data_1I4L
#
_model_server_result.job_id            IvGiHAOACY8CA9cy8cmjKQ 
_model_server_result.datetime_utc      '2024-10-18 16:30:52' 
_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          1i4l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":200}' 
#
_entry.id    1I4L 
#
_exptl.entry_id    1I4L 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            1I4L 
_cell.length_a            112.379 
_cell.length_b            112.379 
_cell.length_c            68.242 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1I4L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41' 
#
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 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,D,E,F,G,H 1 1 
C,D,E,H 2 1 
A,B,F,G 2 2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_554 y,-x,z-1/4 0 1 0 -1 0 0 0 0 1 0 0 -17.0605 
#
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc2 E O2B GDP . D GDP 200 1_555 D MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
#
_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                     1I4L 
_atom_sites.fract_transf_matrix[1][1]    0.008898 
_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]    0.008898 
_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]    0.014654 
_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 1 HOH HOH . 
F 5 HOH A 2 247 2 HOH HOH . 
F 5 HOH A 3 248 3 HOH HOH . 
F 5 HOH A 4 249 4 HOH HOH . 
F 5 HOH A 5 250 5 HOH HOH . 
F 5 HOH A 6 251 6 HOH HOH . 
F 5 HOH A 7 252 7 HOH HOH . 
F 5 HOH A 8 253 8 HOH HOH . 
F 5 HOH A 9 254 9 HOH HOH . 
F 5 HOH A 10 255 10 HOH HOH . 
F 5 HOH A 11 256 11 HOH HOH . 
F 5 HOH A 12 257 13 HOH HOH . 
F 5 HOH A 13 258 18 HOH HOH . 
F 5 HOH A 14 259 19 HOH HOH . 
F 5 HOH A 15 260 20 HOH HOH . 
F 5 HOH A 16 261 23 HOH HOH . 
F 5 HOH A 17 262 28 HOH HOH . 
F 5 HOH A 18 263 29 HOH HOH . 
F 5 HOH A 19 264 30 HOH HOH . 
F 5 HOH A 20 265 31 HOH HOH . 
F 5 HOH A 21 266 32 HOH HOH . 
F 5 HOH A 22 267 33 HOH HOH . 
F 5 HOH A 23 268 35 HOH HOH . 
F 5 HOH A 24 269 42 HOH HOH . 
F 5 HOH A 25 270 45 HOH HOH . 
F 5 HOH A 26 271 47 HOH HOH . 
F 5 HOH A 27 272 49 HOH HOH . 
F 5 HOH A 28 273 50 HOH HOH . 
F 5 HOH A 29 274 53 HOH HOH . 
F 5 HOH A 30 275 55 HOH HOH . 
F 5 HOH A 31 276 57 HOH HOH . 
F 5 HOH A 32 277 61 HOH HOH . 
F 5 HOH A 33 278 64 HOH HOH . 
F 5 HOH A 34 279 68 HOH HOH . 
F 5 HOH A 35 280 70 HOH HOH . 
F 5 HOH A 36 281 74 HOH HOH . 
F 5 HOH A 37 282 75 HOH HOH . 
F 5 HOH A 38 283 76 HOH HOH . 
F 5 HOH A 39 284 77 HOH HOH . 
F 5 HOH A 40 285 78 HOH HOH . 
F 5 HOH A 41 286 83 HOH HOH . 
F 5 HOH A 42 287 91 HOH HOH . 
F 5 HOH A 43 288 92 HOH HOH . 
F 5 HOH A 44 289 94 HOH HOH . 
F 5 HOH A 45 290 95 HOH HOH . 
F 5 HOH A 46 291 105 HOH HOH . 
F 5 HOH A 47 292 107 HOH HOH . 
F 5 HOH A 48 293 108 HOH HOH . 
F 5 HOH A 49 294 109 HOH HOH . 
F 5 HOH A 50 295 111 HOH HOH . 
F 5 HOH A 51 296 116 HOH HOH . 
F 5 HOH A 52 297 117 HOH HOH . 
F 5 HOH A 53 298 118 HOH HOH . 
F 5 HOH A 54 299 119 HOH HOH . 
