data_6ZL3
#
_model_server_result.job_id            0oWfxzkwOCpJ9K7OQGx1zA 
_model_server_result.datetime_utc      '2024-11-05 10:40:58' 
_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          6zl3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    6ZL3 
#
_exptl.entry_id    6ZL3 
_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            6ZL3 
_cell.length_a            93.067 
_cell.length_b            93.067 
_cell.length_c            55.441 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6ZL3 
_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    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 
_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
metalc ? metalc1 A OG SER 18 A SER 17 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc2 B NA NA . A NA 201 1_555 C O2B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc3 B NA NA . A NA 201 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? 
metalc ? metalc4 B NA NA . A NA 201 1_555 E O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc5 B NA NA . A NA 201 1_555 E O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc6 B NA NA . A NA 201 1_555 E O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
#
_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 129 n n 
PB O2B GDP sing 130 n n 
PB O3B GDP sing 131 n n 
PB O3A GDP sing 132 n n 
O2B HOB2 GDP sing 133 n n 
O3B HOB3 GDP sing 134 n n 
O3A PA GDP sing 135 n n 
PA O1A GDP doub 136 n n 
PA O2A GDP sing 137 n n 
PA O5' GDP sing 138 n n 
O2A HOA2 GDP sing 139 n n 
O5' C5' GDP sing 140 n n 
C5' C4' GDP sing 141 n n 
C5' H5' GDP sing 142 n n 
C5' "H5''" GDP sing 143 n n 
C4' O4' GDP sing 144 n n 
C4' C3' GDP sing 145 n n 
C4' H4' GDP sing 146 n n 
O4' C1' GDP sing 147 n n 
C3' O3' GDP sing 148 n n 
C3' C2' GDP sing 149 n n 
C3' H3' GDP sing 150 n n 
O3' HO3' GDP sing 151 n n 
C2' O2' GDP sing 152 n n 
C2' C1' GDP sing 153 n n 
C2' H2' GDP sing 154 n n 
O2' HO2' GDP sing 155 n n 
C1' N9 GDP sing 156 n n 
C1' H1' GDP sing 157 n n 
N9 C8 GDP sing 158 n y 
N9 C4 GDP sing 159 n y 
C8 N7 GDP doub 160 n y 
C8 H8 GDP sing 161 n n 
N7 C5 GDP sing 162 n y 
C5 C6 GDP sing 163 n n 
C5 C4 GDP doub 164 n y 
C6 O6 GDP doub 165 n n 
C6 N1 GDP sing 166 n n 
N1 C2 GDP sing 167 n n 
N1 HN1 GDP sing 168 n n 
C2 N2 GDP sing 169 n n 
C2 N3 GDP doub 170 n n 
N2 HN21 GDP sing 171 n n 
N2 HN22 GDP sing 172 n n 
N3 C4 GDP sing 173 n n 
#
_atom_sites.entry_id                     6ZL3 
_atom_sites.fract_transf_matrix[1][1]    0.010745 
_atom_sites.fract_transf_matrix[1][2]    0.006204 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012407 
_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]    0.018037 
_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 NA A 1 201 1 NA NA . 
C 3 GDP A 1 202 1 GDP GDP . 
D 4 EZZ A 1 203 1 EZZ LIG . 
E 5 HOH A 1 301 75 HOH HOH . 
E 5 HOH A 2 302 7 HOH HOH . 
E 5 HOH A 3 303 118 HOH HOH . 
E 5 HOH A 4 304 134 HOH HOH . 
E 5 HOH A 5 305 106 HOH HOH . 
E 5 HOH A 6 306 68 HOH HOH . 
E 5 HOH A 7 307 76 HOH HOH . 
E 5 HOH A 8 308 3 HOH HOH . 
E 5 HOH A 9 309 6 HOH HOH . 
E 5 HOH A 10 310 129 HOH HOH . 
E 5 HOH A 11 311 16 HOH HOH . 
E 5 HOH A 12 312 138 HOH HOH . 
E 5 HOH A 13 313 110 HOH HOH . 
E 5 HOH A 14 314 139 HOH HOH . 
E 5 HOH A 15 315 2 HOH HOH . 
E 5 HOH A 16 316 70 HOH HOH . 
E 5 HOH A 17 317 83 HOH HOH . 
E 5 HOH A 18 318 22 HOH HOH . 
E 5 HOH A 19 319 74 HOH HOH . 
E 5 HOH A 20 320 29 HOH HOH . 
E 5 HOH A 21 321 123 HOH HOH . 
E 5 HOH A 22 322 13 HOH HOH . 
E 5 HOH A 23 323 86 HOH HOH . 
E 5 HOH A 24 324 98 HOH HOH . 
E 5 HOH A 25 325 97 HOH HOH . 
