data_3LZZ
#
_model_server_result.job_id            AfEvtv5Js2PhsiV738mgRw 
_model_server_result.datetime_utc      '2024-11-28 21:16:00' 
_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          3lzz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":173}' 
#
_entry.id    3LZZ 
#
_exptl.entry_id    3LZZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            3LZZ 
_cell.length_a            88.86 
_cell.length_b            88.86 
_cell.length_c            168.17 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LZZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 C N N 
? 2 E N N 
#
_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 89 n n 
PB O2B GDP sing 90 n n 
PB O3B GDP sing 91 n n 
PB O3A GDP sing 92 n n 
O2B HOB2 GDP sing 93 n n 
O3B HOB3 GDP sing 94 n n 
O3A PA GDP sing 95 n n 
PA O1A GDP doub 96 n n 
PA O2A GDP sing 97 n n 
PA O5' GDP sing 98 n n 
O2A HOA2 GDP sing 99 n n 
O5' C5' GDP sing 100 n n 
C5' C4' GDP sing 101 n n 
C5' H5' GDP sing 102 n n 
C5' "H5''" GDP sing 103 n n 
C4' O4' GDP sing 104 n n 
C4' C3' GDP sing 105 n n 
C4' H4' GDP sing 106 n n 
O4' C1' GDP sing 107 n n 
C3' O3' GDP sing 108 n n 
C3' C2' GDP sing 109 n n 
C3' H3' GDP sing 110 n n 
O3' HO3' GDP sing 111 n n 
C2' O2' GDP sing 112 n n 
C2' C1' GDP sing 113 n n 
C2' H2' GDP sing 114 n n 
O2' HO2' GDP sing 115 n n 
C1' N9 GDP sing 116 n n 
C1' H1' GDP sing 117 n n 
N9 C8 GDP sing 118 n y 
N9 C4 GDP sing 119 n y 
C8 N7 GDP doub 120 n y 
C8 H8 GDP sing 121 n n 
N7 C5 GDP sing 122 n y 
C5 C6 GDP sing 123 n n 
C5 C4 GDP doub 124 n y 
C6 O6 GDP doub 125 n n 
C6 N1 GDP sing 126 n n 
N1 C2 GDP sing 127 n n 
N1 HN1 GDP sing 128 n n 
C2 N2 GDP sing 129 n n 
C2 N3 GDP doub 130 n n 
N2 HN21 GDP sing 131 n n 
N2 HN22 GDP sing 132 n n 
N3 C4 GDP sing 133 n n 
#
_atom_sites.entry_id                     3LZZ 
_atom_sites.fract_transf_matrix[1][1]    0.011254 
_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]    0.011254 
_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]    0.005946 
_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 2 GDP A 1 173 1 GDP GDP . 
D 3 ACT A 1 174 1 ACT ACT . 
E 2 GDP B 1 173 1 GDP GDP . 
F 3 ACT B 1 174 1 ACT ACT . 
G 4 HOH A 1 175 2 HOH HOH . 
G 4 HOH A 2 176 176 HOH HOH . 
G 4 HOH A 3 177 177 HOH HOH . 
G 4 HOH A 4 178 7 HOH HOH . 
G 4 HOH A 5 179 8 HOH HOH . 
G 4 HOH A 6 180 10 HOH HOH . 
G 4 HOH A 7 181 181 HOH HOH . 
G 4 HOH A 8 182 11 HOH HOH . 
G 4 HOH A 9 183 12 HOH HOH . 
G 4 HOH A 10 184 13 HOH HOH . 
G 4 HOH A 11 185 14 HOH HOH . 
G 4 HOH A 12 186 15 HOH HOH . 
G 4 HOH A 13 187 21 HOH HOH . 
G 4 HOH A 14 188 22 HOH HOH . 
G 4 HOH A 15 189 24 HOH HOH . 
G 4 HOH A 16 190 25 HOH HOH . 
G 4 HOH A 17 191 28 HOH HOH . 
G 4 HOH A 18 192 32 HOH HOH . 
G 4 HOH A 19 193 34 HOH HOH . 
G 4 HOH A 20 194 35 HOH HOH . 
G 4 HOH A 21 195 36 HOH HOH . 
G 4 HOH A 22 196 39 HOH HOH . 
