data_1Z2A
#
_model_server_result.job_id            '_KVCePlYzcSYmSEJnHHYfA' 
_model_server_result.datetime_utc      '2024-11-06 14:26:59' 
_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          1z2a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    1Z2A 
#
_exptl.entry_id    1Z2A 
_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          89.99 
_cell.angle_gamma         90 
_cell.entry_id            1Z2A 
_cell.length_a            40.281 
_cell.length_b            61.44 
_cell.length_c            63.854 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Z2A 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 19 A SER 23 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc2 C O3B GDP . A GDP 201 1_555 B MG MG . A MG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc3 B MG MG . A MG 300 1_555 D O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc4 B MG MG . A MG 300 1_555 D O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc5 B MG MG . A MG 300 1_555 D O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
metalc ? metalc6 B MG MG . A MG 300 1_555 D O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
#
_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 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     1Z2A 
_atom_sites.fract_transf_matrix[1][1]    0.024826 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    -0.000005 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016276 
_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]    0.015661 
_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 MG A 1 300 300 MG MG . 
C 3 GDP A 1 201 201 GDP GDP . 
D 4 HOH A 1 301 2 HOH HOH . 
D 4 HOH A 2 302 5 HOH HOH . 
D 4 HOH A 3 303 8 HOH HOH . 
D 4 HOH A 4 304 9 HOH HOH . 
D 4 HOH A 5 305 10 HOH HOH . 
D 4 HOH A 6 306 14 HOH HOH . 
D 4 HOH A 7 307 17 HOH HOH . 
D 4 HOH A 8 308 18 HOH HOH . 
D 4 HOH A 9 309 21 HOH HOH . 
D 4 HOH A 10 310 23 HOH HOH . 
D 4 HOH A 11 311 25 HOH HOH . 
D 4 HOH A 12 312 26 HOH HOH . 
D 4 HOH A 13 313 27 HOH HOH . 
D 4 HOH A 14 314 30 HOH HOH . 
D 4 HOH A 15 315 31 HOH HOH . 
D 4 HOH A 16 316 32 HOH HOH . 
D 4 HOH A 17 317 36 HOH HOH . 
D 4 HOH A 18 318 37 HOH HOH . 
D 4 HOH A 19 319 39 HOH HOH . 
D 4 HOH A 20 320 44 HOH HOH . 
D 4 HOH A 21 321 47 HOH HOH . 
D 4 HOH A 22 322 48 HOH HOH . 
D 4 HOH A 23 323 49 HOH HOH . 
D 4 HOH A 24 324 51 HOH HOH . 
D 4 HOH A 25 325 55 HOH HOH . 
D 4 HOH A 26 326 57 HOH HOH . 
D 4 HOH A 27 327 60 HOH HOH . 
D 4 HOH A 28 328 61 HOH HOH . 
D 4 HOH A 29 329 65 HOH HOH . 
D 4 HOH A 30 330 66 HOH HOH . 
D 4 HOH A 31 331 67 HOH HOH . 
D 4 HOH A 32 332 68 HOH HOH . 
D 4 HOH A 33 333 69 HOH HOH . 
D 4 HOH A 34 334 74 HOH HOH . 
D 4 HOH A 35 335 75 HOH HOH . 
D 4 HOH A 36 336 78 HOH HOH . 
D 4 HOH A 37 337 81 HOH HOH . 
D 4 HOH A 38 338 82 HOH HOH . 
D 4 HOH A 39 339 83 HOH HOH . 
D 4 HOH A 40 340 86 HOH HOH . 
D 4 HOH A 41 341 88 HOH HOH . 
D 4 HOH A 42 342 89 HOH HOH . 
D 4 HOH A 43 343 101 HOH HOH . 
D 4 HOH A 44 344 106 HOH HOH . 
D 4 HOH A 45 345 107 HOH HOH . 
D 4 HOH A 46 346 108 HOH HOH . 
D 4 HOH A 47 347 109 HOH HOH . 
D 4 HOH A 48 348 111 HOH HOH . 
D 4 HOH A 49 349 112 HOH HOH . 
D 4 HOH A 50 350 113 HOH HOH . 
D 4 HOH A 51 351 115 HOH HOH . 
D 4 HOH A 52 352 116 HOH HOH . 
