data_5XCO
#
_model_server_result.job_id            yjbjjrndvVe0kgReViAnaw 
_model_server_result.datetime_utc      '2024-11-04 22:18:51' 
_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          5xco 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    5XCO 
#
_exptl.entry_id    5XCO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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            5XCO 
_cell.length_a            51.529 
_cell.length_b            51.529 
_cell.length_c            129.741 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XCO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 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,E,F 
_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                      3 
_struct_asym.id                             C 
_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
disulf ? disulf1 B SG CYS 6 B CYS 5 1_555 B SG CYS 16 B CYS 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
covale ? covale1 B C ACE 1 B ACE 0 1_555 B N ARG 2 B ARG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
covale ? covale2 B C ARG 20 B ARG 19 1_555 B N NH2 21 B NH2 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
#
_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 98 n n 
PB O2B GDP sing 99 n n 
PB O3B GDP sing 100 n n 
PB O3A GDP sing 101 n n 
O2B HOB2 GDP sing 102 n n 
O3B HOB3 GDP sing 103 n n 
O3A PA GDP sing 104 n n 
PA O1A GDP doub 105 n n 
PA O2A GDP sing 106 n n 
PA O5' GDP sing 107 n n 
O2A HOA2 GDP sing 108 n n 
O5' C5' GDP sing 109 n n 
C5' C4' GDP sing 110 n n 
C5' H5' GDP sing 111 n n 
C5' "H5''" GDP sing 112 n n 
C4' O4' GDP sing 113 n n 
C4' C3' GDP sing 114 n n 
C4' H4' GDP sing 115 n n 
O4' C1' GDP sing 116 n n 
C3' O3' GDP sing 117 n n 
C3' C2' GDP sing 118 n n 
C3' H3' GDP sing 119 n n 
O3' HO3' GDP sing 120 n n 
C2' O2' GDP sing 121 n n 
C2' C1' GDP sing 122 n n 
C2' H2' GDP sing 123 n n 
O2' HO2' GDP sing 124 n n 
C1' N9 GDP sing 125 n n 
C1' H1' GDP sing 126 n n 
N9 C8 GDP sing 127 n y 
N9 C4 GDP sing 128 n y 
C8 N7 GDP doub 129 n y 
C8 H8 GDP sing 130 n n 
N7 C5 GDP sing 131 n y 
C5 C6 GDP sing 132 n n 
C5 C4 GDP doub 133 n y 
C6 O6 GDP doub 134 n n 
C6 N1 GDP sing 135 n n 
N1 C2 GDP sing 136 n n 
N1 HN1 GDP sing 137 n n 
C2 N2 GDP sing 138 n n 
C2 N3 GDP doub 139 n n 
N2 HN21 GDP sing 140 n n 
N2 HN22 GDP sing 141 n n 
N3 C4 GDP sing 142 n n 
#
_atom_sites.entry_id                     5XCO 
_atom_sites.fract_transf_matrix[1][1]    0.019407 
_atom_sites.fract_transf_matrix[1][2]    0.011204 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022409 
_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]    0.007708 
_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 3 GDP A 1 201 201 GDP GDP . 
D 4 EDO A 1 202 202 EDO EDO . 
E 5 HOH A 1 301 108 HOH HOH . 
E 5 HOH A 2 302 128 HOH HOH . 
E 5 HOH A 3 303 35 HOH HOH . 
E 5 HOH A 4 304 129 HOH HOH . 
E 5 HOH A 5 305 117 HOH HOH . 
E 5 HOH A 6 306 5 HOH HOH . 
E 5 HOH A 7 307 105 HOH HOH . 
E 5 HOH A 8 308 84 HOH HOH . 
E 5 HOH A 9 309 8 HOH HOH . 
E 5 HOH A 10 310 65 HOH HOH . 
E 5 HOH A 11 311 21 HOH HOH . 
E 5 HOH A 12 312 33 HOH HOH . 
E 5 HOH A 13 313 32 HOH HOH . 
E 5 HOH A 14 314 27 HOH HOH . 
E 5 HOH A 15 315 103 HOH HOH . 
E 5 HOH A 16 316 43 HOH HOH . 
E 5 HOH A 17 317 36 HOH HOH . 
E 5 HOH A 18 318 77 HOH HOH . 
E 5 HOH A 19 319 86 HOH HOH . 
E 5 HOH A 20 320 49 HOH HOH . 
E 5 HOH A 21 321 3 HOH HOH . 
