data_8E0B
#
_model_server_result.job_id            2jwPOHBYNe47omUVQtCyzw 
_model_server_result.datetime_utc      '2024-10-11 06:17:01' 
_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          8e0b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":204}' 
#
_entry.id    8E0B 
#
_exptl.entry_id    8E0B 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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          106.17 
_cell.angle_gamma         90 
_cell.entry_id            8E0B 
_cell.length_a            52.971 
_cell.length_b            61.814 
_cell.length_c            70.681 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8E0B 
_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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,J 1 1 
B,F,G,H,I,K 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
? 3 E N N 
? 3 I 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 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                     8E0B 
_atom_sites.fract_transf_matrix[1][1]    0.018878 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005472 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016178 
_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]    0.014731 
_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 SO4 A 1 201 5 SO4 SO4 . 
D 2 SO4 A 1 202 3 SO4 SO4 . 
E 3 GDP A 1 203 1 GDP GDP . 
F 2 SO4 B 1 201 1 SO4 SO4 . 
G 2 SO4 B 1 202 2 SO4 SO4 . 
H 2 SO4 B 1 203 4 SO4 SO4 . 
I 3 GDP B 1 204 2 GDP GDP . 
J 4 HOH A 1 301 131 HOH HOH . 
J 4 HOH A 2 302 81 HOH HOH . 
J 4 HOH A 3 303 78 HOH HOH . 
J 4 HOH A 4 304 94 HOH HOH . 
J 4 HOH A 5 305 80 HOH HOH . 
J 4 HOH A 6 306 48 HOH HOH . 
J 4 HOH A 7 307 65 HOH HOH . 
J 4 HOH A 8 308 73 HOH HOH . 
J 4 HOH A 9 309 67 HOH HOH . 
J 4 HOH A 10 310 43 HOH HOH . 
J 4 HOH A 11 311 11 HOH HOH . 
J 4 HOH A 12 312 1 HOH HOH . 
J 4 HOH A 13 313 55 HOH HOH . 
J 4 HOH A 14 314 18 HOH HOH . 
J 4 HOH A 15 315 23 HOH HOH . 
J 4 HOH A 16 316 37 HOH HOH . 
J 4 HOH A 17 317 126 HOH HOH . 
J 4 HOH A 18 318 6 HOH HOH . 
J 4 HOH A 19 319 91 HOH HOH . 
J 4 HOH A 20 320 15 HOH HOH . 
J 4 HOH A 21 321 74 HOH HOH . 
J 4 HOH A 22 322 127 HOH HOH . 
J 4 HOH A 23 323 28 HOH HOH . 
J 4 HOH A 24 324 14 HOH HOH . 
J 4 HOH A 25 325 39 HOH HOH . 
J 4 HOH A 26 326 79 HOH HOH . 
J 4 HOH A 27 327 3 HOH HOH . 
J 4 HOH A 28 328 109 HOH HOH . 
J 4 HOH A 29 329 20 HOH HOH . 
J 4 HOH A 30 330 115 HOH HOH . 
J 4 HOH A 31 331 29 HOH HOH . 
J 4 HOH A 32 332 103 HOH HOH . 
J 4 HOH A 33 333 35 HOH HOH . 
J 4 HOH A 34 334 85 HOH HOH . 
J 4 HOH A 35 335 116 HOH HOH . 
J 4 HOH A 36 336 129 HOH HOH . 
J 4 HOH A 37 337 68 HOH HOH . 
J 4 HOH A 38 338 122 HOH HOH . 
J 4 HOH A 39 339 128 HOH HOH . 
J 4 HOH A 40 340 132 HOH HOH . 
J 4 HOH A 41 341 46 HOH HOH . 
J 4 HOH A 42 342 100 HOH HOH . 
J 4 HOH A 43 343 7 HOH HOH . 
J 4 HOH A 44 344 45 HOH HOH . 
J 4 HOH A 45 345 24 HOH HOH . 
J 4 HOH A 46 346 118 HOH HOH . 
J 4 HOH A 47 347 124 HOH HOH . 