D 4 HOH A 53 353 117 HOH HOH . 
D 4 HOH A 54 354 119 HOH HOH . 
D 4 HOH A 55 355 121 HOH HOH . 
D 4 HOH A 56 356 122 HOH HOH . 
D 4 HOH A 57 357 123 HOH HOH . 
D 4 HOH A 58 358 126 HOH HOH . 
D 4 HOH A 59 359 127 HOH HOH . 
D 4 HOH A 60 360 128 HOH HOH . 
D 4 HOH A 61 361 129 HOH HOH . 
D 4 HOH A 62 362 130 HOH HOH . 
D 4 HOH A 63 363 131 HOH HOH . 
D 4 HOH A 64 364 132 HOH HOH . 
D 4 HOH A 65 365 134 HOH HOH . 
D 4 HOH A 66 366 136 HOH HOH . 
D 4 HOH A 67 367 137 HOH HOH . 
D 4 HOH A 68 368 140 HOH HOH . 
D 4 HOH A 69 369 141 HOH HOH . 
D 4 HOH A 70 370 142 HOH HOH . 
D 4 HOH A 71 371 143 HOH HOH . 
D 4 HOH A 72 372 144 HOH HOH . 
D 4 HOH A 73 373 145 HOH HOH . 
D 4 HOH A 74 374 146 HOH HOH . 
D 4 HOH A 75 375 147 HOH HOH . 
D 4 HOH A 76 376 148 HOH HOH . 
D 4 HOH A 77 377 149 HOH HOH . 
D 4 HOH A 78 378 152 HOH HOH . 
D 4 HOH A 79 379 153 HOH HOH . 
D 4 HOH A 80 380 155 HOH HOH . 
D 4 HOH A 81 381 159 HOH HOH . 
D 4 HOH A 82 382 161 HOH HOH . 
D 4 HOH A 83 383 163 HOH HOH . 
D 4 HOH A 84 384 165 HOH HOH . 
D 4 HOH A 85 385 166 HOH HOH . 
D 4 HOH A 86 386 167 HOH HOH . 
D 4 HOH A 87 387 168 HOH HOH . 
D 4 HOH A 88 388 172 HOH HOH . 
D 4 HOH A 89 389 173 HOH HOH . 
D 4 HOH A 90 390 174 HOH HOH . 
D 4 HOH A 91 391 176 HOH HOH . 
D 4 HOH A 92 392 177 HOH HOH . 
D 4 HOH A 93 393 178 HOH HOH . 
D 4 HOH A 94 394 180 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 12.393 4.312 12.627 1 20.25 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . C 3 13.005 3.214 11.783 1 18.18 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . C 3 10.995 3.914 13.005 1 20.39 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . C 3 13.244 4.558 13.859 1 20.04 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . C 3 12.293 5.65 11.741 1 19.27 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . C 3 13.42 6.78 11.584 1 19.01 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . C 3 14.781 6.204 11.294 1 18.56 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . C 3 13.465 7.665 12.815 1 20.63 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . C 3 12.884 7.637 10.331 1 20.79 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . C 3 12.753 7.037 9.038 1 21.44 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . C 3 12.639 8.126 7.97 1 21.58 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . C 3 11.388 8.801 8.1 1 21.35 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . C 3 13.718 9.184 8.097 1 22.28 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . C 3 14.088 9.592 6.778 1 23.14 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . C 3 13.015 10.317 8.832 1 21.98 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . C 3 13.584 11.597 8.58 1 23.73 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . C 3 11.608 10.205 8.279 1 21.77 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . C 3 10.58 10.807 9.167 1 21.94 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . C 3 10.439 10.638 10.501 1 22.17 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . C 3 9.383 11.354 10.968 1 21.79 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . C 3 8.821 11.998 9.92 1 21.38 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . C 3 7.672 12.924 9.698 1 22.14 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . C 3 6.923 13.299 10.637 1 21.2 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . C 3 7.448 13.355 8.445 1 22.02 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . C 3 8.223 12.983 7.399 1 22.22 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . C 3 7.934 13.456 6.166 1 21.74 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . C 3 9.281 12.146 7.532 1 22.29 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . C 3 9.621 11.629 8.74 1 22.11 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              48 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           343 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#