data_1ZD9
#
_model_server_result.job_id            5c656MnxdylyZeGw5aQ2dw 
_model_server_result.datetime_utc      '2024-11-15 11:31:11' 
_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          1zd9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    1ZD9 
#
_exptl.entry_id    1ZD9 
_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         90 
_cell.entry_id            1ZD9 
_cell.length_a            61.731 
_cell.length_b            72.092 
_cell.length_c            36.416 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ZD9 
_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 OG1 THR 36 A THR 33 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc2 C O1B GDP . A GDP 201 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc3 B MG MG . A MG 202 1_555 D O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc4 B MG MG . A MG 202 1_555 D O HOH . A HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc5 B MG MG . A MG 202 1_555 D O HOH . A HOH 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc6 B MG MG . A MG 202 1_555 D O HOH . A HOH 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
#
_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                     1ZD9 
_atom_sites.fract_transf_matrix[1][1]    0.016199 
_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]    0.013871 
_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]    0.02746 
_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 1 202 202 MG MG . 
C 3 GDP A 1 201 201 GDP GDP . 
D 4 HOH A 1 301 301 HOH HOH . 
D 4 HOH A 2 302 302 HOH HOH . 
D 4 HOH A 3 303 303 HOH HOH . 
D 4 HOH A 4 304 304 HOH HOH . 
D 4 HOH A 5 305 305 HOH HOH . 
D 4 HOH A 6 306 306 HOH HOH . 
D 4 HOH A 7 307 307 HOH HOH . 
D 4 HOH A 8 308 308 HOH HOH . 
D 4 HOH A 9 309 309 HOH HOH . 
D 4 HOH A 10 310 310 HOH HOH . 
D 4 HOH A 11 311 311 HOH HOH . 
D 4 HOH A 12 312 312 HOH HOH . 
D 4 HOH A 13 313 313 HOH HOH . 
D 4 HOH A 14 314 314 HOH HOH . 
D 4 HOH A 15 315 315 HOH HOH . 
D 4 HOH A 16 316 316 HOH HOH . 
D 4 HOH A 17 317 317 HOH HOH . 
D 4 HOH A 18 318 318 HOH HOH . 
D 4 HOH A 19 319 319 HOH HOH . 
D 4 HOH A 20 320 320 HOH HOH . 
D 4 HOH A 21 321 321 HOH HOH . 
D 4 HOH A 22 322 322 HOH HOH . 
D 4 HOH A 23 323 323 HOH HOH . 
D 4 HOH A 24 324 324 HOH HOH . 
D 4 HOH A 25 325 325 HOH HOH . 
D 4 HOH A 26 326 326 HOH HOH . 
D 4 HOH A 27 327 327 HOH HOH . 
D 4 HOH A 28 328 328 HOH HOH . 
D 4 HOH A 29 329 329 HOH HOH . 
D 4 HOH A 30 330 330 HOH HOH . 
D 4 HOH A 31 331 331 HOH HOH . 
D 4 HOH A 32 332 332 HOH HOH . 
D 4 HOH A 33 333 333 HOH HOH . 
D 4 HOH A 34 334 334 HOH HOH . 
D 4 HOH A 35 335 335 HOH HOH . 
D 4 HOH A 36 336 336 HOH HOH . 
D 4 HOH A 37 337 337 HOH HOH . 
D 4 HOH A 38 338 338 HOH HOH . 
D 4 HOH A 39 339 339 HOH HOH . 
D 4 HOH A 40 340 340 HOH HOH . 
D 4 HOH A 41 341 341 HOH HOH . 
D 4 HOH A 42 342 342 HOH HOH . 
D 4 HOH A 43 343 343 HOH HOH . 
D 4 HOH A 44 344 344 HOH HOH . 
D 4 HOH A 45 345 345 HOH HOH . 
D 4 HOH A 46 346 346 HOH HOH . 
D 4 HOH A 47 347 347 HOH HOH . 
D 4 HOH A 48 348 348 HOH HOH . 
D 4 HOH A 49 349 349 HOH HOH . 
D 4 HOH A 50 350 350 HOH HOH . 
D 4 HOH A 51 351 351 HOH HOH . 
D 4 HOH A 52 352 352 HOH HOH . 
D 4 HOH A 53 353 353 HOH HOH . 
D 4 HOH A 54 354 354 HOH HOH . 
D 4 HOH A 55 355 355 HOH HOH . 
D 4 HOH A 56 356 356 HOH HOH . 
D 4 HOH A 57 357 357 HOH HOH . 
D 4 HOH A 58 358 358 HOH HOH . 
D 4 HOH A 59 359 359 HOH HOH . 
D 4 HOH A 60 360 360 HOH HOH . 
D 4 HOH A 61 361 361 HOH HOH . 
D 4 HOH A 62 362 362 HOH HOH . 
D 4 HOH A 63 363 363 HOH HOH . 
D 4 HOH A 64 364 364 HOH HOH . 
D 4 HOH A 65 365 365 HOH HOH . 
D 4 HOH A 66 366 366 HOH HOH . 
D 4 HOH A 67 367 367 HOH HOH . 
D 4 HOH A 68 368 368 HOH HOH . 
D 4 HOH A 69 369 369 HOH HOH . 
D 4 HOH A 70 370 370 HOH HOH . 
D 4 HOH A 71 371 371 HOH HOH . 
D 4 HOH A 72 372 372 HOH HOH . 
D 4 HOH A 73 373 373 HOH HOH . 
