data_8CPR
#
_model_server_result.job_id            XI6UHp-GS6rwTml8ngvQvw 
_model_server_result.datetime_utc      '2024-11-26 05:49:19' 
_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          8cpr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    8CPR 
#
_exptl.entry_id    8CPR 
_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         120 
_cell.entry_id            8CPR 
_cell.length_a            76.413 
_cell.length_b            76.413 
_cell.length_c            55.862 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8CPR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_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    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 OH TYR 33 A TYR 32 1_555 C NA NA . A NA 202 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? 
metalc ? metalc2 A O GLY 61 A GLY 60 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? 
metalc ? metalc3 A OE2 GLU 64 A GLU 63 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? 
#
_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                     8CPR 
_atom_sites.fract_transf_matrix[1][1]    0.013087 
_atom_sites.fract_transf_matrix[1][2]    0.007556 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015111 
_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]    0.017901 
_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 NA A 1 202 1 NA NA . 
D 4 HOH A 1 301 70 HOH HOH . 
D 4 HOH A 2 302 8 HOH HOH . 
D 4 HOH A 3 303 28 HOH HOH . 
D 4 HOH A 4 304 100 HOH HOH . 
D 4 HOH A 5 305 24 HOH HOH . 
D 4 HOH A 6 306 115 HOH HOH . 
D 4 HOH A 7 307 5 HOH HOH . 
D 4 HOH A 8 308 23 HOH HOH . 
D 4 HOH A 9 309 7 HOH HOH . 
D 4 HOH A 10 310 10 HOH HOH . 
D 4 HOH A 11 311 16 HOH HOH . 
D 4 HOH A 12 312 77 HOH HOH . 
D 4 HOH A 13 313 58 HOH HOH . 
D 4 HOH A 14 314 68 HOH HOH . 
D 4 HOH A 15 315 33 HOH HOH . 
D 4 HOH A 16 316 107 HOH HOH . 
D 4 HOH A 17 317 26 HOH HOH . 
D 4 HOH A 18 318 13 HOH HOH . 
D 4 HOH A 19 319 32 HOH HOH . 
D 4 HOH A 20 320 75 HOH HOH . 
D 4 HOH A 21 321 9 HOH HOH . 
D 4 HOH A 22 322 25 HOH HOH . 
D 4 HOH A 23 323 49 HOH HOH . 
D 4 HOH A 24 324 27 HOH HOH . 
D 4 HOH A 25 325 6 HOH HOH . 
D 4 HOH A 26 326 17 HOH HOH . 
D 4 HOH A 27 327 113 HOH HOH . 
D 4 HOH A 28 328 56 HOH HOH . 
D 4 HOH A 29 329 31 HOH HOH . 
D 4 HOH A 30 330 20 HOH HOH . 
D 4 HOH A 31 331 35 HOH HOH . 
D 4 HOH A 32 332 42 HOH HOH . 
D 4 HOH A 33 333 4 HOH HOH . 
D 4 HOH A 34 334 15 HOH HOH . 
D 4 HOH A 35 335 11 HOH HOH . 
D 4 HOH A 36 336 41 HOH HOH . 
D 4 HOH A 37 337 52 HOH HOH . 
D 4 HOH A 38 338 95 HOH HOH . 
D 4 HOH A 39 339 63 HOH HOH . 
D 4 HOH A 40 340 54 HOH HOH . 
D 4 HOH A 41 341 89 HOH HOH . 
D 4 HOH A 42 342 59 HOH HOH . 
D 4 HOH A 43 343 62 HOH HOH . 
D 4 HOH A 44 344 66 HOH HOH . 
D 4 HOH A 45 345 2 HOH HOH . 
D 4 HOH A 46 346 18 HOH HOH . 
D 4 HOH A 47 347 47 HOH HOH . 
D 4 HOH A 48 348 76 HOH HOH . 
D 4 HOH A 49 349 40 HOH HOH . 
D 4 HOH A 50 350 39 HOH HOH . 
D 4 HOH A 51 351 104 HOH HOH . 
D 4 HOH A 52 352 21 HOH HOH . 
D 4 HOH A 53 353 67 HOH HOH . 
D 4 HOH A 54 354 73 HOH HOH . 
D 4 HOH A 55 355 51 HOH HOH . 
D 4 HOH A 56 356 57 HOH HOH . 
D 4 HOH A 57 357 74 HOH HOH . 
D 4 HOH A 58 358 91 HOH HOH . 
D 4 HOH A 59 359 61 HOH HOH . 
D 4 HOH A 60 360 90 HOH HOH . 
D 4 HOH A 61 361 43 HOH HOH . 
D 4 HOH A 62 362 98 HOH HOH . 
D 4 HOH A 63 363 110 HOH HOH . 
D 4 HOH A 64 364 37 HOH HOH . 