F 5 HOH A 55 300 121 HOH HOH . 
F 5 HOH A 56 301 125 HOH HOH . 
F 5 HOH A 57 302 126 HOH HOH . 
F 5 HOH A 58 303 134 HOH HOH . 
F 5 HOH A 59 304 138 HOH HOH . 
F 5 HOH A 60 305 145 HOH HOH . 
F 5 HOH A 61 306 149 HOH HOH . 
F 5 HOH A 62 307 150 HOH HOH . 
F 5 HOH A 63 308 151 HOH HOH . 
F 5 HOH A 64 309 153 HOH HOH . 
F 5 HOH A 65 310 154 HOH HOH . 
F 5 HOH A 66 311 156 HOH HOH . 
F 5 HOH A 67 312 161 HOH HOH . 
F 5 HOH A 68 313 163 HOH HOH . 
F 5 HOH A 69 314 168 HOH HOH . 
F 5 HOH A 70 315 173 HOH HOH . 
F 5 HOH A 71 316 178 HOH HOH . 
G 5 HOH B 1 246 12 HOH HOH . 
G 5 HOH B 2 247 22 HOH HOH . 
G 5 HOH B 3 248 26 HOH HOH . 
G 5 HOH B 4 249 27 HOH HOH . 
G 5 HOH B 5 250 36 HOH HOH . 
G 5 HOH B 6 251 41 HOH HOH . 
G 5 HOH B 7 252 46 HOH HOH . 
G 5 HOH B 8 253 51 HOH HOH . 
G 5 HOH B 9 254 52 HOH HOH . 
G 5 HOH B 10 255 56 HOH HOH . 
G 5 HOH B 11 256 58 HOH HOH . 
G 5 HOH B 12 257 59 HOH HOH . 
G 5 HOH B 13 258 62 HOH HOH . 
G 5 HOH B 14 259 63 HOH HOH . 
G 5 HOH B 15 260 66 HOH HOH . 
G 5 HOH B 16 261 72 HOH HOH . 
G 5 HOH B 17 262 85 HOH HOH . 
G 5 HOH B 18 263 88 HOH HOH . 
G 5 HOH B 19 264 93 HOH HOH . 
G 5 HOH B 20 265 97 HOH HOH . 
G 5 HOH B 21 266 98 HOH HOH . 
G 5 HOH B 22 267 99 HOH HOH . 
G 5 HOH B 23 268 100 HOH HOH . 
G 5 HOH B 24 269 104 HOH HOH . 
G 5 HOH B 25 270 115 HOH HOH . 
G 5 HOH B 26 271 124 HOH HOH . 
G 5 HOH B 27 272 129 HOH HOH . 
G 5 HOH B 28 273 130 HOH HOH . 
G 5 HOH B 29 274 132 HOH HOH . 
G 5 HOH B 30 275 135 HOH HOH . 
G 5 HOH B 31 276 148 HOH HOH . 
G 5 HOH B 32 277 152 HOH HOH . 
G 5 HOH B 33 278 160 HOH HOH . 
G 5 HOH B 34 279 162 HOH HOH . 
G 5 HOH B 35 280 167 HOH HOH . 
G 5 HOH B 36 281 171 HOH HOH . 
H 5 HOH D 1 202 15 HOH HOH . 
H 5 HOH D 2 203 17 HOH HOH . 
H 5 HOH D 3 204 25 HOH HOH . 
H 5 HOH D 4 205 34 HOH HOH . 
H 5 HOH D 5 206 54 HOH HOH . 
H 5 HOH D 6 207 71 HOH HOH . 
H 5 HOH D 7 208 79 HOH HOH . 
H 5 HOH D 8 209 80 HOH HOH . 
H 5 HOH D 9 210 81 HOH HOH . 
H 5 HOH D 10 211 122 HOH HOH . 
H 5 HOH D 11 212 123 HOH HOH . 
H 5 HOH D 12 213 141 HOH HOH . 
H 5 HOH D 13 214 142 HOH HOH . 
H 5 HOH D 14 215 155 HOH HOH . 
H 5 HOH D 15 216 164 HOH HOH . 
