data_6L6O
#
_model_server_result.job_id            ar33YaIBkDI109pTpIZ1ow 
_model_server_result.datetime_utc      '2024-10-20 18:42:54' 
_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          6l6o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    6L6O 
#
_exptl.entry_id    6L6O 
_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            6L6O 
_cell.length_a            58.018 
_cell.length_b            58.018 
_cell.length_c            103.418 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6L6O 
_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    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
metalc ? metalc1 A OG SER 29 A SER 27 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc2 B O2B GDP . A GDP 201 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
#
_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 89 n n 
PB O2B GDP sing 90 n n 
PB O3B GDP sing 91 n n 
PB O3A GDP sing 92 n n 
O2B HOB2 GDP sing 93 n n 
O3B HOB3 GDP sing 94 n n 
O3A PA GDP sing 95 n n 
PA O1A GDP doub 96 n n 
PA O2A GDP sing 97 n n 
PA O5' GDP sing 98 n n 
O2A HOA2 GDP sing 99 n n 
O5' C5' GDP sing 100 n n 
C5' C4' GDP sing 101 n n 
C5' H5' GDP sing 102 n n 
C5' "H5''" GDP sing 103 n n 
C4' O4' GDP sing 104 n n 
C4' C3' GDP sing 105 n n 
C4' H4' GDP sing 106 n n 
O4' C1' GDP sing 107 n n 
C3' O3' GDP sing 108 n n 
C3' C2' GDP sing 109 n n 
C3' H3' GDP sing 110 n n 
O3' HO3' GDP sing 111 n n 
C2' O2' GDP sing 112 n n 
C2' C1' GDP sing 113 n n 
C2' H2' GDP sing 114 n n 
O2' HO2' GDP sing 115 n n 
C1' N9 GDP sing 116 n n 
C1' H1' GDP sing 117 n n 
N9 C8 GDP sing 118 n y 
N9 C4 GDP sing 119 n y 
C8 N7 GDP doub 120 n y 
C8 H8 GDP sing 121 n n 
N7 C5 GDP sing 122 n y 
C5 C6 GDP sing 123 n n 
C5 C4 GDP doub 124 n y 
C6 O6 GDP doub 125 n n 
C6 N1 GDP sing 126 n n 
N1 C2 GDP sing 127 n n 
N1 HN1 GDP sing 128 n n 
C2 N2 GDP sing 129 n n 
C2 N3 GDP doub 130 n n 
N2 HN21 GDP sing 131 n n 
N2 HN22 GDP sing 132 n n 
N3 C4 GDP sing 133 n n 
#
_atom_sites.entry_id                     6L6O 
_atom_sites.fract_transf_matrix[1][1]    0.017236 
_atom_sites.fract_transf_matrix[1][2]    0.009951 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019902 
_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]    0.009669 
_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 1 201 166 GDP GDP . 
C 3 GOL A 1 202 167 GOL GOL . 
D 4 ACT A 1 203 168 ACT ACT . 
E 5 MG A 1 204 1 MG MG . 
F 6 HOH A 1 301 108 HOH HOH . 
F 6 HOH A 2 302 84 HOH HOH . 
F 6 HOH A 3 303 125 HOH HOH . 
F 6 HOH A 4 304 67 HOH HOH . 
F 6 HOH A 5 305 69 HOH HOH . 
F 6 HOH A 6 306 41 HOH HOH . 
F 6 HOH A 7 307 101 HOH HOH . 
F 6 HOH A 8 308 26 HOH HOH . 
F 6 HOH A 9 309 50 HOH HOH . 
F 6 HOH A 10 310 60 HOH HOH . 
F 6 HOH A 11 311 20 HOH HOH . 
F 6 HOH A 12 312 121 HOH HOH . 
F 6 HOH A 13 313 4 HOH HOH . 
F 6 HOH A 14 314 36 HOH HOH . 
F 6 HOH A 15 315 34 HOH HOH . 
F 6 HOH A 16 316 22 HOH HOH . 
F 6 HOH A 17 317 71 HOH HOH . 
F 6 HOH A 18 318 17 HOH HOH . 
F 6 HOH A 19 319 56 HOH HOH . 
