data_4CK7
#
_model_server_result.job_id            3gidZMkhYzrmg3fcKkzOOg 
_model_server_result.datetime_utc      '2024-10-22 03:31:27' 
_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          4ck7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1210}' 
#
_entry.id    4CK7 
#
_exptl.entry_id    4CK7 
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            4CK7 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4CK7 
_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        PQS 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J 
_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 
#
_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 MG MG . A MG 1208 1_555 E O1G GTP . A GTP 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc2 H MG MG . C MG 1205 1_555 I AL AF3 . C AF3 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? 
metalc ? metalc3 H MG MG . C MG 1205 1_555 J O3B ADP . C ADP 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc4 I AL AF3 . C AF3 1206 1_555 J O3B ADP . C ADP 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
#
_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 130 n n 
PB O2B GDP sing 131 n n 
PB O3B GDP sing 132 n n 
PB O3A GDP sing 133 n n 
O2B HOB2 GDP sing 134 n n 
O3B HOB3 GDP sing 135 n n 
O3A PA GDP sing 136 n n 
PA O1A GDP doub 137 n n 
PA O2A GDP sing 138 n n 
PA O5' GDP sing 139 n n 
O2A HOA2 GDP sing 140 n n 
O5' C5' GDP sing 141 n n 
C5' C4' GDP sing 142 n n 
C5' H5' GDP sing 143 n n 
C5' "H5''" GDP sing 144 n n 
C4' O4' GDP sing 145 n n 
C4' C3' GDP sing 146 n n 
C4' H4' GDP sing 147 n n 
O4' C1' GDP sing 148 n n 
C3' O3' GDP sing 149 n n 
C3' C2' GDP sing 150 n n 
C3' H3' GDP sing 151 n n 
O3' HO3' GDP sing 152 n n 
C2' O2' GDP sing 153 n n 
C2' C1' GDP sing 154 n n 
C2' H2' GDP sing 155 n n 
O2' HO2' GDP sing 156 n n 
C1' N9 GDP sing 157 n n 
C1' H1' GDP sing 158 n n 
N9 C8 GDP sing 159 n y 
N9 C4 GDP sing 160 n y 
C8 N7 GDP doub 161 n y 
C8 H8 GDP sing 162 n n 
N7 C5 GDP sing 163 n y 
C5 C6 GDP sing 164 n n 
C5 C4 GDP doub 165 n y 
C6 O6 GDP doub 166 n n 
C6 N1 GDP sing 167 n n 
N1 C2 GDP sing 168 n n 
N1 HN1 GDP sing 169 n n 
C2 N2 GDP sing 170 n n 
C2 N3 GDP doub 171 n n 
N2 HN21 GDP sing 172 n n 
N2 HN22 GDP sing 173 n n 
N3 C4 GDP sing 174 n n 
#
_atom_sites.entry_id                     4CK7 
_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 MG A 1 1208 1208 MG MG . 
E 5 GTP A 1 1209 1209 GTP GTP . 
F 6 GDP B 1 1210 1210 GDP GDP . 
G 7 TA1 B 1 1211 1211 TA1 TA1 . 
H 4 MG C 1 1205 1205 MG MG . 
I 8 AF3 C 1 1206 1206 AF3 AF3 . 
J 9 ADP C 1 1207 1207 ADP ADP . 
#
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 6 194.598 266.334 442.219 1 22.28 ? PB GDP 1210 B 1 
HETATM 2 O O1B GDP . . . F 6 193.884 266.877 441.048 1 23.59 ? O1B GDP 1210 B 1 
HETATM 3 O O2B GDP . . . F 6 195.888 266.829 442.437 1 23.44 ? O2B GDP 1210 B 1 
HETATM 4 O O3B GDP . . . F 6 193.616 266.451 443.519 1 25.3 ? O3B GDP 1210 B 1 
HETATM 5 O O3A GDP . . . F 6 194.806 264.799 441.929 1 19.52 ? O3A GDP 1210 B 1 
HETATM 6 P PA GDP . . . F 6 196.213 263.898 441.859 1 20.51 ? PA GDP 1210 B 1 
HETATM 7 O O1A GDP . . . F 6 197.027 264.359 440.699 1 23.36 ? O1A GDP 1210 B 1 
HETATM 8 O O2A GDP . . . F 6 196.875 264.044 443.22 1 18 ? O2A GDP 1210 B 1 
HETATM 9 O O5' GDP . . . F 6 195.645 262.488 441.541 1 16.66 ? O5' GDP 1210 B 1 
HETATM 10 C C5' GDP . . . F 6 196.388 261.276 441.88 1 7.65 ? C5' GDP 1210 B 1 
HETATM 11 C C4' GDP . . . F 6 196.685 260.406 440.757 1 2.51 ? C4' GDP 1210 B 1 
HETATM 12 O O4' GDP . . . F 6 197.584 261.127 439.825 1 2 ? O4' GDP 1210 B 1 
HETATM 13 C C3' GDP . . . F 6 197.551 259.14 441.101 1 3.46 ? C3' GDP 1210 B 1 
HETATM 14 O O3' GDP . . . F 6 197.021 258.051 440.261 1 2.32 ? O3' GDP 1210 B 1 
HETATM 15 C C2' GDP . . . F 6 199.02 259.401 440.688 1 2.23 ? C2' GDP 1210 B 1 
HETATM 16 O O2' GDP . . . F 6 199.824 258.3 440.228 1 2 ? O2' GDP 1210 B 1 
HETATM 17 C C1' GDP . . . F 6 198.881 260.433 439.571 1 2 ? C1' GDP 1210 B 1 
HETATM 18 N N9 GDP . . . F 6 199.933 261.448 439.548 1 5.88 ? N9 GDP 1210 B 1 
HETATM 19 C C8 GDP . . . F 6 199.971 262.488 440.63 1 9.42 ? C8 GDP 1210 B 1 
HETATM 20 N N7 GDP . . . F 6 201.098 263.133 440.09 1 10.36 ? N7 GDP 1210 B 1 
HETATM 21 C C5 GDP . . . F 6 201.673 262.678 438.984 1 10.45 ? C5 GDP 1210 B 1 
HETATM 22 C C6 GDP . . . F 6 202.72 262.853 438.051 1 13.51 ? C6 GDP 1210 B 1 
HETATM 23 O O6 GDP . . . F 6 203.533 263.902 438.268 1 11.34 ? O6 GDP 1210 B 1 
HETATM 24 N N1 GDP . . . F 6 202.924 262.072 436.968 1 10.31 ? N1 GDP 1210 B 1 
HETATM 25 C C2 GDP . . . F 6 202.001 260.927 436.743 1 5.81 ? C2 GDP 1210 B 1 
HETATM 26 N N2 GDP . . . F 6 202.4 260.299 435.656 1 6.23 ? N2 GDP 1210 B 1 
HETATM 27 N N3 GDP . . . F 6 201.054 260.703 437.551 1 4.23 ? N3 GDP 1210 B 1 
HETATM 28 C C4 GDP . . . F 6 200.865 261.53 438.596 1 7.64 ? C4 GDP 1210 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#