data_3JD3
#
_model_server_result.job_id            j30LpWBNydHrYOnuNko_ow 
_model_server_result.datetime_utc      '2025-04-28 03:17:51' 
_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          3jd3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":602}' 
#
_entry.id    3JD3 
#
_exptl.entry_id    3JD3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_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            3JD3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3JD3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X 
_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
? 2 G N N 
? 2 J N N 
? 2 N N N 
? 2 P N N 
? 2 S N N 
? 2 W N N 
#
_chem_comp.formula           'C10 H16 N5 O14 P3' 
_chem_comp.formula_weight    523.18 
_chem_comp.id                GTP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "GUANOSINE-5'-TRIPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
PG O1G GTP doub 129 n n 
PG O2G GTP sing 130 n n 
PG O3G GTP sing 131 n n 
PG O3B GTP sing 132 n n 
O2G HOG2 GTP sing 133 n n 
O3G HOG3 GTP sing 134 n n 
O3B PB GTP sing 135 n n 
PB O1B GTP doub 136 n n 
PB O2B GTP sing 137 n n 
PB O3A GTP sing 138 n n 
O2B HOB2 GTP sing 139 n n 
O3A PA GTP sing 140 n n 
PA O1A GTP doub 141 n n 
PA O2A GTP sing 142 n n 
PA O5' GTP sing 143 n n 
O2A HOA2 GTP sing 144 n n 
O5' C5' GTP sing 145 n n 
C5' C4' GTP sing 146 n n 
C5' H5' GTP sing 147 n n 
C5' "H5''" GTP sing 148 n n 
C4' O4' GTP sing 149 n n 
C4' C3' GTP sing 150 n n 
C4' H4' GTP sing 151 n n 
O4' C1' GTP sing 152 n n 
C3' O3' GTP sing 153 n n 
C3' C2' GTP sing 154 n n 
C3' H3' GTP sing 155 n n 
O3' HO3' GTP sing 156 n n 
C2' O2' GTP sing 157 n n 
C2' C1' GTP sing 158 n n 
C2' H2' GTP sing 159 n n 
O2' HO2' GTP sing 160 n n 
C1' N9 GTP sing 161 n n 
C1' H1' GTP sing 162 n n 
N9 C8 GTP sing 163 n y 
N9 C4 GTP sing 164 n y 
C8 N7 GTP doub 165 n y 
C8 H8 GTP sing 166 n n 
N7 C5 GTP sing 167 n y 
C5 C6 GTP sing 168 n n 
C5 C4 GTP doub 169 n y 
C6 O6 GTP doub 170 n n 
C6 N1 GTP sing 171 n n 
N1 C2 GTP sing 172 n n 
N1 HN1 GTP sing 173 n n 
C2 N2 GTP sing 174 n n 
C2 N3 GTP doub 175 n n 
N2 HN21 GTP sing 176 n n 
N2 HN22 GTP sing 177 n n 
N3 C4 GTP sing 178 n n 
#
_atom_sites.entry_id                     3JD3 
_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
G 2 GTP A 1 601 503 GTP GTP . 
H 3 NAI A 1 602 505 NAI NAI . 
I 3 NAI A 1 603 504 NAI NAI . 
J 2 GTP B 1 601 503 GTP GTP . 
K 3 NAI B 1 602 505 NAI NAI . 
L 3 NAI B 1 603 504 NAI NAI . 
M 3 NAI C 1 601 504 NAI NAI . 
N 2 GTP C 1 602 503 GTP GTP . 
O 3 NAI C 1 603 505 NAI NAI . 
P 2 GTP D 1 601 503 GTP GTP . 
Q 3 NAI D 1 602 505 NAI NAI . 
R 3 NAI D 1 603 504 NAI NAI . 
S 2 GTP E 1 601 503 GTP GTP . 
T 3 NAI E 1 602 505 NAI NAI . 
U 3 NAI E 1 603 504 NAI NAI . 
V 3 NAI F 1 601 504 NAI NAI . 
W 2 GTP F 1 602 503 GTP GTP . 
X 3 NAI F 1 603 505 NAI NAI . 