E 5 HOH A 22 322 114 HOH HOH . 
E 5 HOH A 23 323 28 HOH HOH . 
E 5 HOH A 24 324 85 HOH HOH . 
E 5 HOH A 25 325 79 HOH HOH . 
E 5 HOH A 26 326 57 HOH HOH . 
E 5 HOH A 27 327 137 HOH HOH . 
E 5 HOH A 28 328 34 HOH HOH . 
E 5 HOH A 29 329 2 HOH HOH . 
E 5 HOH A 30 330 53 HOH HOH . 
E 5 HOH A 31 331 7 HOH HOH . 
E 5 HOH A 32 332 101 HOH HOH . 
E 5 HOH A 33 333 70 HOH HOH . 
E 5 HOH A 34 334 45 HOH HOH . 
E 5 HOH A 35 335 37 HOH HOH . 
E 5 HOH A 36 336 67 HOH HOH . 
E 5 HOH A 37 337 83 HOH HOH . 
E 5 HOH A 38 338 115 HOH HOH . 
E 5 HOH A 39 339 13 HOH HOH . 
E 5 HOH A 40 340 1 HOH HOH . 
E 5 HOH A 41 341 30 HOH HOH . 
E 5 HOH A 42 342 68 HOH HOH . 
E 5 HOH A 43 343 62 HOH HOH . 
E 5 HOH A 44 344 119 HOH HOH . 
E 5 HOH A 45 345 4 HOH HOH . 
E 5 HOH A 46 346 29 HOH HOH . 
E 5 HOH A 47 347 47 HOH HOH . 
E 5 HOH A 48 348 52 HOH HOH . 
E 5 HOH A 49 349 61 HOH HOH . 
E 5 HOH A 50 350 20 HOH HOH . 
E 5 HOH A 51 351 124 HOH HOH . 
E 5 HOH A 52 352 123 HOH HOH . 
E 5 HOH A 53 353 60 HOH HOH . 
E 5 HOH A 54 354 14 HOH HOH . 
E 5 HOH A 55 355 82 HOH HOH . 
E 5 HOH A 56 356 17 HOH HOH . 
E 5 HOH A 57 357 72 HOH HOH . 
E 5 HOH A 58 358 38 HOH HOH . 
E 5 HOH A 59 359 51 HOH HOH . 
E 5 HOH A 60 360 74 HOH HOH . 
E 5 HOH A 61 361 111 HOH HOH . 
E 5 HOH A 62 362 89 HOH HOH . 
E 5 HOH A 63 363 76 HOH HOH . 
E 5 HOH A 64 364 100 HOH HOH . 
E 5 HOH A 65 365 113 HOH HOH . 
E 5 HOH A 66 366 80 HOH HOH . 
E 5 HOH A 67 367 96 HOH HOH . 
E 5 HOH A 68 368 55 HOH HOH . 
E 5 HOH A 69 369 59 HOH HOH . 
E 5 HOH A 70 370 18 HOH HOH . 
E 5 HOH A 71 371 23 HOH HOH . 
E 5 HOH A 72 372 10 HOH HOH . 
E 5 HOH A 73 373 24 HOH HOH . 
E 5 HOH A 74 374 6 HOH HOH . 
E 5 HOH A 75 375 44 HOH HOH . 
E 5 HOH A 76 376 110 HOH HOH . 
E 5 HOH A 77 377 87 HOH HOH . 
E 5 HOH A 78 378 71 HOH HOH . 
E 5 HOH A 79 379 26 HOH HOH . 
E 5 HOH A 80 380 48 HOH HOH . 
E 5 HOH A 81 381 11 HOH HOH . 
E 5 HOH A 82 382 130 HOH HOH . 
E 5 HOH A 83 383 42 HOH HOH . 
E 5 HOH A 84 384 31 HOH HOH . 
E 5 HOH A 85 385 75 HOH HOH . 
E 5 HOH A 86 386 9 HOH HOH . 
E 5 HOH A 87 387 40 HOH HOH . 
E 5 HOH A 88 388 19 HOH HOH . 
E 5 HOH A 89 389 39 HOH HOH . 
E 5 HOH A 90 390 15 HOH HOH . 
E 5 HOH A 91 391 58 HOH HOH . 
E 5 HOH A 92 392 99 HOH HOH . 
E 5 HOH A 93 393 122 HOH HOH . 
E 5 HOH A 94 394 73 HOH HOH . 
