data_1I4D
#
_model_server_result.job_id            Hg26LveeuJ6OPZaTDxL5sA 
_model_server_result.datetime_utc      '2024-12-22 01:20:00' 
_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          1i4d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":200}' 
#
_entry.id    1I4D 
#
_exptl.entry_id    1I4D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_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          97.51 
_cell.angle_gamma         90 
_cell.entry_id            1I4D 
_cell.length_a            63.566 
_cell.length_b            47.462 
_cell.length_c            125.311 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1I4D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_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                      4 
_struct_asym.id                             E 
_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 C OG1 THR 17 D THR 17 1_555 D MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc2 E O3B GDP . D GDP 200 1_555 D MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
#
_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 83 n n 
PB O2B GDP sing 84 n n 
PB O3B GDP sing 85 n n 
PB O3A GDP sing 86 n n 
O2B HOB2 GDP sing 87 n n 
O3B HOB3 GDP sing 88 n n 
O3A PA GDP sing 89 n n 
PA O1A GDP doub 90 n n 
PA O2A GDP sing 91 n n 
PA O5' GDP sing 92 n n 
O2A HOA2 GDP sing 93 n n 
O5' C5' GDP sing 94 n n 
C5' C4' GDP sing 95 n n 
C5' H5' GDP sing 96 n n 
C5' "H5''" GDP sing 97 n n 
C4' O4' GDP sing 98 n n 
C4' C3' GDP sing 99 n n 
C4' H4' GDP sing 100 n n 
O4' C1' GDP sing 101 n n 
C3' O3' GDP sing 102 n n 
C3' C2' GDP sing 103 n n 
C3' H3' GDP sing 104 n n 
O3' HO3' GDP sing 105 n n 
C2' O2' GDP sing 106 n n 
C2' C1' GDP sing 107 n n 
C2' H2' GDP sing 108 n n 
O2' HO2' GDP sing 109 n n 
C1' N9 GDP sing 110 n n 
C1' H1' GDP sing 111 n n 
N9 C8 GDP sing 112 n y 
N9 C4 GDP sing 113 n y 
C8 N7 GDP doub 114 n y 
C8 H8 GDP sing 115 n n 
N7 C5 GDP sing 116 n y 
C5 C6 GDP sing 117 n n 
C5 C4 GDP doub 118 n y 
C6 O6 GDP doub 119 n n 
C6 N1 GDP sing 120 n n 
N1 C2 GDP sing 121 n n 
N1 HN1 GDP sing 122 n n 
C2 N2 GDP sing 123 n n 
C2 N3 GDP doub 124 n n 
N2 HN21 GDP sing 125 n n 
N2 HN22 GDP sing 126 n n 
N3 C4 GDP sing 127 n n 
#
_atom_sites.entry_id                     1I4D 
_atom_sites.fract_transf_matrix[1][1]    0.015732 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002074 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021069 
_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]    0.008049 
_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 3 MG D 1 201 201 MG MG . 
E 4 GDP D 1 200 200 GDP GDP . 
F 5 HOH A 1 246 3 HOH HOH . 
F 5 HOH A 2 247 7 HOH HOH . 
F 5 HOH A 3 248 13 HOH HOH . 
F 5 HOH A 4 249 15 HOH HOH . 
F 5 HOH A 5 250 16 HOH HOH . 
F 5 HOH A 6 251 17 HOH HOH . 
F 5 HOH A 7 252 18 HOH HOH . 
F 5 HOH A 8 253 22 HOH HOH . 
F 5 HOH A 9 254 24 HOH HOH . 
F 5 HOH A 10 255 31 HOH HOH . 
F 5 HOH A 11 256 38 HOH HOH . 
F 5 HOH A 12 257 43 HOH HOH . 
F 5 HOH A 13 258 47 HOH HOH . 
F 5 HOH A 14 259 51 HOH HOH . 
F 5 HOH A 15 260 54 HOH HOH . 
F 5 HOH A 16 261 56 HOH HOH . 
