH . 
E 5 HOH A 107 407 104 HOH HOH . 
E 5 HOH A 108 408 98 HOH HOH . 
E 5 HOH A 109 409 44 HOH HOH . 
E 5 HOH A 110 410 86 HOH HOH . 
E 5 HOH A 111 411 112 HOH HOH . 
E 5 HOH A 112 412 95 HOH HOH . 
E 5 HOH A 113 413 13 HOH HOH . 
E 5 HOH A 114 414 72 HOH HOH . 
E 5 HOH A 115 415 87 HOH HOH . 
E 5 HOH A 116 416 89 HOH HOH . 
E 5 HOH A 117 417 97 HOH HOH . 
E 5 HOH A 118 418 73 HOH HOH . 
E 5 HOH A 119 419 55 HOH HOH . 
E 5 HOH A 120 420 65 HOH HOH . 
E 5 HOH A 121 421 70 HOH HOH . 
E 5 HOH A 122 422 114 HOH HOH . 
E 5 HOH A 123 423 31 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 -28.026 4.041 -16.028 1 10.45 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . B 2 -27.392 5.369 -16.462 1 10.58 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . B 2 -28.956 3.469 -17.051 1 11.53 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . B 2 -27.073 3.034 -15.482 1 10.28 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . B 2 -28.962 4.377 -14.719 1 11.39 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . B 2 -29.675 5.774 -14.355 1 12.74 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . B 2 -28.721 6.714 -13.699 1 12.81 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . B 2 -30.498 6.205 -15.538 1 13.9 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . B 2 -30.646 5.298 -13.174 1 12.69 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . B 2 -31.742 4.376 -13.422 1 12.86 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . B 2 -32.878 4.672 -12.486 1 14.88 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . B 2 -32.484 4.383 -11.115 1 14.66 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . B 2 -33.343 6.129 -12.455 1 17.07 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . B 2 -34.753 6.191 -12.231 1 20.87 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . B 2 -32.586 6.745 -11.274 1 16.62 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . B 2 -33.207 7.867 -10.651 1 20.02 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . B 2 -32.553 5.557 -10.335 1 15.37 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . B 2 -31.395 5.516 -9.443 1 13.94 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . B 2 -30.081 5.529 -9.828 1 12.36 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . B 2 -29.246 5.438 -8.833 1 11.85 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . B 2 -30.052 5.33 -7.717 1 12.82 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . B 2 -29.729 5.139 -6.34 1 13.35 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . B 2 -28.613 5.033 -5.803 1 13.28 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . B 2 -30.87 5.042 -5.536 1 15.14 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . B 2 -32.175 5.137 -5.973 1 16.14 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . B 2 -33.144 5.014 -5.064 1 18.75 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . B 2 -32.468 5.308 -7.261 1 15.45 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . B 2 -31.38 5.353 -8.087 1 13.64 ? 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    2 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#