#
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 PG GTP . . . N 2 63.463 97.895 44.665 1 21.31 ? PG GTP 602 C 1 
HETATM 2 O O1G GTP . . . N 2 63.54 97.703 46.156 1 21.22 ? O1G GTP 602 C 1 
HETATM 3 O O2G GTP . . . N 2 63.801 99.309 44.269 1 13.22 ? O2G GTP 602 C 1 
HETATM 4 O O3G GTP . . . N 2 62.058 97.602 44.208 1 16.62 ? O3G GTP 602 C 1 
HETATM 5 O O3B GTP . . . N 2 64.477 96.873 43.959 1 25.78 ? O3B GTP 602 C 1 
HETATM 6 P PB GTP . . . N 2 66.063 96.945 44.206 1 25.81 ? PB GTP 602 C 1 
HETATM 7 O O1B GTP . . . N 2 66.374 96.287 45.523 1 23.12 ? O1B GTP 602 C 1 
HETATM 8 O O2B GTP . . . N 2 66.794 96.273 43.073 1 21.25 ? O2B GTP 602 C 1 
HETATM 9 O O3A GTP . . . N 2 66.461 98.503 44.277 1 17.09 ? O3A GTP 602 C 1 
HETATM 10 P PA GTP . . . N 2 66.974 99.21 45.629 1 23.93 ? PA GTP 602 C 1 
HETATM 11 O O1A GTP . . . N 2 68.117 98.443 46.224 1 20.63 ? O1A GTP 602 C 1 
HETATM 12 O O2A GTP . . . N 2 67.361 100.645 45.386 1 27.04 ? O2A GTP 602 C 1 
HETATM 13 O O5' GTP . . . N 2 65.728 99.136 46.624 1 17.92 ? O5' GTP 602 C 1 
HETATM 14 C C5' GTP . . . N 2 65.06 100.328 46.941 1 12.02 ? C5' GTP 602 C 1 
HETATM 15 C C4' GTP . . . N 2 64.837 100.382 48.436 1 2.85 ? C4' GTP 602 C 1 
HETATM 16 O O4' GTP . . . N 2 64.043 101.509 48.728 1 8.57 ? O4' GTP 602 C 1 
HETATM 17 C C3' GTP . . . N 2 64.074 99.164 48.911 1 5.16 ? C3' GTP 602 C 1 
HETATM 18 O O3' GTP . . . N 2 64.945 98.235 49.508 1 4.24 ? O3' GTP 602 C 1 
HETATM 19 C C2' GTP . . . N 2 63.129 99.704 49.954 1 7.39 ? C2' GTP 602 C 1 
HETATM 20 O O2' GTP . . . N 2 63.63 99.364 51.223 1 2 ? O2' GTP 602 C 1 
HETATM 21 C C1' GTP . . . N 2 63.135 101.212 49.764 1 13.6 ? C1' GTP 602 C 1 
HETATM 22 N N9 GTP . . . N 2 61.802 101.668 49.357 1 22.89 ? N9 GTP 602 C 1 
HETATM 23 C C8 GTP . . . N 2 60.916 102.378 50.122 1 20.3 ? C8 GTP 602 C 1 
HETATM 24 N N7 GTP . . . N 2 59.806 102.605 49.392 1 30.17 ? N7 GTP 602 C 1 
HETATM 25 C C5 GTP . . . N 2 59.979 102.052 48.172 1 33.02 ? C5 GTP 602 C 1 
HETATM 26 C C6 GTP . . . N 2 59.162 101.992 47.059 1 34.48 ? C6 GTP 602 C 1 
HETATM 27 O O6 GTP . . . N 2 58.055 102.519 47.095 1 37.56 ? O6 GTP 602 C 1 
HETATM 28 N N1 GTP . . . N 2 59.598 101.354 45.922 1 33.91 ? N1 GTP 602 C 1 
HETATM 29 C C2 GTP . . . N 2 60.845 100.773 45.903 1 34.61 ? C2 GTP 602 C 1 
HETATM 30 N N2 GTP . . . N 2 61.262 100.16 44.803 1 41.83 ? N2 GTP 602 C 1 
HETATM 31 N N3 GTP . . . N 2 61.657 100.832 47.015 1 34.29 ? N3 GTP 602 C 1 
HETATM 32 C C4 GTP . . . N 2 61.23 101.464 48.133 1 29.47 ? C4 GTP 602 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           32 
#