F 5 HOH A 17 262 59 HOH HOH . 
F 5 HOH A 18 263 60 HOH HOH . 
F 5 HOH A 19 264 66 HOH HOH . 
F 5 HOH A 20 265 68 HOH HOH . 
F 5 HOH A 21 266 75 HOH HOH . 
F 5 HOH A 22 267 77 HOH HOH . 
F 5 HOH A 23 268 78 HOH HOH . 
F 5 HOH A 24 269 80 HOH HOH . 
F 5 HOH A 25 270 83 HOH HOH . 
F 5 HOH A 26 271 84 HOH HOH . 
F 5 HOH A 27 272 89 HOH HOH . 
F 5 HOH A 28 273 96 HOH HOH . 
F 5 HOH A 29 274 99 HOH HOH . 
F 5 HOH A 30 275 103 HOH HOH . 
F 5 HOH A 31 276 104 HOH HOH . 
F 5 HOH A 32 277 109 HOH HOH . 
F 5 HOH A 33 278 112 HOH HOH . 
F 5 HOH A 34 279 119 HOH HOH . 
F 5 HOH A 35 280 121 HOH HOH . 
F 5 HOH A 36 281 123 HOH HOH . 
F 5 HOH A 37 282 126 HOH HOH . 
F 5 HOH A 38 283 128 HOH HOH . 
F 5 HOH A 39 284 136 HOH HOH . 
F 5 HOH A 40 285 138 HOH HOH . 
F 5 HOH A 41 286 139 HOH HOH . 
F 5 HOH A 42 287 148 HOH HOH . 
F 5 HOH A 43 288 150 HOH HOH . 
F 5 HOH A 44 289 152 HOH HOH . 
F 5 HOH A 45 290 156 HOH HOH . 
F 5 HOH A 46 291 157 HOH HOH . 
G 5 HOH B 1 246 1 HOH HOH . 
G 5 HOH B 2 247 2 HOH HOH . 
G 5 HOH B 3 248 6 HOH HOH . 
G 5 HOH B 4 249 8 HOH HOH . 
G 5 HOH B 5 250 12 HOH HOH . 
G 5 HOH B 6 251 19 HOH HOH . 
G 5 HOH B 7 252 26 HOH HOH . 
G 5 HOH B 8 253 28 HOH HOH . 
G 5 HOH B 9 254 29 HOH HOH . 
G 5 HOH B 10 255 30 HOH HOH . 
G 5 HOH B 11 256 32 HOH HOH . 
G 5 HOH B 12 257 33 HOH HOH . 
G 5 HOH B 13 258 34 HOH HOH . 
G 5 HOH B 14 259 35 HOH HOH . 
G 5 HOH B 15 260 44 HOH HOH . 
G 5 HOH B 16 261 48 HOH HOH . 
G 5 HOH B 17 262 49 HOH HOH . 
G 5 HOH B 18 263 58 HOH HOH . 
G 5 HOH B 19 264 61 HOH HOH . 
G 5 HOH B 20 265 65 HOH HOH . 
G 5 HOH B 21 266 69 HOH HOH . 
G 5 HOH B 22 267 70 HOH HOH . 
G 5 HOH B 23 268 71 HOH HOH . 
G 5 HOH B 24 269 79 HOH HOH . 
G 5 HOH B 25 270 87 HOH HOH . 
G 5 HOH B 26 271 88 HOH HOH . 
G 5 HOH B 27 272 91 HOH HOH . 
G 5 HOH B 28 273 93 HOH HOH . 
G 5 HOH B 29 274 94 HOH HOH . 
G 5 HOH B 30 275 101 HOH HOH . 
G 5 HOH B 31 276 106 HOH HOH . 
G 5 HOH B 32 277 108 HOH HOH . 
G 5 HOH B 33 278 110 HOH HOH . 
G 5 HOH B 34 279 114 HOH HOH . 
G 5 HOH B 35 280 115 HOH HOH . 