F 6 HOH A 20 320 3 HOH HOH . 
F 6 HOH A 21 321 105 HOH HOH . 
F 6 HOH A 22 322 119 HOH HOH . 
F 6 HOH A 23 323 31 HOH HOH . 
F 6 HOH A 24 324 66 HOH HOH . 
F 6 HOH A 25 325 115 HOH HOH . 
F 6 HOH A 26 326 10 HOH HOH . 
F 6 HOH A 27 327 25 HOH HOH . 
F 6 HOH A 28 328 47 HOH HOH . 
F 6 HOH A 29 329 86 HOH HOH . 
F 6 HOH A 30 330 46 HOH HOH . 
F 6 HOH A 31 331 23 HOH HOH . 
F 6 HOH A 32 332 58 HOH HOH . 
F 6 HOH A 33 333 118 HOH HOH . 
F 6 HOH A 34 334 45 HOH HOH . 
F 6 HOH A 35 335 83 HOH HOH . 
F 6 HOH A 36 336 53 HOH HOH . 
F 6 HOH A 37 337 64 HOH HOH . 
F 6 HOH A 38 338 123 HOH HOH . 
F 6 HOH A 39 339 100 HOH HOH . 
F 6 HOH A 40 340 21 HOH HOH . 
F 6 HOH A 41 341 96 HOH HOH . 
F 6 HOH A 42 342 62 HOH HOH . 
F 6 HOH A 43 343 15 HOH HOH . 
F 6 HOH A 44 344 54 HOH HOH . 
F 6 HOH A 45 345 65 HOH HOH . 
F 6 HOH A 46 346 38 HOH HOH . 
F 6 HOH A 47 347 12 HOH HOH . 
F 6 HOH A 48 348 30 HOH HOH . 
F 6 HOH A 49 349 9 HOH HOH . 
F 6 HOH A 50 350 1 HOH HOH . 
F 6 HOH A 51 351 120 HOH HOH . 
F 6 HOH A 52 352 18 HOH HOH . 
F 6 HOH A 53 353 2 HOH HOH . 
F 6 HOH A 54 354 6 HOH HOH . 
F 6 HOH A 55 355 52 HOH HOH . 
F 6 HOH A 56 356 113 HOH HOH . 
F 6 HOH A 57 357 19 HOH HOH . 
F 6 HOH A 58 358 8 HOH HOH . 
F 6 HOH A 59 359 5 HOH HOH . 
F 6 HOH A 60 360 74 HOH HOH . 
F 6 HOH A 61 361 39 HOH HOH . 
F 6 HOH A 62 362 13 HOH HOH . 
F 6 HOH A 63 363 97 HOH HOH . 
F 6 HOH A 64 364 88 HOH HOH . 
F 6 HOH A 65 365 24 HOH HOH . 
F 6 HOH A 66 366 73 HOH HOH . 
F 6 HOH A 67 367 68 HOH HOH . 
F 6 HOH A 68 368 16 HOH HOH . 
F 6 HOH A 69 369 55 HOH HOH . 
F 6 HOH A 70 370 102 HOH HOH . 
F 6 HOH A 71 371 43 HOH HOH . 
F 6 HOH A 72 372 7 HOH HOH . 
F 6 HOH A 73 373 32 HOH HOH . 
F 6 HOH A 74 374 44 HOH HOH . 
F 6 HOH A 75 375 40 HOH HOH . 
F 6 HOH A 76 376 14 HOH HOH . 
F 6 HOH A 77 377 27 HOH HOH . 
F 6 HOH A 78 378 81 HOH HOH . 
F 6 HOH A 79 379 61 HOH HOH . 
F 6 HOH A 80 380 77 HOH HOH . 
F 6 HOH A 81 381 48 HOH HOH . 
F 6 HOH A 82 382 91 HOH HOH . 
F 6 HOH A 83 383 103 HOH HOH . 
F 6 HOH A 84 384 11 HOH HOH . 
F 6 HOH A 85 385 59 HOH HOH . 
F 6 HOH A 86 386 112 HOH HOH . 
F 6 HOH A 87 387 35 HOH HOH . 
F 6 HOH A 88 388 70 HOH HOH . 
