data_3U2Q
#
_model_server_result.job_id            ID8onmfgee28_n8_ExD8hA 
_model_server_result.datetime_utc      '2025-02-05 10:56:51' 
_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          3u2q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    3U2Q 
#
_exptl.entry_id    3U2Q 
_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            3U2Q 
_cell.length_a            83.303 
_cell.length_b            132.473 
_cell.length_c            37.433 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3U2Q 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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                      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
covale ? covale1 B C SER 1 B SER 1 1_555 B N BB9 2 B BB9 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 sing 
covale ? covale2 B C SER 1 B SER 1 1_555 B SG BB9 2 B BB9 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.717 sing 
covale ? covale3 B CA SER 1 B SER 1 1_555 B C BB9 10 B BB9 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 sing 
covale ? covale4 B CB SER 1 B SER 1 1_555 B CB MH6 11 B MH6 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 sing 
covale ? covale5 B C BB9 2 B BB9 2 1_555 B N MEN 3 B MEN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 sing 
covale ? covale6 B C MEN 3 B MEN 3 1_555 B SG BB6 4 B BB6 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 sing 
covale ? covale7 B C MEN 3 B MEN 3 1_555 B N BB6 4 B BB6 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 sing 
covale ? covale8 B C BB6 4 B BB6 4 1_555 B N VAL 5 B VAL 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 sing 
covale ? covale9 B C VAL 5 B VAL 5 1_555 B SG BB7 6 B BB7 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.786 sing 
covale ? covale10 B C VAL 5 B VAL 5 1_555 B N BB7 6 B BB7 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 sing 
covale ? covale11 B C BB7 6 B BB7 6 1_555 B N GLY 7 B GLY 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 sing 
covale ? covale12 B C GLY 7 B GLY 7 1_555 B N BB8 8 B BB8 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 sing 
covale ? covale13 B C BB8 8 B BB8 8 1_555 B N BB9 9 B BB9 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 sing 
covale ? covale14 B C BB8 8 B BB8 8 1_555 B SG BB9 9 B BB9 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.781 sing 
covale ? covale15 B C BB9 9 B BB9 9 1_555 B N BB9 10 B BB9 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 sing 
covale ? covale16 B C BB9 9 B BB9 9 1_555 B SG BB9 10 B BB9 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.738 sing 
covale ? covale17 B C BB9 10 B BB9 10 1_555 B N MH6 11 B MH6 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 sing 
covale ? covale18 B C MH6 11 B MH6 11 1_555 B SG 7BB 12 B 7BB 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 sing 
covale ? covale19 B C MH6 11 B MH6 11 1_555 B N 7BB 12 B 7BB 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 sing 
metalc ? metalc1 A OG1 THR 26 A THR 25 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc2 E O HOH . A HOH 405 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc3 E O HOH . A HOH 433 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc4 C O2B GDP . A GDP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc5 C O2A GDP . A GDP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? 
metalc ? metalc6 C O1B GDP . A GDP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
#
_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 198 n n 
PB O2B GDP sing 199 n n 
PB O3B GDP sing 200 n n 
PB O3A GDP sing 201 n n 
O2B HOB2 GDP sing 202 n n 
O3B HOB3 GDP sing 203 n n 
O3A PA GDP sing 204 n n 
PA O1A GDP doub 205 n n 
PA O2A GDP sing 206 n n 
PA O5' GDP sing 207 n n 
O2A HOA2 GDP sing 208 n n 
O5' C5' GDP sing 209 n n 
C5' C4' GDP sing 210 n n 
C5' H5' GDP sing 211 n n 
C5' "H5''" GDP sing 212 n n 
C4' O4' GDP sing 213 n n 
C4' C3' GDP sing 214 n n 
C4' H4' GDP sing 215 n n 
O4' C1' GDP sing 216 n n 
C3' O3' GDP sing 217 n n 
C3' C2' GDP sing 218 n n 
C3' H3' GDP sing 219 n n 
O3' HO3' GDP sing 220 n n 
C2' O2' GDP sing 221 n n 
C2' C1' GDP sing 222 n n 
C2' H2' GDP sing 223 n n 
O2' HO2' GDP sing 224 n n 
C1' N9 GDP sing 225 n n 
C1' H1' GDP sing 226 n n 
N9 C8 GDP sing 227 n y 
N9 C4 GDP sing 228 n y 
C8 N7 GDP doub 229 n y 
C8 H8 GDP sing 230 n n 
N7 C5 GDP sing 231 n y 
C5 C6 GDP sing 232 n n 
C5 C4 GDP doub 233 n y 
C6 O6 GDP doub 234 n n 
C6 N1 GDP sing 235 n n 
N1 C2 GDP sing 236 n n 
N1 HN1 GDP sing 237 n n 
C2 N2 GDP sing 238 n n 
C2 N3 GDP doub 239 n n 
N2 HN21 GDP sing 240 n n 
N2 HN22 GDP sing 241 n n 
N3 C4 GDP sing 242 n n 
#
_atom_sites.entry_id                     3U2Q 
_atom_sites.fract_transf_matrix[1][1]    0.012004 
_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]    0.007549 
_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]    0.026714 
_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
C 3 GDP A 1 501 501 GDP GDP . 