J 4 HOH A 48 348 44 HOH HOH . 
J 4 HOH A 49 349 130 HOH HOH . 
J 4 HOH A 50 350 60 HOH HOH . 
J 4 HOH A 51 351 12 HOH HOH . 
J 4 HOH A 52 352 99 HOH HOH . 
J 4 HOH A 53 353 77 HOH HOH . 
J 4 HOH A 54 354 120 HOH HOH . 
J 4 HOH A 55 355 72 HOH HOH . 
J 4 HOH A 56 356 58 HOH HOH . 
J 4 HOH A 57 357 51 HOH HOH . 
J 4 HOH A 58 358 125 HOH HOH . 
J 4 HOH A 59 359 117 HOH HOH . 
J 4 HOH A 60 360 108 HOH HOH . 
J 4 HOH A 61 361 19 HOH HOH . 
J 4 HOH A 62 362 54 HOH HOH . 
J 4 HOH A 63 363 69 HOH HOH . 
J 4 HOH A 64 364 135 HOH HOH . 
J 4 HOH A 65 365 105 HOH HOH . 
J 4 HOH A 66 366 113 HOH HOH . 
J 4 HOH A 67 367 57 HOH HOH . 
J 4 HOH A 68 368 133 HOH HOH . 
J 4 HOH A 69 369 104 HOH HOH . 
J 4 HOH A 70 370 59 HOH HOH . 
J 4 HOH A 71 371 121 HOH HOH . 
J 4 HOH A 72 372 22 HOH HOH . 
J 4 HOH A 73 373 96 HOH HOH . 
J 4 HOH A 74 374 136 HOH HOH . 
K 4 HOH B 1 301 50 HOH HOH . 
K 4 HOH B 2 302 93 HOH HOH . 
K 4 HOH B 3 303 110 HOH HOH . 
K 4 HOH B 4 304 31 HOH HOH . 
K 4 HOH B 5 305 92 HOH HOH . 
K 4 HOH B 6 306 83 HOH HOH . 
K 4 HOH B 7 307 38 HOH HOH . 
K 4 HOH B 8 308 17 HOH HOH . 
K 4 HOH B 9 309 21 HOH HOH . 
K 4 HOH B 10 310 62 HOH HOH . 
K 4 HOH B 11 311 9 HOH HOH . 
K 4 HOH B 12 312 8 HOH HOH . 
K 4 HOH B 13 313 75 HOH HOH . 
K 4 HOH B 14 314 87 HOH HOH . 
K 4 HOH B 15 315 41 HOH HOH . 
K 4 HOH B 16 316 36 HOH HOH . 
K 4 HOH B 17 317 84 HOH HOH . 
K 4 HOH B 18 318 119 HOH HOH . 
K 4 HOH B 19 319 13 HOH HOH . 
K 4 HOH B 20 320 5 HOH HOH . 
K 4 HOH B 21 321 52 HOH HOH . 
K 4 HOH B 22 322 40 HOH HOH . 
K 4 HOH B 23 323 4 HOH HOH . 
K 4 HOH B 24 324 70 HOH HOH . 
K 4 HOH B 25 325 106 HOH HOH . 
K 4 HOH B 26 326 66 HOH HOH . 
K 4 HOH B 27 327 26 HOH HOH . 
K 4 HOH B 28 328 27 HOH HOH . 
K 4 HOH B 29 329 16 HOH HOH . 
K 4 HOH B 30 330 89 HOH HOH . 
K 4 HOH B 31 331 25 HOH HOH . 
K 4 HOH B 32 332 114 HOH HOH . 
K 4 HOH B 33 333 76 HOH HOH . 
K 4 HOH B 34 334 64 HOH HOH . 
K 4 HOH B 35 335 49 HOH HOH . 
K 4 HOH B 36 336 56 HOH HOH . 
K 4 HOH B 37 337 10 HOH HOH . 
K 4 HOH B 38 338 42 HOH HOH . 
K 4 HOH B 39 339 61 HOH HOH . 
K 4 HOH B 40 340 97 HOH HOH . 
K 4 HOH B 41 341 86 HOH HOH . 