G 4 HOH A 23 197 40 HOH HOH . 
G 4 HOH A 24 198 41 HOH HOH . 
G 4 HOH A 25 199 42 HOH HOH . 
G 4 HOH A 26 200 43 HOH HOH . 
G 4 HOH A 27 201 45 HOH HOH . 
G 4 HOH A 28 202 46 HOH HOH . 
G 4 HOH A 29 203 47 HOH HOH . 
G 4 HOH A 30 204 54 HOH HOH . 
G 4 HOH A 31 205 55 HOH HOH . 
G 4 HOH A 32 206 57 HOH HOH . 
G 4 HOH A 33 207 58 HOH HOH . 
G 4 HOH A 34 208 60 HOH HOH . 
G 4 HOH A 35 209 62 HOH HOH . 
G 4 HOH A 36 210 65 HOH HOH . 
G 4 HOH A 37 211 67 HOH HOH . 
G 4 HOH A 38 212 73 HOH HOH . 
G 4 HOH A 39 213 75 HOH HOH . 
G 4 HOH A 40 214 76 HOH HOH . 
G 4 HOH A 41 215 78 HOH HOH . 
G 4 HOH A 42 216 81 HOH HOH . 
G 4 HOH A 43 217 83 HOH HOH . 
G 4 HOH A 44 218 87 HOH HOH . 
G 4 HOH A 45 219 91 HOH HOH . 
G 4 HOH A 46 220 93 HOH HOH . 
G 4 HOH A 47 221 96 HOH HOH . 
G 4 HOH A 48 222 103 HOH HOH . 
G 4 HOH A 49 223 105 HOH HOH . 
G 4 HOH A 50 224 107 HOH HOH . 
G 4 HOH A 51 225 110 HOH HOH . 
G 4 HOH A 52 226 112 HOH HOH . 
G 4 HOH A 53 227 114 HOH HOH . 
G 4 HOH A 54 228 116 HOH HOH . 
G 4 HOH A 55 229 117 HOH HOH . 
G 4 HOH A 56 230 119 HOH HOH . 
G 4 HOH A 57 231 120 HOH HOH . 
G 4 HOH A 58 232 121 HOH HOH . 
G 4 HOH A 59 233 122 HOH HOH . 
G 4 HOH A 60 234 123 HOH HOH . 
G 4 HOH A 61 235 126 HOH HOH . 
G 4 HOH A 62 236 130 HOH HOH . 
G 4 HOH A 63 237 132 HOH HOH . 
G 4 HOH A 64 238 137 HOH HOH . 
G 4 HOH A 65 239 145 HOH HOH . 
G 4 HOH A 66 240 146 HOH HOH . 
G 4 HOH A 67 241 149 HOH HOH . 
G 4 HOH A 68 242 150 HOH HOH . 
G 4 HOH A 69 243 152 HOH HOH . 
G 4 HOH A 70 244 154 HOH HOH . 
G 4 HOH A 71 245 155 HOH HOH . 
G 4 HOH A 72 246 157 HOH HOH . 
G 4 HOH A 73 247 158 HOH HOH . 
G 4 HOH A 74 248 159 HOH HOH . 
G 4 HOH A 75 249 162 HOH HOH . 
G 4 HOH A 76 250 163 HOH HOH . 
G 4 HOH A 77 251 166 HOH HOH . 
G 4 HOH A 78 252 170 HOH HOH . 
G 4 HOH A 79 253 171 HOH HOH . 
G 4 HOH A 80 254 172 HOH HOH . 
G 4 HOH A 81 255 174 HOH HOH . 
H 4 HOH B 1 175 175 HOH HOH . 
H 4 HOH B 2 176 1 HOH HOH . 
H 4 HOH B 3 177 3 HOH HOH . 
H 4 HOH B 4 178 4 HOH HOH . 
H 4 HOH B 5 179 179 HOH HOH . 
H 4 HOH B 6 180 180 HOH HOH . 
H 4 HOH B 7 181 5 HOH HOH . 
H 4 HOH B 8 182 182 HOH HOH . 
H 4 HOH B 9 183 6 HOH HOH . 
H 4 HOH B 10 184 9 HOH HOH . 
H 4 HOH B 11 185 16 HOH HOH . 
H 4 HOH B 12 186 17 HOH HOH . 
