data_5VYU
#
_model_server_result.job_id            XCV7xV3qn0ZQYjko8xdn1A 
_model_server_result.datetime_utc      '2024-11-25 08:54:55' 
_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          5vyu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    5VYU 
#
_exptl.entry_id    5VYU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_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            5VYU 
_cell.length_a            66.835 
_cell.length_b            66.835 
_cell.length_c            235.947 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VYU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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,G,H 
_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                      4 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 142 n n 
PB O2B GDP sing 143 n n 
PB O3B GDP sing 144 n n 
PB O3A GDP sing 145 n n 
O2B HOB2 GDP sing 146 n n 
O3B HOB3 GDP sing 147 n n 
O3A PA GDP sing 148 n n 
PA O1A GDP doub 149 n n 
PA O2A GDP sing 150 n n 
PA O5' GDP sing 151 n n 
O2A HOA2 GDP sing 152 n n 
O5' C5' GDP sing 153 n n 
C5' C4' GDP sing 154 n n 
C5' H5' GDP sing 155 n n 
C5' "H5''" GDP sing 156 n n 
C4' O4' GDP sing 157 n n 
C4' C3' GDP sing 158 n n 
C4' H4' GDP sing 159 n n 
O4' C1' GDP sing 160 n n 
C3' O3' GDP sing 161 n n 
C3' C2' GDP sing 162 n n 
C3' H3' GDP sing 163 n n 
O3' HO3' GDP sing 164 n n 
C2' O2' GDP sing 165 n n 
C2' C1' GDP sing 166 n n 
C2' H2' GDP sing 167 n n 
O2' HO2' GDP sing 168 n n 
C1' N9 GDP sing 169 n n 
C1' H1' GDP sing 170 n n 
N9 C8 GDP sing 171 n y 
N9 C4 GDP sing 172 n y 
C8 N7 GDP doub 173 n y 
C8 H8 GDP sing 174 n n 
N7 C5 GDP sing 175 n y 
C5 C6 GDP sing 176 n n 
C5 C4 GDP doub 177 n y 
C6 O6 GDP doub 178 n n 
C6 N1 GDP sing 179 n n 
N1 C2 GDP sing 180 n n 
N1 HN1 GDP sing 181 n n 
C2 N2 GDP sing 182 n n 
C2 N3 GDP doub 183 n n 
N2 HN21 GDP sing 184 n n 
N2 HN22 GDP sing 185 n n 
N3 C4 GDP sing 186 n n 
#
_atom_sites.entry_id                     5VYU 
_atom_sites.fract_transf_matrix[1][1]    0.014962 
_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]    0.014962 
_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]    0.004238 
_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 1YA A 1 301 300 1YA 1YA . 
D 3 JB2 A 1 302 2002 JB2 JB2 . 
E 2 1YA B 1 301 300 1YA 1YA . 
F 4 GDP B 1 302 1 GDP GDP . 
G 5 HOH A 1 401 187 HOH HOH . 
G 5 HOH A 2 402 44 HOH HOH . 
G 5 HOH A 3 403 28 HOH HOH . 
G 5 HOH A 4 404 198 HOH HOH . 
G 5 HOH A 5 405 213 HOH HOH . 
G 5 HOH A 6 406 237 HOH HOH . 
G 5 HOH A 7 407 221 HOH HOH . 
G 5 HOH A 8 408 177 HOH HOH . 
G 5 HOH A 9 409 96 HOH HOH . 
G 5 HOH A 10 410 191 HOH HOH . 
G 5 HOH A 11 411 74 HOH HOH . 
G 5 HOH A 12 412 210 HOH HOH . 
G 5 HOH A 13 413 216 HOH HOH . 
G 5 HOH A 14 414 37 HOH HOH . 
G 5 HOH A 15 415 203 HOH HOH . 
G 5 HOH A 16 416 222 HOH HOH . 
G 5 HOH A 17 417 78 HOH HOH . 
G 5 HOH A 18 418 50 HOH HOH . 
G 5 HOH A 19 419 29 HOH HOH . 
G 5 HOH A 20 420 223 HOH HOH . 
G 5 HOH A 21 421 10 HOH HOH . 
G 5 HOH A 22 422 188 HOH HOH . 
G 5 HOH A 23 423 184 HOH HOH . 