E 5 HOH A 26 326 100 HOH HOH . 
E 5 HOH A 27 327 87 HOH HOH . 
E 5 HOH A 28 328 143 HOH HOH . 
E 5 HOH A 29 329 17 HOH HOH . 
E 5 HOH A 30 330 78 HOH HOH . 
E 5 HOH A 31 331 19 HOH HOH . 
E 5 HOH A 32 332 113 HOH HOH . 
E 5 HOH A 33 333 95 HOH HOH . 
E 5 HOH A 34 334 11 HOH HOH . 
E 5 HOH A 35 335 79 HOH HOH . 
E 5 HOH A 36 336 40 HOH HOH . 
E 5 HOH A 37 337 65 HOH HOH . 
E 5 HOH A 38 338 23 HOH HOH . 
E 5 HOH A 39 339 80 HOH HOH . 
E 5 HOH A 40 340 102 HOH HOH . 
E 5 HOH A 41 341 27 HOH HOH . 
E 5 HOH A 42 342 90 HOH HOH . 
E 5 HOH A 43 343 91 HOH HOH . 
E 5 HOH A 44 344 14 HOH HOH . 
E 5 HOH A 45 345 20 HOH HOH . 
E 5 HOH A 46 346 94 HOH HOH . 
E 5 HOH A 47 347 15 HOH HOH . 
E 5 HOH A 48 348 121 HOH HOH . 
E 5 HOH A 49 349 1 HOH HOH . 
E 5 HOH A 50 350 125 HOH HOH . 
E 5 HOH A 51 351 89 HOH HOH . 
E 5 HOH A 52 352 107 HOH HOH . 
E 5 HOH A 53 353 41 HOH HOH . 
E 5 HOH A 54 354 128 HOH HOH . 
E 5 HOH A 55 355 114 HOH HOH . 
E 5 HOH A 56 356 39 HOH HOH . 
E 5 HOH A 57 357 4 HOH HOH . 
E 5 HOH A 58 358 105 HOH HOH . 
E 5 HOH A 59 359 84 HOH HOH . 
E 5 HOH A 60 360 9 HOH HOH . 
E 5 HOH A 61 361 127 HOH HOH . 
E 5 HOH A 62 362 130 HOH HOH . 
E 5 HOH A 63 363 45 HOH HOH . 
E 5 HOH A 64 364 24 HOH HOH . 
E 5 HOH A 65 365 141 HOH HOH . 
E 5 HOH A 66 366 124 HOH HOH . 
E 5 HOH A 67 367 81 HOH HOH . 
E 5 HOH A 68 368 10 HOH HOH . 
E 5 HOH A 69 369 26 HOH HOH . 
E 5 HOH A 70 370 18 HOH HOH . 
E 5 HOH A 71 371 122 HOH HOH . 
E 5 HOH A 72 372 5 HOH HOH . 
E 5 HOH A 73 373 33 HOH HOH . 
E 5 HOH A 74 374 12 HOH HOH . 
E 5 HOH A 75 375 137 HOH HOH . 
E 5 HOH A 76 376 104 HOH HOH . 
E 5 HOH A 77 377 37 HOH HOH . 
E 5 HOH A 78 378 131 HOH HOH . 
E 5 HOH A 79 379 120 HOH HOH . 
E 5 HOH A 80 380 42 HOH HOH . 
E 5 HOH A 81 381 43 HOH HOH . 
E 5 HOH A 82 382 61 HOH HOH . 
E 5 HOH A 83 383 140 HOH HOH . 
E 5 HOH A 84 384 32 HOH HOH . 
E 5 HOH A 85 385 101 HOH HOH . 
E 5 HOH A 86 386 63 HOH HOH . 
E 5 HOH A 87 387 88 HOH HOH . 
E 5 HOH A 88 388 93 HOH HOH . 
E 5 HOH A 89 389 109 HOH HOH . 
E 5 HOH A 90 390 92 HOH HOH . 
E 5 HOH A 91 391 133 HOH HOH . 
E 5 HOH A 92 392 46 HOH HOH . 
E 5 HOH A 93 393 96 HOH HOH . 
E 5 HOH A 94 394 66 HOH HOH . 
E 5 HOH A 95 395 119 HOH HOH . 
E 5 HOH A 96 396 116 HOH HOH . 
E 5 HOH A 97 397 142 HOH HOH . 
E 5 HOH A 98 398 77 HOH HOH . 
E 5 HOH A 99 399 38 HOH HOH . 
E 5 HOH A 100 400 126 HOH HOH . 
E 5 HOH A 101 401 82 HOH HOH . 
E 5 HOH A 102 402 111 HOH HOH . 
E 5 HOH A 103 403 73 HOH HOH . 