E 5 HOH A 95 395 78 HOH HOH . 
E 5 HOH A 96 396 56 HOH HOH . 
E 5 HOH A 97 397 127 HOH HOH . 
E 5 HOH A 98 398 126 HOH HOH . 
E 5 HOH A 99 399 22 HOH HOH . 
E 5 HOH A 100 400 88 HOH HOH . 
E 5 HOH A 101 401 132 HOH HOH . 
E 5 HOH A 102 402 41 HOH HOH . 
E 5 HOH A 103 403 69 HOH HOH . 
E 5 HOH A 104 404 63 HOH HOH . 
E 5 HOH A 105 405 81 HOH HOH . 
E 5 HOH A 106 406 107 HOH HOH . 
E 5 HOH A 107 407 118 HOH HOH . 
E 5 HOH A 108 408 102 HOH HOH . 
E 5 HOH A 109 409 112 HOH HOH . 
E 5 HOH A 110 410 133 HOH HOH . 
E 5 HOH A 111 411 104 HOH HOH . 
E 5 HOH A 112 412 131 HOH HOH . 
E 5 HOH A 113 413 135 HOH HOH . 
E 5 HOH A 114 414 125 HOH HOH . 
E 5 HOH A 115 415 116 HOH HOH . 
E 5 HOH A 116 416 98 HOH HOH . 
E 5 HOH A 117 417 109 HOH HOH . 
E 5 HOH A 118 418 138 HOH HOH . 
E 5 HOH A 119 419 50 HOH HOH . 
E 5 HOH A 120 420 106 HOH HOH . 
F 5 HOH B 1 101 97 HOH HOH . 
F 5 HOH B 2 102 16 HOH HOH . 
F 5 HOH B 3 103 12 HOH HOH . 
F 5 HOH B 4 104 46 HOH HOH . 
F 5 HOH B 5 105 92 HOH HOH . 
F 5 HOH B 6 106 95 HOH HOH . 
F 5 HOH B 7 107 66 HOH HOH . 
F 5 HOH B 8 108 90 HOH HOH . 
F 5 HOH B 9 109 25 HOH HOH . 
F 5 HOH B 10 110 136 HOH HOH . 
F 5 HOH B 11 111 54 HOH HOH . 
F 5 HOH B 12 112 134 HOH HOH . 
F 5 HOH B 13 113 94 HOH HOH . 
F 5 HOH B 14 114 64 HOH HOH . 
F 5 HOH B 15 115 91 HOH HOH . 
F 5 HOH B 16 116 93 HOH HOH . 
F 5 HOH B 17 117 120 HOH HOH . 
F 5 HOH B 18 118 121 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 3 19.797 -18.095 -8.171 1 13.22 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . C 3 18.841 -17.616 -9.233 1 13.97 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . C 3 20.231 -17.014 -7.189 1 13.42 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . C 3 19.314 -19.365 -7.484 1 13.76 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . C 3 21.103 -18.51 -8.984 1 15.02 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . C 3 22.611 -18.058 -8.89 1 14.21 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . C 3 22.705 -16.558 -8.999 1 14.08 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . C 3 23.246 -18.76 -7.739 1 16.1 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . C 3 23.186 -18.658 -10.26 1 14.58 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . C 3 23.14 -20.087 -10.513 1 15.1 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . C 3 24.291 -20.534 -11.397 1 15.9 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . C 3 24.174 -19.916 -12.681 1 15.41 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . C 3 25.675 -20.179 -10.883 1 16.67 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . C 3 26.589 -21.227 -11.259 1 18.26 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . C 3 26.004 -18.927 -11.654 1 16.28 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . C 3 27.395 -18.676 -11.838 1 17.14 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . C 3 25.374 -19.252 -12.985 1 15.33 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . C 3 25 -18.043 -13.732 1 14.34 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . C 3 24.233 -17.018 -13.261 1 14.11 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . C 3 24.062 -16.089 -14.196 1 13.86 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . C 3 24.728 -16.526 -15.279 1 14.57 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . C 3 24.989 -15.992 -16.593 1 14.58 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . C 3 24.499 -14.923 -17.035 1 14.66 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . C 3 25.74 -16.756 -17.418 1 14.76 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . C 3 26.272 -17.947 -17.056 1 15.66 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . C 3 27.004 -18.613 -17.983 1 16.09 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . C 3 26.093 -18.494 -15.854 1 15.56 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . C 3 25.359 -17.78 -14.964 1 14.93 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#