data_8WB1
#
_model_server_result.job_id            B0qTx-A_YMeWqaSSCzWhJA 
_model_server_result.datetime_utc      '2024-11-14 10:49:59' 
_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          8wb1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    8WB1 
#
_exptl.entry_id    8WB1 
_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            8WB1 
_cell.length_a            40.099 
_cell.length_b            51.955 
_cell.length_c            90.475 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8WB1 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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                      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
covale ? covale1 A OD2 ASP 13 A ASP 12 1_555 E C15 W3T . A W3T 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
metalc ? metalc1 A OG SER 18 A SER 18 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc3 C MG MG . A MG 202 1_555 F O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc4 C MG MG . A MG 202 1_555 F O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? 
metalc ? metalc5 C MG MG . A MG 202 1_555 F O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
metalc ? metalc6 C MG MG . A MG 202 1_555 F O HOH . A HOH 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
#
_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 92 n n 
PB O2B GDP sing 93 n n 
PB O3B GDP sing 94 n n 
PB O3A GDP sing 95 n n 
O2B HOB2 GDP sing 96 n n 
O3B HOB3 GDP sing 97 n n 
O3A PA GDP sing 98 n n 
PA O1A GDP doub 99 n n 
PA O2A GDP sing 100 n n 
PA O5' GDP sing 101 n n 
O2A HOA2 GDP sing 102 n n 
O5' C5' GDP sing 103 n n 
C5' C4' GDP sing 104 n n 
C5' H5' GDP sing 105 n n 
C5' "H5''" GDP sing 106 n n 
C4' O4' GDP sing 107 n n 
C4' C3' GDP sing 108 n n 
C4' H4' GDP sing 109 n n 
O4' C1' GDP sing 110 n n 
C3' O3' GDP sing 111 n n 
C3' C2' GDP sing 112 n n 
C3' H3' GDP sing 113 n n 
O3' HO3' GDP sing 114 n n 
C2' O2' GDP sing 115 n n 
C2' C1' GDP sing 116 n n 
C2' H2' GDP sing 117 n n 
O2' HO2' GDP sing 118 n n 
C1' N9 GDP sing 119 n n 
C1' H1' GDP sing 120 n n 
N9 C8 GDP sing 121 n y 
N9 C4 GDP sing 122 n y 
C8 N7 GDP doub 123 n y 
C8 H8 GDP sing 124 n n 
N7 C5 GDP sing 125 n y 
C5 C6 GDP sing 126 n n 
C5 C4 GDP doub 127 n y 
C6 O6 GDP doub 128 n n 
C6 N1 GDP sing 129 n n 
N1 C2 GDP sing 130 n n 
N1 HN1 GDP sing 131 n n 
C2 N2 GDP sing 132 n n 
C2 N3 GDP doub 133 n n 
N2 HN21 GDP sing 134 n n 
N2 HN22 GDP sing 135 n n 
N3 C4 GDP sing 136 n n 
#
_atom_sites.entry_id                     8WB1 
_atom_sites.fract_transf_matrix[1][1]    0.024938 
_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]    0.019247 
_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]    0.011053 
_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 1 202 203 MG MG . 
D 4 EDO A 1 203 204 EDO EDO . 
E 5 W3T A 1 204 12 W3T N2D . 
F 6 HOH A 1 301 374 HOH HOH . 
F 6 HOH A 2 302 345 HOH HOH . 
F 6 HOH A 3 303 365 HOH HOH . 
F 6 HOH A 4 304 332 HOH HOH . 
F 6 HOH A 5 305 334 HOH HOH . 
F 6 HOH A 6 306 319 HOH HOH . 
F 6 HOH A 7 307 333 HOH HOH . 
F 6 HOH A 8 308 318 HOH HOH . 
F 6 HOH A 9 309 331 HOH HOH . 
F 6 HOH A 10 310 312 HOH HOH . 
F 6 HOH A 11 311 303 HOH HOH . 
F 6 HOH A 12 312 308 HOH HOH . 
F 6 HOH A 13 313 391 HOH HOH . 
F 6 HOH A 14 314 338 HOH HOH . 
F 6 HOH A 15 315 398 HOH HOH . 
F 6 HOH A 16 316 335 HOH HOH . 
F 6 HOH A 17 317 324 HOH HOH . 
F 6 HOH A 18 318 400 HOH HOH . 
F 6 HOH A 19 319 356 HOH HOH . 
F 6 HOH A 20 320 397 HOH HOH . 
F 6 HOH A 21 321 327 HOH HOH . 
F 6 HOH A 22 322 313 HOH HOH . 
F 6 HOH A 23 323 325 HOH HOH . 
F 6 HOH A 24 324 349 HOH HOH . 
F 6 HOH A 25 325 358 HOH HOH . 
F 6 HOH A 26 326 311 HOH HOH . 
F 6 HOH A 27 327 317 HOH HOH . 
F 6 HOH A 28 328 354 HOH HOH . 
F 6 HOH A 29 329 371 HOH HOH . 
F 6 HOH A 30 330 314 HOH HOH . 
F 6 HOH A 31 331 336 HOH HOH . 
F 6 HOH A 32 332 301 HOH HOH . 
F 6 HOH A 33 333 306 HOH HOH . 
F 6 HOH A 34 334 320 HOH HOH . 
F 6 HOH A 35 335 384 HOH HOH . 
F 6 HOH A 36 336 340 HOH HOH . 
F 6 HOH A 37 337 387 HOH HOH . 
F 6 HOH A 38 338 377 HOH HOH . 
F 6 HOH A 39 339 321 HOH HOH . 
