data_6B0I
#
_model_server_result.job_id            js_3ddDFGgf8Ys-tmLFjVA 
_model_server_result.datetime_utc      '2025-07-07 17:25:07' 
_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          6b0i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":501}' 
#
_entry.id    6B0I 
#
_exptl.entry_id    6B0I 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          6 
_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                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? 105-meric 105 'representative helical assembly' 1 
? trimeric 3 'helical asymmetric unit' 2 
? trimeric 3 'helical asymmetric unit, std helical frame' 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G 1 (1-35) 
A,B,C,D,E,F,G 2 27 
A,B,C,D,E,F,G 3 H 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
1 'helical symmetry operation' ? ? 0.923284 -0.384118 0 0.384118 0.923284 0 0 0 1 126.58559 -84.43966 -93.5 
2 'helical symmetry operation' ? ? 0.999764 0.021728 0 -0.021728 0.999764 0 0 0 1 -5.90348 6.03317 -82.5 
3 'helical symmetry operation' ? ? 0.905724 0.423867 0 -0.423867 0.905724 0 0 0 1 -90.53489 142.32774 -71.5 
4 'helical symmetry operation' ? ? 0.657204 0.753713 0 -0.753713 0.657204 0 0 0 1 -112.87391 301.19766 -60.5 
5 'helical symmetry operation' ? ? 0.296592 0.955004 0 -0.955004 0.296592 0 0 0 1 -69.1104 455.54611 -49.5 
6 'helical symmetry operation' ? ? -0.114608 0.993411 0 -0.993411 -0.114608 0 0 0 1 33.29133 579.0474 -38.5 
7 'helical symmetry operation' ? ? -0.50626 0.862381 0 -0.862381 -0.50626 0 0 0 1 176.86567 650.63718 -27.5 
8 'helical symmetry operation' ? ? -0.811564 0.584264 0 -0.584264 -0.811564 0 0 0 1 337.12457 658.1051 -16.5 
9 'helical symmetry operation' ? ? -0.978448 0.206495 0 -0.206495 -0.978448 0 0 0 1 486.7343 600.17742 -5.5 
10 'helical symmetry operation' ? ? -0.978448 -0.206495 0 0.206495 -0.978448 0 0 0 1 600.17742 486.7343 5.5 
11 'helical symmetry operation' ? ? -0.811564 -0.584264 0 0.584264 -0.811564 0 0 0 1 658.1051 337.12457 16.5 
12 'helical symmetry operation' ? ? -0.50626 -0.862381 0 0.862381 -0.50626 0 0 0 1 650.63718 176.86567 27.5 
13 'helical symmetry operation' ? ? -0.114608 -0.993411 0 0.993411 -0.114608 0 0 0 1 579.0474 33.29133 38.5 
14 'helical symmetry operation' ? ? 0.296592 -0.955004 0 0.955004 0.296592 0 0 0 1 455.54611 -69.1104 49.5 
15 'helical symmetry operation' ? ? 0.657204 -0.753713 0 0.753713 0.657204 0 0 0 1 301.19766 -112.87391 60.5 
16 'helical symmetry operation' ? ? 0.905724 -0.423867 0 0.423867 0.905724 0 0 0 1 142.32774 -90.53489 71.5 
17 'helical symmetry operation' ? ? 0.999764 -0.021728 0 0.021728 0.999764 0 0 0 1 6.03317 -5.90348 82.5 
18 'helical symmetry operation' ? ? 0.923284 0.384118 0 -0.384118 0.923284 0 0 0 1 -84.43966 126.58559 93.5 
19 'helical symmetry operation' ? ? -0.982703 0.185186 0 -0.185186 -0.982703 0 0 0 1 493.75635 595.49332 -88 
20 'helical symmetry operation' ? ? -0.97373 -0.227705 0 0.227705 -0.97373 0 0 0 1 604.70785 479.61212 -77 
21 'helical symmetry operation' ? ? -0.798678 -0.601759 0 0.601759 -0.798678 0 0 0 1 659.37118 328.77908 -66 
22 'helical symmetry operation' ? ? -0.487403 -0.873177 0 0.873177 -0.487403 0 0 0 1 648.42298 168.72027 -55 
23 'helical symmetry operation' ? ? -0.092996 -0.995666 0 0.995666 -0.092996 0 0 0 1 573.73057 26.73531 -44 
24 'helical symmetry operation' ? ? 0.317272 -0.948335 0 0.948335 0.317272 0 0 0 1 448.03348 -72.95886 -33 
25 'helical symmetry operation' ? ? 0.673425 -0.739255 0 0.739255 0.673425 0 0 0 1 292.7706 -113.35841 -22 
26 'helical symmetry operation' ? ? 0.91472 -0.404088 0 0.404088 0.91472 0 0 0 1 134.42355 -87.57279 -11 
27 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
28 'helical symmetry operation' ? ? 0.91472 0.404088 0 -0.404088 0.91472 0 0 0 1 -87.57279 134.42355 11 
29 'helical symmetry operation' ? ? 0.673425 0.739255 0 -0.739255 0.673425 0 0 0 1 -113.35841 292.7706 22 
30 'helical symmetry operation' ? ? 0.317272 0.948335 0 -0.948335 0.317272 0 0 0 1 -72.95886 448.03348 33 
31 'helical symmetry operation' ? ? -0.092996 0.995666 0 -0.995666 -0.092996 0 0 0 1 26.73531 573.73057 44 
32 'helical symmetry operation' ? ? -0.487403 0.873177 0 -0.873177 -0.487403 0 0 0 1 168.72027 648.42298 55 
33 'helical symmetry operation' ? ? -0.798678 0.601759 0 -0.601759 -0.798678 0 0 0 1 328.77908 659.37118 66 
34 'helical symmetry operation' ? ? -0.97373 0.227705 0 -0.227705 -0.97373 0 0 0 1 479.61212 604.70785 77 
35 'helical symmetry operation' ? ? -0.982703 -0.185186 0 0.185186 -0.982703 0 0 0 1 595.49332 493.75635 88 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             F 
_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 D O2G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
#
_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                     6B0I 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
D 4 GTP A 1 501 501 GTP GTP . 