H 5 HOH D 16 217 174 HOH HOH . 
H 5 HOH D 17 218 176 HOH HOH . 
H 5 HOH D 18 219 179 HOH HOH . 
H 5 HOH D 19 220 183 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 7.433 30.429 -9.515 1 75.39 ? PB GDP 200 D 1 
HETATM 2 O O1B GDP . . . E 4 8.085 30.599 -10.832 1 75.33 ? O1B GDP 200 D 1 
HETATM 3 O O2B GDP . . . E 4 8.117 31.274 -8.414 1 72.8 ? O2B GDP 200 D 1 
HETATM 4 O O3B GDP . . . E 4 5.964 30.855 -9.658 1 74.77 ? O3B GDP 200 D 1 
HETATM 5 O O3A GDP . . . E 4 7.526 28.871 -9.174 1 77.03 ? O3A GDP 200 D 1 
HETATM 6 P PA GDP . . . E 4 8.058 28.317 -7.768 1 80.45 ? PA GDP 200 D 1 
HETATM 7 O O1A GDP . . . E 4 9.52 28.465 -7.621 1 79.59 ? O1A GDP 200 D 1 
HETATM 8 O O2A GDP . . . E 4 7.283 28.917 -6.575 1 80.54 ? O2A GDP 200 D 1 
HETATM 9 O O5' GDP . . . E 4 7.691 26.762 -7.928 1 82.43 ? O5' GDP 200 D 1 
HETATM 10 C C5' GDP . . . E 4 6.337 26.372 -7.881 1 84.01 ? C5' GDP 200 D 1 
HETATM 11 C C4' GDP . . . E 4 6.277 24.922 -7.434 1 85.41 ? C4' GDP 200 D 1 
HETATM 12 O O4' GDP . . . E 4 7.159 24.181 -8.248 1 85.95 ? O4' GDP 200 D 1 
HETATM 13 C C3' GDP . . . E 4 6.741 24.74 -5.998 1 86.22 ? C3' GDP 200 D 1 
HETATM 14 O O3' GDP . . . E 4 5.855 23.837 -5.361 1 86.77 ? O3' GDP 200 D 1 
HETATM 15 C C2' GDP . . . E 4 8.155 24.192 -6.141 1 86.44 ? C2' GDP 200 D 1 
HETATM 16 O O2' GDP . . . E 4 8.545 23.307 -5.116 1 86.9 ? O2' GDP 200 D 1 
HETATM 17 C C1' GDP . . . E 4 8.086 23.468 -7.467 1 86.63 ? C1' GDP 200 D 1 
HETATM 18 N N9 GDP . . . E 4 9.355 23.493 -8.188 1 87.71 ? N9 GDP 200 D 1 
HETATM 19 C C8 GDP . . . E 4 10.047 24.6 -8.593 1 88.44 ? C8 GDP 200 D 1 
HETATM 20 N N7 GDP . . . E 4 11.158 24.181 -9.246 1 88.8 ? N7 GDP 200 D 1 
HETATM 21 C C5 GDP . . . E 4 11.168 22.83 -9.271 1 89.22 ? C5 GDP 200 D 1 
HETATM 22 C C6 GDP . . . E 4 12.055 21.901 -9.806 1 90.09 ? C6 GDP 200 D 1 
HETATM 23 O O6 GDP . . . E 4 13.139 22.269 -10.273 1 90.24 ? O6 GDP 200 D 1 
HETATM 24 N N1 GDP . . . E 4 11.779 20.552 -9.664 1 89.68 ? N1 GDP 200 D 1 
HETATM 25 C C2 GDP . . . E 4 10.638 20.144 -9 1 89.06 ? C2 GDP 200 D 1 
HETATM 26 N N2 GDP . . . E 4 10.473 18.866 -8.678 1 88.56 ? N2 GDP 200 D 1 
HETATM 27 N N3 GDP . . . E 4 9.769 21.074 -8.48 1 88.99 ? N3 GDP 200 D 1 
HETATM 28 C C4 GDP . . . E 4 10.033 22.39 -8.611 1 88.59 ? C4 GDP 200 D 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#