data_3QE0
#
_model_server_result.job_id            AAuq3DrNriWLS4E9LzEPVw 
_model_server_result.datetime_utc      '2025-07-16 17:38:36' 
_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          3qe0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":551}' 
#
_entry.id    3QE0 
#
_exptl.entry_id    3QE0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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         120 
_cell.entry_id            3QE0 
_cell.length_a            106.637 
_cell.length_b            106.637 
_cell.length_c            455.062 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QE0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,L 1 1 
B,D,H,I,M 2 1 
C,J,K,N 3 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
? 4 G N N 
? 4 I N N 
? 4 K N 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 18 A SER 47 1_555 F MG MG . A MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? 
metalc ? metalc2 A OG1 THR 152 A THR 181 1_555 F MG MG . A MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? 
metalc ? metalc3 G O1B GDP . A GDP 555 1_555 F MG MG . A MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? 
metalc ? metalc4 B OG SER 18 B SER 47 1_555 H MG MG . B MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? 
metalc ? metalc5 I O1B GDP . B GDP 355 1_555 H MG MG . B MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? 
metalc ? metalc6 I O2B GDP . B GDP 355 1_555 H MG MG . B MG 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? 
metalc ? metalc7 C OG SER 18 C SER 47 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc8 C OG1 THR 152 C THR 181 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc9 K O1B GDP . C GDP 551 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? 
metalc ? metalc10 K O2B GDP . C GDP 551 1_555 J MG MG . C MG 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
#
_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                     3QE0 
_atom_sites.fract_transf_matrix[1][1]    0.009378 
_atom_sites.fract_transf_matrix[1][2]    0.005414 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010828 
_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]    0.002198 
_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
F 3 MG A 1 556 556 MG MG . 
G 4 GDP A 1 555 555 GDP GDP . 
H 3 MG B 1 556 556 MG MG . 
I 4 GDP B 1 355 355 GDP GDP . 
J 3 MG C 1 552 552 MG MG . 
K 4 GDP C 1 551 551 GDP GDP . 
L 5 HOH A 1 1 1 HOH HOH . 
L 5 HOH A 2 2 2 HOH HOH . 
L 5 HOH A 3 6 6 HOH HOH . 
L 5 HOH A 4 7 7 HOH HOH . 
L 5 HOH A 5 8 8 HOH HOH . 
L 5 HOH A 6 9 9 HOH HOH . 
L 5 HOH A 7 11 11 HOH HOH . 
M 5 HOH B 1 3 3 HOH HOH . 
M 5 HOH B 2 4 4 HOH HOH . 
M 5 HOH B 3 10 10 HOH HOH . 
M 5 HOH B 4 12 12 HOH HOH . 
N 5 HOH C 1 5 5 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 . . . K 4 82.766 -27.476 14.85 1 90.31 ? PB GDP 551 C 1 
HETATM 2 O O1B GDP . . . K 4 82.334 -27.968 13.488 1 88.9 ? O1B GDP 551 C 1 
HETATM 3 O O2B GDP . . . K 4 83.303 -26.065 14.771 1 86.66 ? O2B GDP 551 C 1 
HETATM 4 O O3B GDP . . . K 4 83.873 -28.372 15.355 1 61.16 ? O3B GDP 551 C 1 
HETATM 5 O O3A GDP . . . K 4 81.514 -27.524 15.873 1 29.92 ? O3A GDP 551 C 1 
HETATM 6 P PA GDP . . . K 4 80.026 -27.175 15.353 1 89.67 ? PA GDP 551 C 1 
HETATM 7 O O1A GDP . . . K 4 79.936 -27.255 13.846 1 71.72 ? O1A GDP 551 C 1 
HETATM 8 O O2A GDP . . . K 4 79.658 -25.798 15.85 1 19.65 ? O2A GDP 551 C 1 
HETATM 9 O O5' GDP . . . K 4 79.048 -28.248 16.052 1 20.65 ? O5' GDP 551 C 1 
HETATM 10 C C5' GDP . . . K 4 78.462 -29.277 15.255 1 66.97 ? C5' GDP 551 C 1 
HETATM 11 C C4' GDP . . . K 4 77.102 -29.627 15.833 1 71.32 ? C4' GDP 551 C 1 
HETATM 12 O O4' GDP . . . K 4 77.239 -30.044 17.193 1 69.75 ? O4' GDP 551 C 1 
HETATM 13 C C3' GDP . . . K 4 76.228 -28.389 15.837 1 41.27 ? C3' GDP 551 C 1 
HETATM 14 O O3' GDP . . . K 4 74.963 -28.705 15.244 1 67.64 ? O3' GDP 551 C 1 
HETATM 15 C C2' GDP . . . K 4 76.04 -28.039 17.298 1 25.03 ? C2' GDP 551 C 1 
HETATM 16 O O2' GDP . . . K 4 74.715 -27.557 17.549 1 49.32 ? O2' GDP 551 C 1 
HETATM 17 C C1' GDP . . . K 4 76.278 -29.36 18.004 1 52.16 ? C1' GDP 551 C 1 
HETATM 18 N N9 GDP . . . K 4 76.78 -29.137 19.383 1 57.26 ? N9 GDP 551 C 1 
HETATM 19 C C8 GDP . . . K 4 77.9 -28.47 19.722 1 63.87 ? C8 GDP 551 C 1 
HETATM 20 N N7 GDP . . . K 4 78.068 -28.46 21.07 1 67.38 ? N7 GDP 551 C 1 
HETATM 21 C C5 GDP . . . K 4 77.039 -29.139 21.613 1 78.22 ? C5 GDP 551 C 1 
HETATM 22 C C6 GDP . . . K 4 76.61 -29.507 22.983 1 64.62 ? C6 GDP 551 C 1 
HETATM 23 O O6 GDP . . . K 4 77.277 -29.163 23.983 1 55.85 ? O6 GDP 551 C 1 
HETATM 24 N N1 GDP . . . K 4 75.483 -30.22 23.116 1 40.83 ? N1 GDP 551 C 1 
HETATM 25 C C2 GDP . . . K 4 74.738 -30.603 22.057 1 73.39 ? C2 GDP 551 C 1 
HETATM 26 N N2 GDP . . . K 4 73.608 -31.32 22.292 1 27.71 ? N2 GDP 551 C 1 
HETATM 27 N N3 GDP . . . K 4 75.073 -30.303 20.77 1 36.59 ? N3 GDP 551 C 1 
HETATM 28 C C4 GDP . . . K 4 76.192 -29.586 20.497 1 43.7 ? C4 GDP 551 C 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           261 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#