E 5 MG A 1 502 502 MG MG . 
F 6 GDP B 1 501 501 GDP GDP . 
G 7 TA1 B 1 502 502 TA1 TA1 . 
#
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 . . . F 6 162.13 216.315 302.817 1 24.07 ? PB GDP 501 B 1 
HETATM 2 O O1B GDP . . . F 6 161.614 216.359 301.398 1 24.48 ? O1B GDP 501 B 1 
HETATM 3 O O2B GDP . . . F 6 163.01 217.48 303.146 1 24.05 ? O2B GDP 501 B 1 
HETATM 4 O O3B GDP . . . F 6 160.949 216.125 303.752 1 22.73 ? O3B GDP 501 B 1 
HETATM 5 O O3A GDP . . . F 6 162.898 214.902 302.935 1 23.77 ? O3A GDP 501 B 1 
HETATM 6 P PA GDP . . . F 6 164.177 214.411 302.081 1 24.19 ? PA GDP 501 B 1 
HETATM 7 O O1A GDP . . . F 6 164.343 215.178 300.8 1 25.64 ? O1A GDP 501 B 1 
HETATM 8 O O2A GDP . . . F 6 165.442 214.546 302.901 1 25.05 ? O2A GDP 501 B 1 
HETATM 9 O O5' GDP . . . F 6 163.667 212.94 301.848 1 24.37 ? O5' GDP 501 B 1 
HETATM 10 C C5' GDP . . . F 6 164.388 211.753 302.207 1 22.94 ? C5' GDP 501 B 1 
HETATM 11 C C4' GDP . . . F 6 164.678 210.994 300.912 1 22.74 ? C4' GDP 501 B 1 
HETATM 12 O O4' GDP . . . F 6 165.538 211.789 300.099 1 22.76 ? O4' GDP 501 B 1 
HETATM 13 C C3' GDP . . . F 6 165.448 209.726 301.226 1 25.17 ? C3' GDP 501 B 1 
HETATM 14 O O3' GDP . . . F 6 165.099 208.716 300.285 1 29.23 ? O3' GDP 501 B 1 
HETATM 15 C C2' GDP . . . F 6 166.905 210.132 301.143 1 28.88 ? C2' GDP 501 B 1 
HETATM 16 O O2' GDP . . . F 6 167.778 209.048 300.819 1 26.96 ? O2' GDP 501 B 1 
HETATM 17 C C1' GDP . . . F 6 166.85 211.15 300.032 1 23.02 ? C1' GDP 501 B 1 
HETATM 18 N N9 GDP . . . F 6 167.78 212.261 300.085 1 27.46 ? N9 GDP 501 B 1 
HETATM 19 C C8 GDP . . . F 6 167.857 213.248 301.007 1 29.95 ? C8 GDP 501 B 1 
HETATM 20 N N7 GDP . . . F 6 168.812 214.144 300.632 1 25.68 ? N7 GDP 501 B 1 
HETATM 21 C C5 GDP . . . F 6 169.29 213.724 299.442 1 29.92 ? C5 GDP 501 B 1 
HETATM 22 C C6 GDP . . . F 6 170.293 214.196 298.484 1 30.94 ? C6 GDP 501 B 1 
HETATM 23 O O6 GDP . . . F 6 170.908 215.247 298.726 1 30.62 ? O6 GDP 501 B 1 
HETATM 24 N N1 GDP . . . F 6 170.508 213.475 297.384 1 30.82 ? N1 GDP 501 B 1 
HETATM 25 C C2 GDP . . . F 6 169.852 212.338 297.113 1 31.52 ? C2 GDP 501 B 1 
HETATM 26 N N2 GDP . . . F 6 170.125 211.685 295.957 1 31.05 ? N2 GDP 501 B 1 
HETATM 27 N N3 GDP . . . F 6 168.907 211.836 297.934 1 26.49 ? N3 GDP 501 B 1 
HETATM 28 C C4 GDP . . . F 6 168.61 212.495 299.089 1 25.97 ? C4 GDP 501 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           342 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#