G 5 HOH B 36 281 116 HOH HOH . 
G 5 HOH B 37 282 117 HOH HOH . 
G 5 HOH B 38 283 118 HOH HOH . 
G 5 HOH B 39 284 120 HOH HOH . 
G 5 HOH B 40 285 124 HOH HOH . 
G 5 HOH B 41 286 125 HOH HOH . 
G 5 HOH B 42 287 127 HOH HOH . 
G 5 HOH B 43 288 129 HOH HOH . 
G 5 HOH B 44 289 130 HOH HOH . 
G 5 HOH B 45 290 132 HOH HOH . 
G 5 HOH B 46 291 135 HOH HOH . 
G 5 HOH B 47 292 141 HOH HOH . 
G 5 HOH B 48 293 144 HOH HOH . 
G 5 HOH B 49 294 147 HOH HOH . 
G 5 HOH B 50 295 149 HOH HOH . 
G 5 HOH B 51 296 154 HOH HOH . 
G 5 HOH B 52 297 155 HOH HOH . 
G 5 HOH B 53 298 158 HOH HOH . 
G 5 HOH B 54 299 159 HOH HOH . 
G 5 HOH B 55 300 160 HOH HOH . 
G 5 HOH B 56 301 161 HOH HOH . 
H 5 HOH D 1 202 4 HOH HOH . 
H 5 HOH D 2 203 5 HOH HOH . 
H 5 HOH D 3 204 10 HOH HOH . 
H 5 HOH D 4 205 11 HOH HOH . 
H 5 HOH D 5 206 14 HOH HOH . 
H 5 HOH D 6 207 20 HOH HOH . 
H 5 HOH D 7 208 21 HOH HOH . 
H 5 HOH D 8 209 23 HOH HOH . 
H 5 HOH D 9 210 25 HOH HOH . 
H 5 HOH D 10 211 36 HOH HOH . 
H 5 HOH D 11 212 37 HOH HOH . 
H 5 HOH D 12 213 39 HOH HOH . 
H 5 HOH D 13 214 40 HOH HOH . 
H 5 HOH D 14 215 42 HOH HOH . 
H 5 HOH D 15 216 45 HOH HOH . 
H 5 HOH D 16 217 46 HOH HOH . 
H 5 HOH D 17 218 50 HOH HOH . 
H 5 HOH D 18 219 52 HOH HOH . 
H 5 HOH D 19 220 53 HOH HOH . 
H 5 HOH D 20 221 55 HOH HOH . 
H 5 HOH D 21 222 57 HOH HOH . 
H 5 HOH D 22 223 62 HOH HOH . 
H 5 HOH D 23 224 63 HOH HOH . 
H 5 HOH D 24 225 67 HOH HOH . 
H 5 HOH D 25 226 72 HOH HOH . 
H 5 HOH D 26 227 74 HOH HOH . 
H 5 HOH D 27 228 76 HOH HOH . 
H 5 HOH D 28 229 82 HOH HOH . 
H 5 HOH D 29 230 85 HOH HOH . 
H 5 HOH D 30 231 86 HOH HOH . 
H 5 HOH D 31 232 90 HOH HOH . 
H 5 HOH D 32 233 95 HOH HOH . 
H 5 HOH D 33 234 97 HOH HOH . 
H 5 HOH D 34 235 98 HOH HOH . 
H 5 HOH D 35 236 100 HOH HOH . 
H 5 HOH D 36 237 102 HOH HOH . 
H 5 HOH D 37 238 111 HOH HOH . 
H 5 HOH D 38 239 113 HOH HOH . 
H 5 HOH D 39 240 122 HOH HOH . 
H 5 HOH D 40 241 133 HOH HOH . 
H 5 HOH D 41 242 134 HOH HOH . 
H 5 HOH D 42 243 140 HOH HOH . 
H 5 HOH D 43 244 142 HOH HOH . 
H 5 HOH D 44 245 143 HOH HOH . 