G 5 HOH A 24 424 55 HOH HOH . 
G 5 HOH A 25 425 104 HOH HOH . 
G 5 HOH A 26 426 174 HOH HOH . 
G 5 HOH A 27 427 105 HOH HOH . 
G 5 HOH A 28 428 3 HOH HOH . 
G 5 HOH A 29 429 41 HOH HOH . 
G 5 HOH A 30 430 86 HOH HOH . 
G 5 HOH A 31 431 114 HOH HOH . 
G 5 HOH A 32 432 90 HOH HOH . 
G 5 HOH A 33 433 139 HOH HOH . 
G 5 HOH A 34 434 93 HOH HOH . 
G 5 HOH A 35 435 196 HOH HOH . 
G 5 HOH A 36 436 110 HOH HOH . 
G 5 HOH A 37 437 18 HOH HOH . 
G 5 HOH A 38 438 66 HOH HOH . 
G 5 HOH A 39 439 45 HOH HOH . 
G 5 HOH A 40 440 21 HOH HOH . 
G 5 HOH A 41 441 98 HOH HOH . 
G 5 HOH A 42 442 186 HOH HOH . 
G 5 HOH A 43 443 8 HOH HOH . 
G 5 HOH A 44 444 131 HOH HOH . 
G 5 HOH A 45 445 181 HOH HOH . 
G 5 HOH A 46 446 211 HOH HOH . 
G 5 HOH A 47 447 64 HOH HOH . 
G 5 HOH A 48 448 4 HOH HOH . 
G 5 HOH A 49 449 42 HOH HOH . 
G 5 HOH A 50 450 103 HOH HOH . 
G 5 HOH A 51 451 53 HOH HOH . 
G 5 HOH A 52 452 75 HOH HOH . 
G 5 HOH A 53 453 199 HOH HOH . 
G 5 HOH A 54 454 65 HOH HOH . 
G 5 HOH A 55 455 243 HOH HOH . 
G 5 HOH A 56 456 14 HOH HOH . 
G 5 HOH A 57 457 244 HOH HOH . 
G 5 HOH A 58 458 80 HOH HOH . 
G 5 HOH A 59 459 207 HOH HOH . 
G 5 HOH A 60 460 52 HOH HOH . 
G 5 HOH A 61 461 5 HOH HOH . 
G 5 HOH A 62 462 239 HOH HOH . 
G 5 HOH A 63 463 220 HOH HOH . 
G 5 HOH A 64 464 51 HOH HOH . 
G 5 HOH A 65 465 94 HOH HOH . 
G 5 HOH A 66 466 142 HOH HOH . 
G 5 HOH A 67 467 152 HOH HOH . 
G 5 HOH A 68 468 85 HOH HOH . 
G 5 HOH A 69 469 122 HOH HOH . 
G 5 HOH A 70 470 70 HOH HOH . 
G 5 HOH A 71 471 208 HOH HOH . 
G 5 HOH A 72 472 11 HOH HOH . 
G 5 HOH A 73 473 48 HOH HOH . 
G 5 HOH A 74 474 151 HOH HOH . 
G 5 HOH A 75 475 1 HOH HOH . 
G 5 HOH A 76 476 26 HOH HOH . 
G 5 HOH A 77 477 62 HOH HOH . 
G 5 HOH A 78 478 240 HOH HOH . 
G 5 HOH A 79 479 39 HOH HOH . 
G 5 HOH A 80 480 100 HOH HOH . 
G 5 HOH A 81 481 46 HOH HOH . 
G 5 HOH A 82 482 192 HOH HOH . 
G 5 HOH A 83 483 54 HOH HOH . 
G 5 HOH A 84 484 47 HOH HOH . 
G 5 HOH A 85 485 215 HOH HOH . 
G 5 HOH A 86 486 16 HOH HOH . 
G 5 HOH A 87 487 189 HOH HOH . 
G 5 HOH A 88 488 212 HOH HOH . 
G 5 HOH A 89 489 200 HOH HOH . 
G 5 HOH A 90 490 190 HOH HOH . 
G 5 HOH A 91 491 115 HOH HOH . 
G 5 HOH A 92 492 204 HOH HOH . 
G 5 HOH A 93 493 102 HOH HOH . 
G 5 HOH A 94 494 238 HOH HOH . 
G 5 HOH A 95 495 32 HOH HOH . 