E 5 HOH A 104 404 34 HOH HOH . 
E 5 HOH A 105 405 25 HOH HOH . 
E 5 HOH A 106 406 59 HOH HOH . 
E 5 HOH A 107 407 8 HOH HOH . 
E 5 HOH A 108 408 132 HOH HOH . 
E 5 HOH A 109 409 103 HOH HOH . 
E 5 HOH A 110 410 135 HOH HOH . 
E 5 HOH A 111 411 35 HOH HOH . 
E 5 HOH A 112 412 44 HOH HOH . 
E 5 HOH A 113 413 64 HOH HOH . 
E 5 HOH A 114 414 112 HOH HOH . 
E 5 HOH A 115 415 117 HOH HOH . 
E 5 HOH A 116 416 62 HOH HOH . 
E 5 HOH A 117 417 67 HOH HOH . 
E 5 HOH A 118 418 57 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 30.452 -26.311 18.321 1 38.98 ? PB GDP 202 A 1 
HETATM 2 O O1B GDP . . . C 3 30.984 -27.371 17.353 1 38.01 ? O1B GDP 202 A 1 
HETATM 3 O O2B GDP . . . C 3 29.15 -26.614 18.992 1 37.5 ? O2B GDP 202 A 1 
HETATM 4 O O3B GDP . . . C 3 31.57 -26.07 19.399 1 39.95 ? O3B GDP 202 A 1 
HETATM 5 O O3A GDP . . . C 3 30.242 -25.004 17.44 1 40.04 ? O3A GDP 202 A 1 
HETATM 6 P PA GDP . . . C 3 29.181 -23.817 17.523 1 41.69 ? PA GDP 202 A 1 
HETATM 7 O O1A GDP . . . C 3 27.831 -24.241 17.092 1 42.62 ? O1A GDP 202 A 1 
HETATM 8 O O2A GDP . . . C 3 29.137 -23.344 18.998 1 42.31 ? O2A GDP 202 A 1 
HETATM 9 O O5' GDP . . . C 3 29.782 -22.707 16.588 1 41.34 ? O5' GDP 202 A 1 
HETATM 10 C C5' GDP . . . C 3 31.111 -22.197 16.834 1 41.92 ? C5' GDP 202 A 1 
HETATM 11 C C4' GDP . . . C 3 31.265 -20.869 16.134 1 42.58 ? C4' GDP 202 A 1 
HETATM 12 O O4' GDP . . . C 3 31.132 -21.054 14.709 1 42.38 ? O4' GDP 202 A 1 
HETATM 13 C C3' GDP . . . C 3 30.262 -19.775 16.506 1 43.37 ? C3' GDP 202 A 1 
HETATM 14 O O3' GDP . . . C 3 30.921 -18.511 16.426 1 44.35 ? O3' GDP 202 A 1 
HETATM 15 C C2' GDP . . . C 3 29.204 -19.908 15.409 1 42.95 ? C2' GDP 202 A 1 
HETATM 16 O O2' GDP . . . C 3 28.52 -18.691 15.137 1 44.11 ? O2' GDP 202 A 1 
HETATM 17 C C1' GDP . . . C 3 30.078 -20.25 14.212 1 42.05 ? C1' GDP 202 A 1 
HETATM 18 N N9 GDP . . . C 3 29.372 -20.994 13.15 1 40.74 ? N9 GDP 202 A 1 
HETATM 19 C C8 GDP . . . C 3 28.72 -22.191 13.275 1 40.09 ? C8 GDP 202 A 1 
HETATM 20 N N7 GDP . . . C 3 28.243 -22.648 12.142 1 39.99 ? N7 GDP 202 A 1 
HETATM 21 C C5 GDP . . . C 3 28.603 -21.691 11.209 1 39.81 ? C5 GDP 202 A 1 
HETATM 22 C C6 GDP . . . C 3 28.403 -21.628 9.79 1 40.28 ? C6 GDP 202 A 1 
HETATM 23 O O6 GDP . . . C 3 27.921 -22.491 9.058 1 40.74 ? O6 GDP 202 A 1 
HETATM 24 N N1 GDP . . . C 3 28.925 -20.472 9.244 1 40.31 ? N1 GDP 202 A 1 
HETATM 25 C C2 GDP . . . C 3 29.583 -19.496 9.941 1 39.83 ? C2 GDP 202 A 1 
HETATM 26 N N2 GDP . . . C 3 30.024 -18.451 9.239 1 39.9 ? N2 GDP 202 A 1 
HETATM 27 N N3 GDP . . . C 3 29.799 -19.548 11.254 1 39.38 ? N3 GDP 202 A 1 
HETATM 28 C C4 GDP . . . C 3 29.291 -20.657 11.821 1 39.9 ? C4 GDP 202 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#