D 4 MG A 1 503 503 MG MG . 
E 5 HOH A 1 394 4 HOH HOH . 
E 5 HOH A 2 395 5 HOH HOH . 
E 5 HOH A 3 396 6 HOH HOH . 
E 5 HOH A 4 397 7 HOH HOH . 
E 5 HOH A 5 398 8 HOH HOH . 
E 5 HOH A 6 399 9 HOH HOH . 
E 5 HOH A 7 400 10 HOH HOH . 
E 5 HOH A 8 401 11 HOH HOH . 
E 5 HOH A 9 402 12 HOH HOH . 
E 5 HOH A 10 403 13 HOH HOH . 
E 5 HOH A 11 404 14 HOH HOH . 
E 5 HOH A 12 405 15 HOH HOH . 
E 5 HOH A 13 406 16 HOH HOH . 
E 5 HOH A 14 407 17 HOH HOH . 
E 5 HOH A 15 408 19 HOH HOH . 
E 5 HOH A 16 409 20 HOH HOH . 
E 5 HOH A 17 410 21 HOH HOH . 
E 5 HOH A 18 411 22 HOH HOH . 
E 5 HOH A 19 412 23 HOH HOH . 
E 5 HOH A 20 413 24 HOH HOH . 
E 5 HOH A 21 414 25 HOH HOH . 
E 5 HOH A 22 415 29 HOH HOH . 
E 5 HOH A 23 416 31 HOH HOH . 
E 5 HOH A 24 417 33 HOH HOH . 
E 5 HOH A 25 418 34 HOH HOH . 
E 5 HOH A 26 419 35 HOH HOH . 
E 5 HOH A 27 420 36 HOH HOH . 
E 5 HOH A 28 421 37 HOH HOH . 
E 5 HOH A 29 422 38 HOH HOH . 
E 5 HOH A 30 423 39 HOH HOH . 
E 5 HOH A 31 424 40 HOH HOH . 
E 5 HOH A 32 425 41 HOH HOH . 
E 5 HOH A 33 426 42 HOH HOH . 
E 5 HOH A 34 427 43 HOH HOH . 
E 5 HOH A 35 428 44 HOH HOH . 
E 5 HOH A 36 429 45 HOH HOH . 
E 5 HOH A 37 430 46 HOH HOH . 
E 5 HOH A 38 431 47 HOH HOH . 
E 5 HOH A 39 432 48 HOH HOH . 
E 5 HOH A 40 433 50 HOH HOH . 
E 5 HOH A 41 434 51 HOH HOH . 
E 5 HOH A 42 435 52 HOH HOH . 
E 5 HOH A 43 436 53 HOH HOH . 
E 5 HOH A 44 437 55 HOH HOH . 
E 5 HOH A 45 438 56 HOH HOH . 
E 5 HOH A 46 439 57 HOH HOH . 
E 5 HOH A 47 440 58 HOH HOH . 
E 5 HOH A 48 441 59 HOH HOH . 
E 5 HOH A 49 442 60 HOH HOH . 
E 5 HOH A 50 443 61 HOH HOH . 
E 5 HOH A 51 444 63 HOH HOH . 
E 5 HOH A 52 445 64 HOH HOH . 
E 5 HOH A 53 446 65 HOH HOH . 
E 5 HOH A 54 447 66 HOH HOH . 
E 5 HOH A 55 448 67 HOH HOH . 
E 5 HOH A 56 449 70 HOH HOH . 
E 5 HOH A 57 450 71 HOH HOH . 
E 5 HOH A 58 451 74 HOH HOH . 
E 5 HOH A 59 452 76 HOH HOH . 
E 5 HOH A 60 453 77 HOH HOH . 
E 5 HOH A 61 454 78 HOH HOH . 
E 5 HOH A 62 455 79 HOH HOH . 
E 5 HOH A 63 456 80 HOH HOH . 
E 5 HOH A 64 457 82 HOH HOH . 
E 5 HOH A 65 458 83 HOH HOH . 
E 5 HOH A 66 459 84 HOH HOH . 
E 5 HOH A 67 460 85 HOH HOH . 
E 5 HOH A 68 461 86 HOH HOH . 
E 5 HOH A 69 462 88 HOH HOH . 
E 5 HOH A 70 463 89 HOH HOH . 
E 5 HOH A 71 464 91 HOH HOH . 
E 5 HOH A 72 465 92 HOH HOH . 
E 5 HOH A 73 466 93 HOH HOH . 