F 6 HOH A 40 340 373 HOH HOH . 
F 6 HOH A 41 341 322 HOH HOH . 
F 6 HOH A 42 342 302 HOH HOH . 
F 6 HOH A 43 343 315 HOH HOH . 
F 6 HOH A 44 344 346 HOH HOH . 
F 6 HOH A 45 345 341 HOH HOH . 
F 6 HOH A 46 346 360 HOH HOH . 
F 6 HOH A 47 347 364 HOH HOH . 
F 6 HOH A 48 348 326 HOH HOH . 
F 6 HOH A 49 349 369 HOH HOH . 
F 6 HOH A 50 350 367 HOH HOH . 
F 6 HOH A 51 351 350 HOH HOH . 
F 6 HOH A 52 352 343 HOH HOH . 
F 6 HOH A 53 353 372 HOH HOH . 
F 6 HOH A 54 354 352 HOH HOH . 
F 6 HOH A 55 355 403 HOH HOH . 
F 6 HOH A 56 356 323 HOH HOH . 
F 6 HOH A 57 357 381 HOH HOH . 
F 6 HOH A 58 358 348 HOH HOH . 
F 6 HOH A 59 359 339 HOH HOH . 
F 6 HOH A 60 360 330 HOH HOH . 
F 6 HOH A 61 361 402 HOH HOH . 
F 6 HOH A 62 362 351 HOH HOH . 
F 6 HOH A 63 363 368 HOH HOH . 
F 6 HOH A 64 364 359 HOH HOH . 
F 6 HOH A 65 365 363 HOH HOH . 
F 6 HOH A 66 366 329 HOH HOH . 
F 6 HOH A 67 367 378 HOH HOH . 
F 6 HOH A 68 368 304 HOH HOH . 
F 6 HOH A 69 369 316 HOH HOH . 
F 6 HOH A 70 370 305 HOH HOH . 
F 6 HOH A 71 371 361 HOH HOH . 
F 6 HOH A 72 372 347 HOH HOH . 
F 6 HOH A 73 373 395 HOH HOH . 
F 6 HOH A 74 374 370 HOH HOH . 
F 6 HOH A 75 375 353 HOH HOH . 
F 6 HOH A 76 376 390 HOH HOH . 
F 6 HOH A 77 377 307 HOH HOH . 
F 6 HOH A 78 378 310 HOH HOH . 
F 6 HOH A 79 379 394 HOH HOH . 
F 6 HOH A 80 380 376 HOH HOH . 
F 6 HOH A 81 381 383 HOH HOH . 
F 6 HOH A 82 382 342 HOH HOH . 
F 6 HOH A 83 383 386 HOH HOH . 
F 6 HOH A 84 384 382 HOH HOH . 
F 6 HOH A 85 385 396 HOH HOH . 
F 6 HOH A 86 386 385 HOH HOH . 
F 6 HOH A 87 387 401 HOH HOH . 
F 6 HOH A 88 388 366 HOH HOH . 
F 6 HOH A 89 389 337 HOH HOH . 
F 6 HOH A 90 390 375 HOH HOH . 
F 6 HOH A 91 391 344 HOH HOH . 
F 6 HOH A 92 392 388 HOH HOH . 
F 6 HOH A 93 393 379 HOH HOH . 
F 6 HOH A 94 394 393 HOH HOH . 
F 6 HOH A 95 395 355 HOH HOH . 
F 6 HOH A 96 396 399 HOH HOH . 
F 6 HOH A 97 397 357 HOH HOH . 
F 6 HOH A 98 398 392 HOH HOH . 
F 6 HOH A 99 399 380 HOH HOH . 
F 6 HOH A 100 400 389 HOH HOH . 
F 6 HOH A 101 401 362 HOH HOH . 
F 6 HOH A 102 402 328 HOH HOH . 
F 6 HOH A 103 403 309 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 8.274 -4.012 -16.137 1 22.89 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . B 2 9.162 -3.404 -17.205 1 23.17 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . B 2 7.336 -2.947 -15.627 1 24.37 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . B 2 7.573 -5.237 -16.67 1 22.33 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . B 2 9.195 -4.399 -14.881 1 23.81 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . B 2 9.789 -5.862 -14.548 1 24.83 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . B 2 10.532 -6.435 -15.73 1 25.11 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . B 2 8.762 -6.819 -13.976 1 24.31 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . B 2 10.823 -5.494 -13.371 1 23.19 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . B 2 12.026 -4.806 -13.707 1 25.76 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . B 2 13.124 -5.179 -12.724 1 27.88 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . B 2 12.698 -4.773 -11.428 1 26.3 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . B 2 13.359 -6.677 -12.652 1 28.69 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . B 2 14.76 -6.916 -12.452 1 30.85 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . B 2 12.63 -7.122 -11.404 1 27.01 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . B 2 13.302 -8.209 -10.769 1 29.97 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . B 2 12.704 -5.89 -10.536 1 26.54 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . B 2 11.529 -5.758 -9.658 1 24.44 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . B 2 10.212 -5.748 -10.025 1 23.31 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . B 2 9.428 -5.58 -8.92 1 21.99 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . B 2 10.254 -5.469 -7.858 1 23.22 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . B 2 10.084 -5.271 -6.414 1 26.26 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . B 2 8.935 -5.158 -5.935 1 25.48 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . B 2 11.193 -5.198 -5.655 1 28.67 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . B 2 12.439 -5.311 -6.169 1 28.3 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . B 2 13.495 -5.236 -5.318 1 30.38 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . B 2 12.682 -5.5 -7.486 1 26.18 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . B 2 11.627 -5.584 -8.352 1 25.16 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#