data_5SYF
#
_model_server_result.job_id            WS1r89-IOVYuRwAYQLK_tQ 
_model_server_result.datetime_utc      '2025-07-03 20:44:00' 
_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          5syf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":501}' 
#
_entry.id    5SYF 
#
_exptl.entry_id    5SYF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    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
? 130-meric 130 'representative helical assembly' 1 
? pentameric 5 'helical asymmetric unit' 2 
? pentameric 5 '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 1 (1-26) 
A,B,C,D,E,F 2 14 
A,B,C,D,E,F 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 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 -56.88 
3 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 24.62 
4 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 -47.4 
5 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 34.1 
6 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 -37.92 
7 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 43.58 
8 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 -28.44 
9 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 53.06 
10 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 -18.96 
11 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 62.54 
12 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 -9.48 
13 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 72.02 
14 'helical symmetry operation' ? ? 1 0 0 0 1 0 0 0 1 0 0 81.5 
15 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 9.48 
16 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 90.98 
17 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 18.96 
18 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 100.46 
19 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 28.44 
20 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 109.94 
21 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 37.92 
22 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 119.42 
23 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 47.4 
24 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 128.9 
25 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 56.88 
26 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 138.38 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_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 A OE2 GLU 71 A GLU 71 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc2 C O3G GTP . A GTP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc3 C O1B GTP . A GTP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? 
#
_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                     5SYF 
_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
C 3 GTP A 1 501 1 GTP GTP . 
D 4 MG A 1 502 2 MG MG . 
E 5 GDP B 1 501 1 GDP GDP . 
F 6 TA1 B 1 502 1 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 . . . E 5 320.96 448.853 308.012 1 60.91 ? PB GDP 501 B 1 
HETATM 2 O O1B GDP . . . E 5 320.256 449.824 307.091 1 60.62 ? O1B GDP 501 B 1 
HETATM 3 O O2B GDP . . . E 5 320.922 447.397 307.609 1 59.88 ? O2B GDP 501 B 1 
HETATM 4 O O3B GDP . . . E 5 320.622 449.126 309.46 1 61.45 ? O3B GDP 501 B 1 
HETATM 5 O O3A GDP . . . E 5 322.508 449.269 307.86 1 58.35 ? O3A GDP 501 B 1 
HETATM 6 P PA GDP . . . E 5 323.692 448.599 308.726 1 56.53 ? PA GDP 501 B 1 
HETATM 7 O O1A GDP . . . E 5 324.384 447.624 307.801 1 55.85 ? O1A GDP 501 B 1 
HETATM 8 O O2A GDP . . . E 5 323.12 447.985 309.983 1 55.2 ? O2A GDP 501 B 1 
HETATM 9 O O5' GDP . . . E 5 324.658 449.847 309.121 1 52.71 ? O5' GDP 501 B 1 
HETATM 10 C C5' GDP . . . E 5 326.061 449.893 308.808 1 49.9 ? C5' GDP 501 B 1 
HETATM 11 C C4' GDP . . . E 5 326.951 449.975 310.048 1 47.76 ? C4' GDP 501 B 1 
HETATM 12 O O4' GDP . . . E 5 326.825 448.765 310.819 1 45.47 ? O4' GDP 501 B 1 
HETATM 13 C C3' GDP . . . E 5 328.421 450.036 309.649 1 47.1 ? C3' GDP 501 B 1 
HETATM 14 O O3' GDP . . . E 5 329.142 450.844 310.591 1 46.71 ? O3' GDP 501 B 1 
HETATM 15 C C2' GDP . . . E 5 328.871 448.571 309.685 1 45.16 ? C2' GDP 501 B 1 
HETATM 16 O O2' GDP . . . E 5 330.272 448.433 309.943 1 45.51 ? O2' GDP 501 B 1 
HETATM 17 C C1' GDP . . . E 5 328.046 448.004 310.822 1 42.81 ? C1' GDP 501 B 1 
HETATM 18 N N9 GDP . . . E 5 327.744 446.564 310.691 1 38.43 ? N9 GDP 501 B 1 
HETATM 19 C C8 GDP . . . E 5 327.03 446.033 309.691 1 36.98 ? C8 GDP 501 B 1 
HETATM 20 N N7 GDP . . . E 5 326.875 444.7 309.871 1 36.15 ? N7 GDP 501 B 1 
HETATM 21 C C5 GDP . . . E 5 327.476 444.364 311.02 1 35.3 ? C5 GDP 501 B 1 
HETATM 22 C C6 GDP . . . E 5 327.68 443.109 311.788 1 34.22 ? C6 GDP 501 B 1 
HETATM 23 O O6 GDP . . . E 5 327.223 442.031 311.367 1 34.08 ? O6 GDP 501 B 1 
HETATM 24 N N1 GDP . . . E 5 328.356 443.158 312.939 1 33.93 ? N1 GDP 501 B 1 
HETATM 25 C C2 GDP . . . E 5 328.861 444.318 313.409 1 34.48 ? C2 GDP 501 B 1 
HETATM 26 N N2 GDP . . . E 5 329.533 444.291 314.588 1 34.07 ? N2 GDP 501 B 1 
HETATM 27 N N3 GDP . . . E 5 328.717 445.513 312.75 1 35.43 ? N3 GDP 501 B 1 
HETATM 28 C C4 GDP . . . E 5 328.048 445.601 311.568 1 36.12 ? C4 GDP 501 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          21 
_model_server_stats.element_count           28 
#