data_8PFH
#
_model_server_result.job_id            saOt35dDyYh4n6oWs1eh2w 
_model_server_result.datetime_utc      '2024-10-20 00:46:25' 
_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          8pfh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    8PFH 
#
_exptl.entry_id    8PFH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.68 
_cell.angle_gamma         90 
_cell.entry_id            8PFH 
_cell.length_a            258.178 
_cell.length_b            69.373 
_cell.length_c            92.533 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PFH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,G,H 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 E N N 
? 5 F N N 
? 5 G N N 
? 5 H N 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                     8PFH 
_atom_sites.fract_transf_matrix[1][1]    0.003873 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001385 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014415 
_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]    0.011477 
_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
E 5 GDP A 1 401 401 GDP GDP . 
F 5 GDP B 1 501 501 GDP GDP . 
G 5 GDP C 1 401 401 GDP GDP . 
H 5 GDP D 1 401 401 GDP GDP . 
#
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 . . . H 5 6.895 -16.868 61.472 1 44.12 ? PB GDP 401 D 1 
HETATM 2 O O1B GDP . . . H 5 5.571 -17.472 61.05 1 46.35 ? O1B GDP 401 D 1 
HETATM 3 O O2B GDP . . . H 5 6.822 -16.193 62.827 1 42.85 -1 O2B GDP 401 D 1 
HETATM 4 O O3B GDP . . . H 5 8.047 -17.842 61.362 1 43.48 ? O3B GDP 401 D 1 
HETATM 5 O O3A GDP . . . H 5 7.195 -15.68 60.401 1 43.97 ? O3A GDP 401 D 1 
HETATM 6 P PA GDP . . . H 5 7.588 -15.377 58.88 1 44.56 ? PA GDP 401 D 1 
HETATM 7 O O1A GDP . . . H 5 7.002 -16.427 58.014 1 46.26 ? O1A GDP 401 D 1 
HETATM 8 O O2A GDP . . . H 5 9.038 -15.104 58.8 1 43.11 -1 O2A GDP 401 D 1 
HETATM 9 O O5' GDP . . . H 5 6.816 -14.003 58.638 1 45.02 ? O5' GDP 401 D 1 
HETATM 10 C C5' GDP . . . H 5 7.53 -12.761 58.796 1 43.64 ? C5' GDP 401 D 1 
HETATM 11 C C4' GDP . . . H 5 6.793 -11.647 58.094 1 44.52 ? C4' GDP 401 D 1 
HETATM 12 O O4' GDP . . . H 5 7.446 -10.393 58.377 1 43.27 ? O4' GDP 401 D 1 
HETATM 13 C C3' GDP . . . H 5 6.801 -11.73 56.575 1 45.68 ? C3' GDP 401 D 1 
HETATM 14 O O3' GDP . . . H 5 5.768 -10.912 56.034 1 46.9 ? O3' GDP 401 D 1 
HETATM 15 C C2' GDP . . . H 5 8.182 -11.164 56.244 1 44.43 ? C2' GDP 401 D 1 
HETATM 16 O O2' GDP . . . H 5 8.225 -10.588 54.942 1 45.2 ? O2' GDP 401 D 1 
HETATM 17 C C1' GDP . . . H 5 8.344 -10.082 57.323 1 43.26 ? C1' GDP 401 D 1 
HETATM 18 N N9 GDP . . . H 5 9.7 -9.979 57.89 1 41.93 ? N9 GDP 401 D 1 
HETATM 19 C C8 GDP . . . H 5 10.643 -10.965 58.032 1 41.47 ? C8 GDP 401 D 1 
HETATM 20 N N7 GDP . . . H 5 11.752 -10.542 58.595 1 40.56 ? N7 GDP 401 D 1 
HETATM 21 C C5 GDP . . . H 5 11.525 -9.197 58.836 1 40.41 ? C5 GDP 401 D 1 
HETATM 22 C C6 GDP . . . H 5 12.352 -8.197 59.436 1 39.88 ? C6 GDP 401 D 1 
HETATM 23 O O6 GDP . . . H 5 13.491 -8.339 59.88 1 39.5 ? O6 GDP 401 D 1 
HETATM 24 N N1 GDP . . . H 5 11.723 -6.967 59.49 1 40.07 ? N1 GDP 401 D 1 
HETATM 25 C C2 GDP . . . H 5 10.459 -6.706 59.032 1 40.69 ? C2 GDP 401 D 1 
HETATM 26 N N2 GDP . . . H 5 9.999 -5.446 59.165 1 40.88 ? N2 GDP 401 D 1 
HETATM 27 N N3 GDP . . . H 5 9.678 -7.629 58.47 1 41.34 ? N3 GDP 401 D 1 
HETATM 28 C C4 GDP . . . H 5 10.267 -8.837 58.405 1 41.16 ? C4 GDP 401 D 1 
HETATM 29 H H5' GDP . . . H 5 7.526 -12.553 59.753 1 38.13 ? H5' GDP 401 D 1 
HETATM 30 H "H5''" GDP . . . H 5 8.48 -12.811 58.568 1 38.13 ? "H5''" GDP 401 D 1 
HETATM 31 H H4' GDP . . . H 5 5.879 -11.583 58.439 1 38.44 ? H4' GDP 401 D 1 
HETATM 32 H H3' GDP . . . H 5 6.621 -12.626 56.223 1 39.12 ? H3' GDP 401 D 1 
HETATM 33 H HO3' GDP . . . H 5 5.885 -11.06 55.205 1 39.12 ? HO3' GDP 401 D 1 
HETATM 34 H H2' GDP . . . H 5 8.887 -11.841 56.293 1 39.15 ? H2' GDP 401 D 1 
HETATM 35 H HO2' GDP . . . H 5 9.062 -10.608 54.794 1 39.15 ? HO2' GDP 401 D 1 
HETATM 36 H H1' GDP . . . H 5 8.095 -9.199 56.982 1 38.77 ? H1' GDP 401 D 1 
HETATM 37 H H8 GDP . . . H 5 10.474 -11.882 57.733 1 38.54 ? H8 GDP 401 D 1 
HETATM 38 H HN1 GDP . . . H 5 12.203 -6.322 59.855 1 38.07 ? HN1 GDP 401 D 1 
HETATM 39 H HN21 GDP . . . H 5 9.2 -5.177 58.902 1 38.18 ? HN21 GDP 401 D 1 
HETATM 40 H HN22 GDP . . . H 5 10.55 -4.869 59.543 1 38.18 ? HN22 GDP 401 D 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           40 
#