G 5 HOH A 96 496 81 HOH HOH . 
G 5 HOH A 97 497 218 HOH HOH . 
G 5 HOH A 98 498 209 HOH HOH . 
H 5 HOH B 1 401 72 HOH HOH . 
H 5 HOH B 2 402 241 HOH HOH . 
H 5 HOH B 3 403 6 HOH HOH . 
H 5 HOH B 4 404 227 HOH HOH . 
H 5 HOH B 5 405 206 HOH HOH . 
H 5 HOH B 6 406 91 HOH HOH . 
H 5 HOH B 7 407 173 HOH HOH . 
H 5 HOH B 8 408 20 HOH HOH . 
H 5 HOH B 9 409 224 HOH HOH . 
H 5 HOH B 10 410 193 HOH HOH . 
H 5 HOH B 11 411 225 HOH HOH . 
H 5 HOH B 12 412 234 HOH HOH . 
H 5 HOH B 13 413 95 HOH HOH . 
H 5 HOH B 14 414 87 HOH HOH . 
H 5 HOH B 15 415 180 HOH HOH . 
H 5 HOH B 16 416 106 HOH HOH . 
H 5 HOH B 17 417 7 HOH HOH . 
H 5 HOH B 18 418 73 HOH HOH . 
H 5 HOH B 19 419 145 HOH HOH . 
H 5 HOH B 20 420 230 HOH HOH . 
H 5 HOH B 21 421 201 HOH HOH . 
H 5 HOH B 22 422 116 HOH HOH . 
H 5 HOH B 23 423 141 HOH HOH . 
H 5 HOH B 24 424 22 HOH HOH . 
H 5 HOH B 25 425 31 HOH HOH . 
H 5 HOH B 26 426 58 HOH HOH . 
H 5 HOH B 27 427 182 HOH HOH . 
H 5 HOH B 28 428 33 HOH HOH . 
H 5 HOH B 29 429 219 HOH HOH . 
H 5 HOH B 30 430 92 HOH HOH . 
H 5 HOH B 31 431 228 HOH HOH . 
H 5 HOH B 32 432 236 HOH HOH . 
H 5 HOH B 33 433 63 HOH HOH . 
H 5 HOH B 34 434 76 HOH HOH . 
H 5 HOH B 35 435 43 HOH HOH . 
H 5 HOH B 36 436 59 HOH HOH . 
H 5 HOH B 37 437 146 HOH HOH . 
H 5 HOH B 38 438 242 HOH HOH . 
H 5 HOH B 39 439 194 HOH HOH . 
H 5 HOH B 40 440 71 HOH HOH . 
H 5 HOH B 41 441 13 HOH HOH . 
H 5 HOH B 42 442 178 HOH HOH . 
H 5 HOH B 43 443 24 HOH HOH . 
H 5 HOH B 44 444 17 HOH HOH . 
H 5 HOH B 45 445 23 HOH HOH . 
H 5 HOH B 46 446 107 HOH HOH . 
H 5 HOH B 47 447 148 HOH HOH . 
H 5 HOH B 48 448 57 HOH HOH . 
H 5 HOH B 49 449 144 HOH HOH . 
H 5 HOH B 50 450 119 HOH HOH . 
H 5 HOH B 51 451 157 HOH HOH . 
H 5 HOH B 52 452 9 HOH HOH . 
H 5 HOH B 53 453 67 HOH HOH . 
H 5 HOH B 54 454 233 HOH HOH . 
H 5 HOH B 55 455 185 HOH HOH . 
H 5 HOH B 56 456 205 HOH HOH . 
H 5 HOH B 57 457 12 HOH HOH . 
H 5 HOH B 58 458 126 HOH HOH . 
H 5 HOH B 59 459 77 HOH HOH . 
H 5 HOH B 60 460 113 HOH HOH . 
H 5 HOH B 61 461 202 HOH HOH . 
H 5 HOH B 62 462 34 HOH HOH . 
H 5 HOH B 63 463 169 HOH HOH . 
H 5 HOH B 64 464 25 HOH HOH . 
H 5 HOH B 65 465 56 HOH HOH . 
H 5 HOH B 66 466 19 HOH HOH . 
H 5 HOH B 67 467 89 HOH HOH . 
H 5 HOH B 68 468 183 HOH HOH . 