H 4 HOH B 13 187 18 HOH HOH . 
H 4 HOH B 14 188 19 HOH HOH . 
H 4 HOH B 15 189 20 HOH HOH . 
H 4 HOH B 16 190 23 HOH HOH . 
H 4 HOH B 17 191 26 HOH HOH . 
H 4 HOH B 18 192 27 HOH HOH . 
H 4 HOH B 19 193 29 HOH HOH . 
H 4 HOH B 20 194 30 HOH HOH . 
H 4 HOH B 21 195 31 HOH HOH . 
H 4 HOH B 22 196 33 HOH HOH . 
H 4 HOH B 23 197 37 HOH HOH . 
H 4 HOH B 24 198 38 HOH HOH . 
H 4 HOH B 25 199 44 HOH HOH . 
H 4 HOH B 26 200 48 HOH HOH . 
H 4 HOH B 27 201 49 HOH HOH . 
H 4 HOH B 28 202 50 HOH HOH . 
H 4 HOH B 29 203 51 HOH HOH . 
H 4 HOH B 30 204 52 HOH HOH . 
H 4 HOH B 31 205 53 HOH HOH . 
H 4 HOH B 32 206 56 HOH HOH . 
H 4 HOH B 33 207 59 HOH HOH . 
H 4 HOH B 34 208 61 HOH HOH . 
H 4 HOH B 35 209 63 HOH HOH . 
H 4 HOH B 36 210 64 HOH HOH . 
H 4 HOH B 37 211 66 HOH HOH . 
H 4 HOH B 38 212 68 HOH HOH . 
H 4 HOH B 39 213 71 HOH HOH . 
H 4 HOH B 40 214 72 HOH HOH . 
H 4 HOH B 41 215 77 HOH HOH . 
H 4 HOH B 42 216 79 HOH HOH . 
H 4 HOH B 43 217 80 HOH HOH . 
H 4 HOH B 44 218 82 HOH HOH . 
H 4 HOH B 45 219 85 HOH HOH . 
H 4 HOH B 46 220 86 HOH HOH . 
H 4 HOH B 47 221 88 HOH HOH . 
H 4 HOH B 48 222 90 HOH HOH . 
H 4 HOH B 49 223 92 HOH HOH . 
H 4 HOH B 50 224 95 HOH HOH . 
H 4 HOH B 51 225 98 HOH HOH . 
H 4 HOH B 52 226 100 HOH HOH . 
H 4 HOH B 53 227 101 HOH HOH . 
H 4 HOH B 54 228 102 HOH HOH . 
H 4 HOH B 55 229 104 HOH HOH . 
H 4 HOH B 56 230 108 HOH HOH . 
H 4 HOH B 57 231 111 HOH HOH . 
H 4 HOH B 58 232 113 HOH HOH . 
H 4 HOH B 59 233 118 HOH HOH . 
H 4 HOH B 60 234 124 HOH HOH . 
H 4 HOH B 61 235 125 HOH HOH . 
H 4 HOH B 62 236 127 HOH HOH . 
H 4 HOH B 63 237 128 HOH HOH . 
H 4 HOH B 64 238 129 HOH HOH . 
H 4 HOH B 65 239 131 HOH HOH . 
H 4 HOH B 66 240 134 HOH HOH . 
H 4 HOH B 67 241 135 HOH HOH . 
H 4 HOH B 68 242 136 HOH HOH . 
H 4 HOH B 69 243 138 HOH HOH . 
H 4 HOH B 70 244 139 HOH HOH . 
H 4 HOH B 71 245 140 HOH HOH . 
H 4 HOH B 72 246 141 HOH HOH . 
H 4 HOH B 73 247 142 HOH HOH . 
H 4 HOH B 74 248 143 HOH HOH . 
H 4 HOH B 75 249 144 HOH HOH . 
H 4 HOH B 76 250 147 HOH HOH . 
H 4 HOH B 77 251 151 HOH HOH . 
H 4 HOH B 78 252 153 HOH HOH . 
H 4 HOH B 79 253 156 HOH HOH . 
H 4 HOH B 80 254 160 HOH HOH . 
H 4 HOH B 81 255 161 HOH HOH . 
H 4 HOH B 82 256 164 HOH HOH . 
