data_3JD4
#
_model_server_result.job_id            N5MMbfIOsFYaJC1YkXCIzw 
_model_server_result.datetime_utc      '2024-11-01 04:41:04' 
_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          3jd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":603}' 
#
_entry.id    3JD4 
#
_exptl.entry_id    3JD4 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          3 
_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            3JD4 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3JD4 
_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
? 3 H N N 
? 3 K N N 
? 3 O N N 
? 3 Q N N 
? 3 T N N 
? 3 X 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                     3JD4 
_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 NAI A 1 601 601 NAI NAI . 
H 3 GTP A 1 602 602 GTP GTP . 
I 2 NAI A 1 603 603 NAI NAI . 
J 2 NAI B 1 602 601 NAI NAI . 
K 3 GTP B 1 603 602 GTP GTP . 
L 2 NAI B 1 601 603 NAI NAI . 
M 2 NAI C 1 601 603 NAI NAI . 
N 2 NAI C 1 602 601 NAI NAI . 
O 3 GTP C 1 603 602 GTP GTP . 
P 2 NAI D 1 601 601 NAI NAI . 
Q 3 GTP D 1 602 602 GTP GTP . 
R 2 NAI D 1 603 603 NAI NAI . 
S 2 NAI E 1 602 601 NAI NAI . 
T 3 GTP E 1 603 602 GTP GTP . 
U 2 NAI E 1 601 603 NAI NAI . 
V 2 NAI F 1 601 603 NAI NAI . 
W 2 NAI F 1 602 601 NAI NAI . 
X 3 GTP F 1 603 602 GTP GTP . 
#
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 . . . K 3 104.823 89.422 44.909 1 66.8 ? PG GTP 603 B 1 
HETATM 2 O O1G GTP . . . K 3 104.007 89.541 43.648 1 61.33 ? O1G GTP 603 B 1 
HETATM 3 O O2G GTP . . . K 3 106.183 90.04 44.71 1 70.56 ? O2G GTP 603 B 1 
HETATM 4 O O3G GTP . . . K 3 104.111 90.122 46.036 1 63.09 ? O3G GTP 603 B 1 
HETATM 5 O O3B GTP . . . K 3 104.977 87.867 45.275 1 62.72 ? O3B GTP 603 B 1 
HETATM 6 P PB GTP . . . K 3 103.685 86.921 45.182 1 64.51 ? PB GTP 603 B 1 
HETATM 7 O O1B GTP . . . K 3 103.229 86.872 43.746 1 72.64 ? O1B GTP 603 B 1 
HETATM 8 O O2B GTP . . . K 3 102.593 87.417 46.093 1 65.11 ? O2B GTP 603 B 1 
HETATM 9 O O3A GTP . . . K 3 104.187 85.456 45.599 1 64.51 ? O3A GTP 603 B 1 
HETATM 10 P PA GTP . . . K 3 105.749 85.108 45.692 1 70.78 ? PA GTP 603 B 1 
HETATM 11 O O1A GTP . . . K 3 106.486 85.744 44.54 1 69.56 ? O1A GTP 603 B 1 
HETATM 12 O O2A GTP . . . K 3 105.942 83.615 45.721 1 58.37 ? O2A GTP 603 B 1 
HETATM 13 O O5' GTP . . . K 3 106.253 85.742 47.074 1 66.04 ? O5' GTP 603 B 1 
HETATM 14 C C5' GTP . . . K 3 105.847 85.173 48.294 1 65.76 ? C5' GTP 603 B 1 
HETATM 15 C C4' GTP . . . K 3 105.609 86.307 49.271 1 67.44 ? C4' GTP 603 B 1 
HETATM 16 O O4' GTP . . . K 3 106.835 86.6 49.902 1 71.54 ? O4' GTP 603 B 1 
HETATM 17 C C3' GTP . . . K 3 105.188 87.554 48.523 1 68.51 ? C3' GTP 603 B 1 
HETATM 18 O O3' GTP . . . K 3 103.804 87.766 48.649 1 64.05 ? O3' GTP 603 B 1 
HETATM 19 C C2' GTP . . . K 3 105.961 88.668 49.187 1 66.21 ? C2' GTP 603 B 1 
HETATM 20 O O2' GTP . . . K 3 105.141 89.287 50.146 1 65.55 ? O2' GTP 603 B 1 
HETATM 21 C C1' GTP . . . K 3 107.117 87.981 49.884 1 68.04 ? C1' GTP 603 B 1 
HETATM 22 N N9 GTP . . . K 3 108.339 88.19 49.098 1 76.14 ? N9 GTP 603 B 1 
HETATM 23 C C8 GTP . . . K 3 108.502 87.901 47.771 1 72.24 ? C8 GTP 603 B 1 
HETATM 24 N N7 GTP . . . K 3 109.761 88.23 47.412 1 66.86 ? N7 GTP 603 B 1 
HETATM 25 C C5 GTP . . . K 3 110.403 88.72 48.494 1 72.25 ? C5 GTP 603 B 1 
HETATM 26 C C6 GTP . . . K 3 111.691 89.199 48.676 1 77.36 ? C6 GTP 603 B 1 
HETATM 27 O O6 GTP . . . K 3 112.481 89.223 47.735 1 81.05 ? O6 GTP 603 B 1 
HETATM 28 N N1 GTP . . . K 3 112.079 89.648 49.919 1 71.29 ? N1 GTP 603 B 1 
HETATM 29 C C2 GTP . . . K 3 111.184 89.615 50.965 1 67.81 ? C2 GTP 603 B 1 
HETATM 30 N N2 GTP . . . K 3 111.553 90.043 52.165 1 66.68 ? N2 GTP 603 B 1 
HETATM 31 N N3 GTP . . . K 3 109.906 89.139 50.777 1 68.94 ? N3 GTP 603 B 1 
HETATM 32 C C4 GTP . . . K 3 109.521 88.698 49.561 1 69.14 ? C4 GTP 603 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#