H 5 HOH B 69 469 179 HOH HOH . 
H 5 HOH B 70 470 226 HOH HOH . 
H 5 HOH B 71 471 30 HOH HOH . 
H 5 HOH B 72 472 83 HOH HOH . 
H 5 HOH B 73 473 68 HOH HOH . 
H 5 HOH B 74 474 101 HOH HOH . 
H 5 HOH B 75 475 36 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 . . . F 4 -2.999 50.306 29.47 1 67.8 ? PB GDP 302 B 1 
HETATM 2 O O1B GDP . . . F 4 -2.349 51.35 28.588 1 64.62 ? O1B GDP 302 B 1 
HETATM 3 O O2B GDP . . . F 4 -3.528 50.821 30.801 1 71.72 ? O2B GDP 302 B 1 
HETATM 4 O O3B GDP . . . F 4 -2.153 49.072 29.674 1 66.58 ? O3B GDP 302 B 1 
HETATM 5 O O3A GDP . . . F 4 -4.354 49.896 28.626 1 65.38 ? O3A GDP 302 B 1 
HETATM 6 P PA GDP . . . F 4 -4.679 48.612 27.658 1 56.55 ? PA GDP 302 B 1 
HETATM 7 O O1A GDP . . . F 4 -6.166 48.525 27.41 1 54.48 ? O1A GDP 302 B 1 
HETATM 8 O O2A GDP . . . F 4 -3.908 47.392 28.125 1 52.6 ? O2A GDP 302 B 1 
HETATM 9 O O5' GDP . . . F 4 -4.084 49.075 26.239 1 58.77 ? O5' GDP 302 B 1 
HETATM 10 C C5' GDP . . . F 4 -2.796 48.665 25.781 1 56.69 ? C5' GDP 302 B 1 
HETATM 11 C C4' GDP . . . F 4 -2.59 49.272 24.403 1 55.4 ? C4' GDP 302 B 1 
HETATM 12 O O4' GDP . . . F 4 -3.863 49.264 23.729 1 52.64 ? O4' GDP 302 B 1 
HETATM 13 C C3' GDP . . . F 4 -2.066 50.719 24.462 1 52.96 ? C3' GDP 302 B 1 
HETATM 14 O O3' GDP . . . F 4 -0.643 50.844 24.209 1 46.72 ? O3' GDP 302 B 1 
HETATM 15 C C2' GDP . . . F 4 -2.916 51.445 23.423 1 52.18 ? C2' GDP 302 B 1 
HETATM 16 O O2' GDP . . . F 4 -2.088 51.878 22.329 1 53.31 ? O2' GDP 302 B 1 
HETATM 17 C C1' GDP . . . F 4 -4.024 50.476 22.971 1 52.49 ? C1' GDP 302 B 1 
HETATM 18 N N9 GDP . . . F 4 -5.379 51.107 23.121 1 51.69 ? N9 GDP 302 B 1 
HETATM 19 C C8 GDP . . . F 4 -6.201 51.079 24.204 1 52.98 ? C8 GDP 302 B 1 
HETATM 20 N N7 GDP . . . F 4 -7.349 51.784 23.96 1 50.64 ? N7 GDP 302 B 1 
HETATM 21 C C5 GDP . . . F 4 -7.272 52.288 22.698 1 48.86 ? C5 GDP 302 B 1 
HETATM 22 C C6 GDP . . . F 4 -8.118 53.129 21.777 1 45.27 ? C6 GDP 302 B 1 
HETATM 23 O O6 GDP . . . F 4 -9.223 53.561 22.142 1 43.4 ? O6 GDP 302 B 1 
HETATM 24 N N1 GDP . . . F 4 -7.671 53.42 20.538 1 43.36 ? N1 GDP 302 B 1 
HETATM 25 C C2 GDP . . . F 4 -6.464 52.959 20.102 1 41.41 ? C2 GDP 302 B 1 
HETATM 26 N N2 GDP . . . F 4 -6.037 53.259 18.85 1 36.1 ? N2 GDP 302 B 1 
HETATM 27 N N3 GDP . . . F 4 -5.645 52.193 20.89 1 43.14 ? N3 GDP 302 B 1 
HETATM 28 C C4 GDP . . . F 4 -5.972 51.834 22.162 1 47.3 ? C4 GDP 302 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           28 
#