data_3FFB
#
_model_server_result.job_id            IgCrAIZPsT4YmUkw9ove4g 
_model_server_result.datetime_utc      '2024-10-18 17:22:47' 
_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          3ffb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1}' 
#
_entry.id    3FFB 
#
_exptl.entry_id    3FFB 
_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         90 
_cell.entry_id            3FFB 
_cell.length_a            121.761 
_cell.length_b            121.761 
_cell.length_c            68.714 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3FFB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
_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 
_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 
#
_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                     3FFB 
_atom_sites.fract_transf_matrix[1][1]    0.008213 
_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]    0.008213 
_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]    0.014553 
_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 1 1 GDP GDP . 
C 3 SO4 A 1 355 47 SO4 SO4 . 
D 4 HOH A 1 2 2 HOH HOH . 
D 4 HOH A 2 3 3 HOH HOH . 
D 4 HOH A 3 4 4 HOH HOH . 
D 4 HOH A 4 5 5 HOH HOH . 
D 4 HOH A 5 356 1 HOH HOH . 
D 4 HOH A 6 357 6 HOH HOH . 
D 4 HOH A 7 358 7 HOH HOH . 
D 4 HOH A 8 359 8 HOH HOH . 
D 4 HOH A 9 360 9 HOH HOH . 
D 4 HOH A 10 361 10 HOH HOH . 
D 4 HOH A 11 362 11 HOH HOH . 
D 4 HOH A 12 363 12 HOH HOH . 
D 4 HOH A 13 364 13 HOH HOH . 
D 4 HOH A 14 365 14 HOH HOH . 
D 4 HOH A 15 366 15 HOH HOH . 
D 4 HOH A 16 367 16 HOH HOH . 
D 4 HOH A 17 368 17 HOH HOH . 
D 4 HOH A 18 369 18 HOH HOH . 
D 4 HOH A 19 370 19 HOH HOH . 
D 4 HOH A 20 371 20 HOH HOH . 
D 4 HOH A 21 372 21 HOH HOH . 
D 4 HOH A 22 373 22 HOH HOH . 
D 4 HOH A 23 374 23 HOH HOH . 
D 4 HOH A 24 375 24 HOH HOH . 
D 4 HOH A 25 376 25 HOH HOH . 
D 4 HOH A 26 377 26 HOH HOH . 
D 4 HOH A 27 378 27 HOH HOH . 
D 4 HOH A 28 379 28 HOH HOH . 
D 4 HOH A 29 380 29 HOH HOH . 
D 4 HOH A 30 381 30 HOH HOH . 
D 4 HOH A 31 382 31 HOH HOH . 
D 4 HOH A 32 383 32 HOH HOH . 
D 4 HOH A 33 384 33 HOH HOH . 
D 4 HOH A 34 385 34 HOH HOH . 
D 4 HOH A 35 386 35 HOH HOH . 
D 4 HOH A 36 387 36 HOH HOH . 
D 4 HOH A 37 388 37 HOH HOH . 
D 4 HOH A 38 389 38 HOH HOH . 
D 4 HOH A 39 390 39 HOH HOH . 
D 4 HOH A 40 391 41 HOH HOH . 
D 4 HOH A 41 392 42 HOH HOH . 
D 4 HOH A 42 393 43 HOH HOH . 
D 4 HOH A 43 394 44 HOH HOH . 
D 4 HOH A 44 395 45 HOH HOH . 
D 4 HOH A 45 396 46 HOH HOH . 
D 4 HOH A 46 397 50 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 -38.779 21.506 -1.829 1 28.55 ? PB GDP 1 A 1 
HETATM 2 O O1B GDP . . . B 2 -39.071 21.12 -3.259 1 28.32 ? O1B GDP 1 A 1 
HETATM 3 O O2B GDP . . . B 2 -37.817 20.537 -1.199 1 27.37 ? O2B GDP 1 A 1 
HETATM 4 O O3B GDP . . . B 2 -38.23 22.911 -1.768 1 29.35 ? O3B GDP 1 A 1 
HETATM 5 O O3A GDP . . . B 2 -40.178 21.373 -1.049 1 29.25 ? O3A GDP 1 A 1 
HETATM 6 P PA GDP . . . B 2 -41.022 22.552 -0.359 1 29.19 ? PA GDP 1 A 1 
HETATM 7 O O1A GDP . . . B 2 -41.628 23.496 -1.366 1 29.84 ? O1A GDP 1 A 1 
HETATM 8 O O2A GDP . . . B 2 -40.287 23.289 0.739 1 29.62 ? O2A GDP 1 A 1 
HETATM 9 O O5' GDP . . . B 2 -42.174 21.638 0.275 1 30.41 ? O5' GDP 1 A 1 
HETATM 10 C C5' GDP . . . B 2 -43.108 20.977 -0.578 1 29.39 ? C5' GDP 1 A 1 
HETATM 11 C C4' GDP . . . B 2 -44.54 21.082 -0.056 1 27.98 ? C4' GDP 1 A 1 
HETATM 12 O O4' GDP . . . B 2 -44.724 20.378 1.178 1 27.58 ? O4' GDP 1 A 1 
HETATM 13 C C3' GDP . . . B 2 -44.987 22.489 0.239 1 28.36 ? C3' GDP 1 A 1 
HETATM 14 O O3' GDP . . . B 2 -46.381 22.431 -0.042 1 30.01 ? O3' GDP 1 A 1 
HETATM 15 C C2' GDP . . . B 2 -44.787 22.649 1.739 1 27.28 ? C2' GDP 1 A 1 
HETATM 16 O O2' GDP . . . B 2 -45.727 23.539 2.33 1 24.46 ? O2' GDP 1 A 1 
HETATM 17 C C1' GDP . . . B 2 -45.061 21.257 2.259 1 26.67 ? C1' GDP 1 A 1 
HETATM 18 N N9 GDP . . . B 2 -44.273 20.851 3.455 1 27.15 ? N9 GDP 1 A 1 
HETATM 19 C C8 GDP . . . B 2 -42.933 20.949 3.647 1 26.84 ? C8 GDP 1 A 1 
HETATM 20 N N7 GDP . . . B 2 -42.574 20.435 4.865 1 26.29 ? N7 GDP 1 A 1 
HETATM 21 C C5 GDP . . . B 2 -43.705 19.988 5.465 1 25.84 ? C5 GDP 1 A 1 
HETATM 22 C C6 GDP . . . B 2 -44.061 19.31 6.734 1 26.64 ? C6 GDP 1 A 1 
HETATM 23 O O6 GDP . . . B 2 -43.19 19.038 7.596 1 26.74 ? O6 GDP 1 A 1 
HETATM 24 N N1 GDP . . . B 2 -45.357 19.016 6.952 1 27.47 ? N1 GDP 1 A 1 
HETATM 25 C C2 GDP . . . B 2 -46.339 19.306 6.068 1 26.55 ? C2 GDP 1 A 1 
HETATM 26 N N2 GDP . . . B 2 -47.626 18.982 6.366 1 25.69 ? N2 GDP 1 A 1 
HETATM 27 N N3 GDP . . . B 2 -46.068 19.913 4.885 1 26.4 ? N3 GDP 1 A 1 
HETATM 28 C C4 GDP . . . B 2 -44.812 20.268 4.537 1 26.36 ? C4 GDP 1 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#