data_3NBY
#
_model_server_result.job_id            BU5TstItxWZl88RA-oVI8g 
_model_server_result.datetime_utc      '2024-11-02 10:26:59' 
_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          3nby 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":217}' 
#
_entry.id    3NBY 
#
_exptl.entry_id    3NBY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              523.18 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          100.63 
_cell.angle_gamma         90 
_cell.entry_id            3NBY 
_cell.length_a            72.09 
_cell.length_b            223.726 
_cell.length_c            163.064 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NBY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,G,H 1 1 
D,E,F,I,J 2 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 J 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 G O3G GTP . C GTP 217 1_555 H MG MG . C MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? 
metalc ? metalc2 G O2B GTP . C GTP 217 1_555 H MG MG . C MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc3 E OG1 THR 20 F THR 24 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc4 E OG1 THR 38 F THR 42 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? 
metalc ? metalc5 J O1B GTP . F GTP 217 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
metalc ? metalc6 J O1G GTP . F GTP 217 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? 
metalc ? metalc7 J O3G GTP . F GTP 217 1_555 I MG MG . F MG 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? 
#
_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                     3NBY 
_atom_sites.fract_transf_matrix[1][1]    0.013872 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002604 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00447 
_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]    0.00624 
_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 4 GTP C 1 217 217 GTP GTP . 
H 5 MG C 1 218 218 MG MG . 
I 5 MG F 1 218 218 MG MG . 
J 4 GTP F 1 217 217 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 . . . J 4 0.248 -109.888 38.989 1 25.98 ? PG GTP 217 F 1 
HETATM 2 O O1G GTP . . . J 4 -1.186 -110.316 38.793 1 29.24 ? O1G GTP 217 F 1 
HETATM 3 O O2G GTP . . . J 4 0.378 -108.405 39.278 1 9.44 ? O2G GTP 217 F 1 
HETATM 4 O O3G GTP . . . J 4 0.765 -110.691 40.158 1 26.95 ? O3G GTP 217 F 1 
HETATM 5 O O3B GTP . . . J 4 1.053 -110.341 37.67 1 24.82 ? O3B GTP 217 F 1 
HETATM 6 P PB GTP . . . J 4 0.744 -111.767 36.975 1 30.5 ? PB GTP 217 F 1 
HETATM 7 O O1B GTP . . . J 4 -0.547 -112.355 37.488 1 24.63 ? O1B GTP 217 F 1 
HETATM 8 O O2B GTP . . . J 4 1.874 -112.751 37.135 1 14.86 ? O2B GTP 217 F 1 
HETATM 9 O O3A GTP . . . J 4 0.457 -111.417 35.439 1 28.96 ? O3A GTP 217 F 1 
HETATM 10 P PA GTP . . . J 4 -0.612 -112.343 34.678 1 29.71 ? PA GTP 217 F 1 
HETATM 11 O O1A GTP . . . J 4 -2.018 -111.932 35.054 1 35.83 ? O1A GTP 217 F 1 
HETATM 12 O O2A GTP . . . J 4 -0.341 -113.771 35.084 1 18.7 ? O2A GTP 217 F 1 
HETATM 13 O O5' GTP . . . J 4 -0.437 -112.094 33.092 1 19.54 ? O5' GTP 217 F 1 
HETATM 14 C C5' GTP . . . J 4 0.821 -112.3 32.488 1 19.26 ? C5' GTP 217 F 1 
HETATM 15 C C4' GTP . . . J 4 0.96 -111.558 31.156 1 21.13 ? C4' GTP 217 F 1 
HETATM 16 O O4' GTP . . . J 4 2.007 -112.223 30.485 1 16 ? O4' GTP 217 F 1 
HETATM 17 C C3' GTP . . . J 4 -0.245 -111.689 30.231 1 17.17 ? C3' GTP 217 F 1 
HETATM 18 O O3' GTP . . . J 4 -0.052 -110.848 29.11 1 7.67 ? O3' GTP 217 F 1 
HETATM 19 C C2' GTP . . . J 4 -0.086 -113.095 29.745 1 14.21 ? C2' GTP 217 F 1 
HETATM 20 O O2' GTP . . . J 4 -0.778 -113.253 28.534 1 9.4 ? O2' GTP 217 F 1 
HETATM 21 C C1' GTP . . . J 4 1.419 -113.085 29.531 1 17.16 ? C1' GTP 217 F 1 
HETATM 22 N N9 GTP . . . J 4 2.037 -114.379 29.77 1 14.1 ? N9 GTP 217 F 1 
HETATM 23 C C8 GTP . . . J 4 1.998 -115.171 30.881 1 12.01 ? C8 GTP 217 F 1 
HETATM 24 N N7 GTP . . . J 4 2.752 -116.257 30.617 1 15.11 ? N7 GTP 217 F 1 
HETATM 25 C C5 GTP . . . J 4 3.273 -116.151 29.372 1 18.76 ? C5 GTP 217 F 1 
HETATM 26 C C6 GTP . . . J 4 4.11 -116.958 28.602 1 18.03 ? C6 GTP 217 F 1 
HETATM 27 O O6 GTP . . . J 4 4.548 -118.028 29.03 1 22.04 ? O6 GTP 217 F 1 
HETATM 28 N N1 GTP . . . J 4 4.453 -116.548 27.331 1 14.07 ? N1 GTP 217 F 1 
HETATM 29 C C2 GTP . . . J 4 3.978 -115.35 26.833 1 17.49 ? C2 GTP 217 F 1 
HETATM 30 N N2 GTP . . . J 4 4.312 -114.944 25.611 1 30.24 ? N2 GTP 217 F 1 
HETATM 31 N N3 GTP . . . J 4 3.158 -114.557 27.602 1 16.26 ? N3 GTP 217 F 1 
HETATM 32 C C4 GTP . . . J 4 2.822 -114.962 28.842 1 16.95 ? C4 GTP 217 F 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           231 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           32 
#