D 4 HOH A 65 365 45 HOH HOH . 
D 4 HOH A 66 366 19 HOH HOH . 
D 4 HOH A 67 367 64 HOH HOH . 
D 4 HOH A 68 368 65 HOH HOH . 
D 4 HOH A 69 369 69 HOH HOH . 
D 4 HOH A 70 370 22 HOH HOH . 
D 4 HOH A 71 371 14 HOH HOH . 
D 4 HOH A 72 372 88 HOH HOH . 
D 4 HOH A 73 373 86 HOH HOH . 
D 4 HOH A 74 374 12 HOH HOH . 
D 4 HOH A 75 375 94 HOH HOH . 
D 4 HOH A 76 376 85 HOH HOH . 
D 4 HOH A 77 377 82 HOH HOH . 
D 4 HOH A 78 378 81 HOH HOH . 
D 4 HOH A 79 379 80 HOH HOH . 
D 4 HOH A 80 380 29 HOH HOH . 
D 4 HOH A 81 381 71 HOH HOH . 
D 4 HOH A 82 382 114 HOH HOH . 
D 4 HOH A 83 383 112 HOH HOH . 
D 4 HOH A 84 384 34 HOH HOH . 
D 4 HOH A 85 385 50 HOH HOH . 
D 4 HOH A 86 386 93 HOH HOH . 
D 4 HOH A 87 387 84 HOH HOH . 
D 4 HOH A 88 388 48 HOH HOH . 
D 4 HOH A 89 389 96 HOH HOH . 
D 4 HOH A 90 390 83 HOH HOH . 
D 4 HOH A 91 391 44 HOH HOH . 
D 4 HOH A 92 392 38 HOH HOH . 
D 4 HOH A 93 393 36 HOH HOH . 
D 4 HOH A 94 394 53 HOH HOH . 
D 4 HOH A 95 395 60 HOH HOH . 
D 4 HOH A 96 396 92 HOH HOH . 
D 4 HOH A 97 397 102 HOH HOH . 
D 4 HOH A 98 398 87 HOH HOH . 
D 4 HOH A 99 399 46 HOH HOH . 
D 4 HOH A 100 400 105 HOH HOH . 
D 4 HOH A 101 401 99 HOH HOH . 
D 4 HOH A 102 402 79 HOH HOH . 
D 4 HOH A 103 403 72 HOH HOH . 
D 4 HOH A 104 404 55 HOH HOH . 
D 4 HOH A 105 405 1 HOH HOH . 
D 4 HOH A 106 406 30 HOH HOH . 
D 4 HOH A 107 407 3 HOH HOH . 
D 4 HOH A 108 408 101 HOH HOH . 
D 4 HOH A 109 409 103 HOH HOH . 
D 4 HOH A 110 410 116 HOH HOH . 
D 4 HOH A 111 411 111 HOH HOH . 
D 4 HOH A 112 412 97 HOH HOH . 
D 4 HOH A 113 413 106 HOH HOH . 
D 4 HOH A 114 414 108 HOH HOH . 
D 4 HOH A 115 415 109 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 14.236 34.564 7.526 1 19.56 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . B 2 13.631 35.198 6.368 1 19.83 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . B 2 13.23 34.107 8.581 1 17.46 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . B 2 15.215 33.471 7.11 1 20.32 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . B 2 15.083 35.731 8.237 1 20.29 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . B 2 16.623 36.119 8.041 1 21.72 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . B 2 16.84 36.413 6.635 1 24.11 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . B 2 17.547 35.171 8.715 1 22.69 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . B 2 16.674 37.491 8.813 1 21.7 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . B 2 15.749 38.543 8.481 1 23.58 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . B 2 16.369 39.852 8.921 1 24.59 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . B 2 16.398 39.913 10.367 1 24.66 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . B 2 17.828 40.074 8.511 1 25.21 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . B 2 18.081 41.462 8.378 1 28.42 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . B 2 18.602 39.534 9.717 1 26.81 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . B 2 19.888 40.094 9.873 1 32.16 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . B 2 17.72 40.036 10.856 1 25.28 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . B 2 17.837 39.296 12.115 1 22.4 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . B 2 17.83 37.924 12.238 1 22.83 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . B 2 17.915 37.505 13.475 1 21.32 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . B 2 17.98 38.668 14.221 1 19.98 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . B 2 18.095 38.823 15.62 1 20.34 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . B 2 18.084 37.934 16.481 1 18.56 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . B 2 18.14 40.183 15.98 1 21.15 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . B 2 18.09 41.241 15.103 1 20.6 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . B 2 18.148 42.468 15.641 1 21.3 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . B 2 17.982 41.096 13.777 1 20.24 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . B 2 17.936 39.786 13.404 1 21.56 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           338 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#