H 4 HOH B 83 257 165 HOH HOH . 
H 4 HOH B 84 258 167 HOH HOH . 
H 4 HOH B 85 259 168 HOH HOH . 
H 4 HOH B 86 260 169 HOH HOH . 
H 4 HOH B 87 261 173 HOH HOH . 
#
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 . . . C 2 -24.958 -7.418 15.694 1 120.26 ? PB GDP 173 A 1 
HETATM 2 O O1B GDP . . . C 2 -26.125 -8.361 15.775 1 119.63 ? O1B GDP 173 A 1 
HETATM 3 O O2B GDP . . . C 2 -25.453 -6.014 15.463 1 120.42 ? O2B GDP 173 A 1 
HETATM 4 O O3B GDP . . . C 2 -24.223 -7.477 16.994 1 119.68 ? O3B GDP 173 A 1 
HETATM 5 O O3A GDP . . . C 2 -24.009 -7.904 14.498 1 118.77 ? O3A GDP 173 A 1 
HETATM 6 P PA GDP . . . C 2 -24.646 -8.739 13.277 1 117.46 ? PA GDP 173 A 1 
HETATM 7 O O1A GDP . . . C 2 -26.123 -8.487 13.239 1 118.27 ? O1A GDP 173 A 1 
HETATM 8 O O2A GDP . . . C 2 -24.269 -10.202 13.284 1 117.08 ? O2A GDP 173 A 1 
HETATM 9 O O5' GDP . . . C 2 -24.091 -8.122 11.944 1 111.39 ? O5' GDP 173 A 1 
HETATM 10 C C5' GDP . . . C 2 -25.12 -7.81 11.045 1 102.76 ? C5' GDP 173 A 1 
HETATM 11 C C4' GDP . . . C 2 -24.704 -8.267 9.68 1 95.36 ? C4' GDP 173 A 1 
HETATM 12 O O4' GDP . . . C 2 -25.875 -8.455 8.91 1 89.9 ? O4' GDP 173 A 1 
HETATM 13 C C3' GDP . . . C 2 -23.854 -7.248 8.945 1 92.89 ? C3' GDP 173 A 1 
HETATM 14 O O3' GDP . . . C 2 -22.492 -7.688 8.842 1 91.97 ? O3' GDP 173 A 1 
HETATM 15 C C2' GDP . . . C 2 -24.5 -7.216 7.579 1 89.62 ? C2' GDP 173 A 1 
HETATM 16 O O2' GDP . . . C 2 -23.49 -7.397 6.631 1 90.19 ? O2' GDP 173 A 1 
HETATM 17 C C1' GDP . . . C 2 -25.339 -8.455 7.621 1 84.21 ? C1' GDP 173 A 1 
HETATM 18 N N9 GDP . . . C 2 -26.245 -8.717 6.503 1 75.62 ? N9 GDP 173 A 1 
HETATM 19 C C8 GDP . . . C 2 -27.464 -9.235 6.474 1 72.7 ? C8 GDP 173 A 1 
HETATM 20 N N7 GDP . . . C 2 -27.877 -9.351 5.203 1 68.88 ? N7 GDP 173 A 1 
HETATM 21 C C5 GDP . . . C 2 -26.893 -8.943 4.399 1 66.54 ? C5 GDP 173 A 1 
HETATM 22 C C6 GDP . . . C 2 -26.601 -8.772 2.954 1 62.43 ? C6 GDP 173 A 1 
HETATM 23 O O6 GDP . . . C 2 -27.374 -9.055 2.073 1 59.35 ? O6 GDP 173 A 1 
HETATM 24 N N1 GDP . . . C 2 -25.446 -8.28 2.609 1 62.23 ? N1 GDP 173 A 1 
HETATM 25 C C2 GDP . . . C 2 -24.547 -7.948 3.532 1 63.92 ? C2 GDP 173 A 1 
HETATM 26 N N2 GDP . . . C 2 -23.361 -7.453 3.198 1 63.15 ? N2 GDP 173 A 1 
HETATM 27 N N3 GDP . . . C 2 -24.727 -8.073 4.825 1 64.65 ? N3 GDP 173 A 1 
HETATM 28 C C4 GDP . . . C 2 -25.846 -8.537 5.299 1 69.12 ? C4 GDP 173 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           28 
#