F 6 HOH A 89 389 28 HOH HOH . 
F 6 HOH A 90 390 72 HOH HOH . 
F 6 HOH A 91 391 85 HOH HOH . 
F 6 HOH A 92 392 76 HOH HOH . 
F 6 HOH A 93 393 109 HOH HOH . 
F 6 HOH A 94 394 79 HOH HOH . 
F 6 HOH A 95 395 89 HOH HOH . 
F 6 HOH A 96 396 93 HOH HOH . 
F 6 HOH A 97 397 37 HOH HOH . 
F 6 HOH A 98 398 63 HOH HOH . 
F 6 HOH A 99 399 99 HOH HOH . 
F 6 HOH A 100 400 92 HOH HOH . 
F 6 HOH A 101 401 107 HOH HOH . 
F 6 HOH A 102 402 78 HOH HOH . 
F 6 HOH A 103 403 75 HOH HOH . 
F 6 HOH A 104 404 42 HOH HOH . 
F 6 HOH A 105 405 95 HOH HOH . 
F 6 HOH A 106 406 57 HOH HOH . 
F 6 HOH A 107 407 87 HOH HOH . 
F 6 HOH A 108 408 90 HOH HOH . 
F 6 HOH A 109 409 82 HOH HOH . 
F 6 HOH A 110 410 126 HOH HOH . 
F 6 HOH A 111 411 114 HOH HOH . 
F 6 HOH A 112 412 98 HOH HOH . 
F 6 HOH A 113 413 51 HOH HOH . 
F 6 HOH A 114 414 116 HOH HOH . 
F 6 HOH A 115 415 104 HOH HOH . 
F 6 HOH A 116 416 124 HOH HOH . 
F 6 HOH A 117 417 29 HOH HOH . 
F 6 HOH A 118 418 106 HOH HOH . 
F 6 HOH A 119 419 33 HOH HOH . 
F 6 HOH A 120 420 110 HOH HOH . 
F 6 HOH A 121 421 49 HOH HOH . 
F 6 HOH A 122 422 94 HOH HOH . 
F 6 HOH A 123 423 80 HOH HOH . 
F 6 HOH A 124 424 111 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 -29.234 14.212 -15.521 1 27.19 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . B 2 -30.594 14.006 -16.1 1 26.04 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . B 2 -29.146 14.149 -13.973 1 24.37 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . B 2 -28.586 15.484 -16.071 1 24.36 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . B 2 -28.288 13.033 -16.068 1 27.98 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . B 2 -27.856 11.62 -15.462 1 29.02 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . B 2 -29.044 10.989 -14.885 1 30.19 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . B 2 -26.711 11.798 -14.574 1 29.39 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . B 2 -27.288 10.845 -16.717 1 27.95 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . B 2 -28.14 10.717 -17.879 1 29.67 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . B 2 -27.671 9.465 -18.66 1 31.98 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . B 2 -26.373 9.676 -19.206 1 32.03 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . B 2 -27.536 8.251 -17.709 1 34.12 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . B 2 -27.911 7.087 -18.356 1 36.65 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . B 2 -26.1 8.171 -17.354 1 33.72 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . B 2 -25.685 6.847 -17.071 1 34.87 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . B 2 -25.459 8.736 -18.646 1 32.19 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . B 2 -24.161 9.425 -18.402 1 30.24 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . B 2 -23.972 10.38 -17.443 1 28.29 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . B 2 -22.761 10.839 -17.469 1 26.49 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . B 2 -22.117 10.147 -18.503 1 26.2 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . B 2 -20.816 10.097 -19.06 1 27.39 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . B 2 -19.92 10.875 -18.65 1 28.15 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . B 2 -20.634 9.318 -20.115 1 28.19 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . B 2 -21.554 8.41 -20.599 1 28.56 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . B 2 -21.247 7.625 -21.593 1 30.54 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . B 2 -22.798 8.39 -20.136 1 27.45 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . B 2 -23.078 9.241 -19.119 1 27.14 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              78 
_model_server_stats.parse_time_ms           103 
_model_server_stats.create_model_time_ms    37 
_model_server_stats.query_time_ms           433 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#