D 4 HOH A 74 374 374 HOH HOH . 
D 4 HOH A 75 375 375 HOH HOH . 
D 4 HOH A 76 376 376 HOH HOH . 
D 4 HOH A 77 377 377 HOH HOH . 
D 4 HOH A 78 378 378 HOH HOH . 
D 4 HOH A 79 379 379 HOH HOH . 
D 4 HOH A 80 380 380 HOH HOH . 
D 4 HOH A 81 381 381 HOH HOH . 
D 4 HOH A 82 382 382 HOH HOH . 
D 4 HOH A 83 383 383 HOH HOH . 
D 4 HOH A 84 384 384 HOH HOH . 
D 4 HOH A 85 385 385 HOH HOH . 
D 4 HOH A 86 386 386 HOH HOH . 
D 4 HOH A 87 387 387 HOH HOH . 
D 4 HOH A 88 388 388 HOH HOH . 
D 4 HOH A 89 389 389 HOH HOH . 
D 4 HOH A 90 390 390 HOH HOH . 
D 4 HOH A 91 391 391 HOH HOH . 
D 4 HOH A 92 392 392 HOH HOH . 
D 4 HOH A 93 393 393 HOH HOH . 
D 4 HOH A 94 394 394 HOH HOH . 
D 4 HOH A 95 395 395 HOH HOH . 
D 4 HOH A 96 396 396 HOH HOH . 
D 4 HOH A 97 397 397 HOH HOH . 
D 4 HOH A 98 398 398 HOH HOH . 
D 4 HOH A 99 399 399 HOH HOH . 
D 4 HOH A 100 400 400 HOH HOH . 
D 4 HOH A 101 401 401 HOH HOH . 
D 4 HOH A 102 402 402 HOH HOH . 
D 4 HOH A 103 403 403 HOH HOH . 
D 4 HOH A 104 404 404 HOH HOH . 
D 4 HOH A 105 405 405 HOH HOH . 
D 4 HOH A 106 406 406 HOH HOH . 
D 4 HOH A 107 407 407 HOH HOH . 
D 4 HOH A 108 408 408 HOH HOH . 
D 4 HOH A 109 409 409 HOH HOH . 
D 4 HOH A 110 410 410 HOH HOH . 
D 4 HOH A 111 411 411 HOH HOH . 
D 4 HOH A 112 412 412 HOH HOH . 
D 4 HOH A 113 413 413 HOH HOH . 
D 4 HOH A 114 414 414 HOH HOH . 
D 4 HOH A 115 415 415 HOH HOH . 
D 4 HOH A 116 416 416 HOH HOH . 
D 4 HOH A 117 417 417 HOH HOH . 
D 4 HOH A 118 418 418 HOH HOH . 
D 4 HOH A 119 419 419 HOH HOH . 
D 4 HOH A 120 420 420 HOH HOH . 
D 4 HOH A 121 421 421 HOH HOH . 
D 4 HOH A 122 422 422 HOH HOH . 
D 4 HOH A 123 423 423 HOH HOH . 
D 4 HOH A 124 424 424 HOH HOH . 
D 4 HOH A 125 425 425 HOH HOH . 
D 4 HOH A 126 426 426 HOH HOH . 
D 4 HOH A 127 427 427 HOH HOH . 
D 4 HOH A 128 428 428 HOH HOH . 
D 4 HOH A 129 429 429 HOH HOH . 
D 4 HOH A 130 430 430 HOH HOH . 
D 4 HOH A 131 431 431 HOH HOH . 
D 4 HOH A 132 432 432 HOH HOH . 
D 4 HOH A 133 433 433 HOH HOH . 
D 4 HOH A 134 434 434 HOH HOH . 
D 4 HOH A 135 435 435 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 44.489 64.483 -13.945 1 15.8 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . C 3 45.308 63.598 -13.037 1 15.18 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . C 3 43.406 63.737 -14.758 1 13.91 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . C 3 45.406 65.217 -14.902 1 17.76 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . C 3 43.671 65.584 -13.119 1 15.44 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . C 3 43.957 66.021 -11.599 1 16.57 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . C 3 43.608 64.94 -10.624 1 17.09 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . C 3 45.31 66.653 -11.437 1 18.01 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . C 3 42.81 67.126 -11.387 1 15.57 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . C 3 42.89 68.307 -12.198 1 17.99 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . C 3 42.282 69.479 -11.425 1 19.45 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . C 3 40.877 69.265 -11.309 1 17.59 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . C 3 42.846 69.623 -10.014 1 21.01 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . C 3 42.938 71.015 -9.657 1 19.85 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . C 3 41.793 68.983 -9.136 1 19.04 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . C 3 41.721 69.592 -7.841 1 21.01 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . C 3 40.54 69.3 -9.921 1 18.62 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . C 3 39.44 68.372 -9.616 1 19.94 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . C 3 39.495 67.007 -9.553 1 17.97 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . C 3 38.264 66.525 -9.262 1 16.67 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . C 3 37.407 67.582 -9.125 1 18.5 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . C 3 35.955 67.77 -8.84 1 19.36 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . C 3 35.181 66.794 -8.62 1 16.8 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . C 3 35.476 69.03 -8.827 1 18.2 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . C 3 36.274 70.111 -9.053 1 19.3 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . C 3 35.737 71.359 -9.01 1 20 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . C 3 37.593 70.019 -9.331 1 18.5 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . C 3 38.196 68.794 -9.376 1 18.54 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          18 
_model_server_stats.element_count           28 
#