H 5 HOH D 45 246 146 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 . . . E 4 -9.349 5.142 53.796 1 44.8 ? PB GDP 200 D 1 
HETATM 2 O O1B GDP . . . E 4 -8.867 6.532 54.022 1 43.72 ? O1B GDP 200 D 1 
HETATM 3 O O2B GDP . . . E 4 -10.747 5.152 53.163 1 47.38 ? O2B GDP 200 D 1 
HETATM 4 O O3B GDP . . . E 4 -8.43 4.327 52.877 1 43.13 ? O3B GDP 200 D 1 
HETATM 5 O O3A GDP . . . E 4 -9.458 4.44 55.198 1 42.68 ? O3A GDP 200 D 1 
HETATM 6 P PA GDP . . . E 4 -9.135 2.872 55.333 1 41.41 ? PA GDP 200 D 1 
HETATM 7 O O1A GDP . . . E 4 -9.863 2.136 54.318 1 40.45 ? O1A GDP 200 D 1 
HETATM 8 O O2A GDP . . . E 4 -7.58 2.712 55.291 1 43.04 ? O2A GDP 200 D 1 
HETATM 9 O O5' GDP . . . E 4 -9.741 2.654 56.8 1 38.28 ? O5' GDP 200 D 1 
HETATM 10 C C5' GDP . . . E 4 -9.481 3.659 57.761 1 38.89 ? C5' GDP 200 D 1 
HETATM 11 C C4' GDP . . . E 4 -9.817 3.101 59.157 1 43.84 ? C4' GDP 200 D 1 
HETATM 12 O O4' GDP . . . E 4 -11.22 2.813 59.228 1 44.55 ? O4' GDP 200 D 1 
HETATM 13 C C3' GDP . . . E 4 -9.073 1.8 59.441 1 42.65 ? C3' GDP 200 D 1 
HETATM 14 O O3' GDP . . . E 4 -8.48 1.804 60.72 1 46.57 ? O3' GDP 200 D 1 
HETATM 15 C C2' GDP . . . E 4 -10.131 0.711 59.341 1 43.69 ? C2' GDP 200 D 1 
HETATM 16 O O2' GDP . . . E 4 -9.887 -0.391 60.211 1 47.39 ? O2' GDP 200 D 1 
HETATM 17 C C1' GDP . . . E 4 -11.414 1.467 59.66 1 43.04 ? C1' GDP 200 D 1 
HETATM 18 N N9 GDP . . . E 4 -12.559 0.907 58.95 1 39.47 ? N9 GDP 200 D 1 
HETATM 19 C C8 GDP . . . E 4 -12.738 0.937 57.607 1 39.02 ? C8 GDP 200 D 1 
HETATM 20 N N7 GDP . . . E 4 -13.919 0.369 57.304 1 37.1 ? N7 GDP 200 D 1 
HETATM 21 C C5 GDP . . . E 4 -14.492 -0.041 58.444 1 39.81 ? C5 GDP 200 D 1 
HETATM 22 C C6 GDP . . . E 4 -15.695 -0.704 58.67 1 42.53 ? C6 GDP 200 D 1 
HETATM 23 O O6 GDP . . . E 4 -16.555 -0.852 57.791 1 44.74 ? O6 GDP 200 D 1 
HETATM 24 N N1 GDP . . . E 4 -16.062 -1.013 59.948 1 43.83 ? N1 GDP 200 D 1 
HETATM 25 C C2 GDP . . . E 4 -15.24 -0.667 60.986 1 41.55 ? C2 GDP 200 D 1 
HETATM 26 N N2 GDP . . . E 4 -15.693 -0.99 62.188 1 42.54 ? N2 GDP 200 D 1 
HETATM 27 N N3 GDP . . . E 4 -14.039 0.016 60.775 1 40.01 ? N3 GDP 200 D 1 
HETATM 28 C C4 GDP . . . E 4 -13.664 0.314 59.503 1 40.27 ? C4 GDP 200 D 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#