E 5 HOH A 74 467 94 HOH HOH . 
E 5 HOH A 75 468 95 HOH HOH . 
E 5 HOH A 76 469 97 HOH HOH . 
E 5 HOH A 77 470 98 HOH HOH . 
E 5 HOH A 78 471 106 HOH HOH . 
E 5 HOH A 79 472 107 HOH HOH . 
E 5 HOH A 80 473 110 HOH HOH . 
E 5 HOH A 81 474 111 HOH HOH . 
E 5 HOH A 82 475 112 HOH HOH . 
F 5 HOH B 1 13 1 HOH HOH . 
F 5 HOH B 2 14 2 HOH HOH . 
F 5 HOH B 3 15 3 HOH HOH . 
F 5 HOH B 4 18 18 HOH HOH . 
F 5 HOH B 5 54 54 HOH HOH . 
F 5 HOH B 6 81 81 HOH HOH . 
F 5 HOH B 7 87 87 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 14.628 1.092 -27.97 1 92.17 ? PB GDP 501 A 1 
HETATM 2 O O1B GDP . . . C 3 14.269 -0.216 -28.72 1 92.48 ? O1B GDP 501 A 1 
HETATM 3 O O2B GDP . . . C 3 16.136 1.083 -27.635 1 92.97 ? O2B GDP 501 A 1 
HETATM 4 O O3B GDP . . . C 3 13.804 1.233 -26.722 1 92.36 ? O3B GDP 501 A 1 
HETATM 5 O O3A GDP . . . C 3 14.389 2.24 -29.021 1 91.24 ? O3A GDP 501 A 1 
HETATM 6 P PA GDP . . . C 3 15.259 3.225 -29.892 1 90.1 ? PA GDP 501 A 1 
HETATM 7 O O1A GDP . . . C 3 16.21 4.046 -29.079 1 90.65 ? O1A GDP 501 A 1 
HETATM 8 O O2A GDP . . . C 3 15.986 2.348 -30.948 1 88.96 ? O2A GDP 501 A 1 
HETATM 9 O O5' GDP . . . C 3 14.302 4.125 -30.739 1 90.8 ? O5' GDP 501 A 1 
HETATM 10 C C5' GDP . . . C 3 13.133 4.738 -30.095 1 91.18 ? C5' GDP 501 A 1 
HETATM 11 C C4' GDP . . . C 3 12.299 5.598 -31.078 1 91.14 ? C4' GDP 501 A 1 
HETATM 12 O O4' GDP . . . C 3 11.787 6.746 -30.39 1 91.5 ? O4' GDP 501 A 1 
HETATM 13 C C3' GDP . . . C 3 13.093 6.12 -32.305 1 91.28 ? C3' GDP 501 A 1 
HETATM 14 O O3' GDP . . . C 3 12.282 6.085 -33.489 1 91.16 ? O3' GDP 501 A 1 
HETATM 15 C C2' GDP . . . C 3 13.461 7.537 -31.923 1 91.97 ? C2' GDP 501 A 1 
HETATM 16 O O2' GDP . . . C 3 13.439 8.462 -33.024 1 92.64 ? O2' GDP 501 A 1 
HETATM 17 C C1' GDP . . . C 3 12.447 7.919 -30.864 1 92.34 ? C1' GDP 501 A 1 
HETATM 18 N N9 GDP . . . C 3 13.249 8.688 -29.886 1 93.04 ? N9 GDP 501 A 1 
HETATM 19 C C8 GDP . . . C 3 13.865 8.245 -28.677 1 93.37 ? C8 GDP 501 A 1 
HETATM 20 N N7 GDP . . . C 3 13.601 8.956 -27.565 1 93.62 ? N7 GDP 501 A 1 
HETATM 21 C C5 GDP . . . C 3 12.686 9.998 -28.052 1 93.67 ? C5 GDP 501 A 1 
HETATM 22 C C6 GDP . . . C 3 11.993 11.127 -27.365 1 93.58 ? C6 GDP 501 A 1 
HETATM 23 O O6 GDP . . . C 3 12.188 11.311 -26.176 1 93.18 ? O6 GDP 501 A 1 
HETATM 24 N N1 GDP . . . C 3 11.158 11.909 -28.127 1 93.61 ? N1 GDP 501 A 1 
HETATM 25 C C2 GDP . . . C 3 10.928 11.727 -29.472 1 93.93 ? C2 GDP 501 A 1 
HETATM 26 N N2 GDP . . . C 3 10.103 12.53 -30.123 1 94.42 ? N2 GDP 501 A 1 
HETATM 27 N N3 GDP . . . C 3 11.567 10.707 -30.134 1 94.04 ? N3 GDP 501 A 1 
HETATM 28 C C4 GDP . . . C 3 12.484 9.823 -29.371 1 93.61 ? C4 GDP 501 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#