K 4 HOH B 42 342 112 HOH HOH . 
K 4 HOH B 43 343 47 HOH HOH . 
K 4 HOH B 44 344 88 HOH HOH . 
K 4 HOH B 45 345 34 HOH HOH . 
K 4 HOH B 46 346 123 HOH HOH . 
K 4 HOH B 47 347 107 HOH HOH . 
K 4 HOH B 48 348 30 HOH HOH . 
K 4 HOH B 49 349 95 HOH HOH . 
K 4 HOH B 50 350 98 HOH HOH . 
K 4 HOH B 51 351 63 HOH HOH . 
K 4 HOH B 52 352 102 HOH HOH . 
K 4 HOH B 53 353 101 HOH HOH . 
K 4 HOH B 54 354 33 HOH HOH . 
K 4 HOH B 55 355 71 HOH HOH . 
K 4 HOH B 56 356 111 HOH HOH . 
K 4 HOH B 57 357 53 HOH HOH . 
K 4 HOH B 58 358 90 HOH HOH . 
K 4 HOH B 59 359 134 HOH HOH . 
K 4 HOH B 60 360 82 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 . . . I 3 20.823 7.646 252.404 1 31.13 ? PB GDP 204 B 1 
HETATM 2 O O1B GDP . . . I 3 20.468 7.153 250.982 1 33.33 ? O1B GDP 204 B 1 
HETATM 3 O O2B GDP . . . I 3 19.549 7.947 253.118 1 22.99 ? O2B GDP 204 B 1 
HETATM 4 O O3B GDP . . . I 3 21.755 8.843 252.305 1 29.74 ? O3B GDP 204 B 1 
HETATM 5 O O3A GDP . . . I 3 21.55 6.505 253.144 1 23.23 ? O3A GDP 204 B 1 
HETATM 6 P PA GDP . . . I 3 22.964 6.536 253.834 1 26.76 ? PA GDP 204 B 1 
HETATM 7 O O1A GDP . . . I 3 24.115 6.971 252.911 1 30.64 ? O1A GDP 204 B 1 
HETATM 8 O O2A GDP . . . I 3 22.889 7.457 255.046 1 23.32 ? O2A GDP 204 B 1 
HETATM 9 O O5' GDP . . . I 3 23.249 5.053 254.317 1 29.58 ? O5' GDP 204 B 1 
HETATM 10 C C5' GDP . . . I 3 22.256 4.438 255.092 1 26.36 ? C5' GDP 204 B 1 
HETATM 11 C C4' GDP . . . I 3 22.851 3.261 255.794 1 30.23 ? C4' GDP 204 B 1 
HETATM 12 O O4' GDP . . . I 3 23.035 2.256 254.97 1 29.66 ? O4' GDP 204 B 1 
HETATM 13 C C3' GDP . . . I 3 24.32 3.691 256.424 1 35.48 ? C3' GDP 204 B 1 
HETATM 14 O O3' GDP . . . I 3 24.389 3.111 257.806 1 29.86 ? O3' GDP 204 B 1 
HETATM 15 C C2' GDP . . . I 3 25.195 3.244 255.639 1 35.98 ? C2' GDP 204 B 1 
HETATM 16 O O2' GDP . . . I 3 26.48 2.918 256.298 1 39.47 ? O2' GDP 204 B 1 
HETATM 17 C C1' GDP . . . I 3 24.495 1.903 255.125 1 28.18 ? C1' GDP 204 B 1 
HETATM 18 N N9 GDP . . . I 3 25.055 1.322 254.091 1 33.7 ? N9 GDP 204 B 1 
HETATM 19 C C8 GDP . . . I 3 25.214 2.286 253.135 1 29.2 ? C8 GDP 204 B 1 
HETATM 20 N N7 GDP . . . I 3 25.813 1.726 252.037 1 25.68 ? N7 GDP 204 B 1 
HETATM 21 C C5 GDP . . . I 3 26.021 0.407 252.32 1 36.06 ? C5 GDP 204 B 1 
HETATM 22 C C6 GDP . . . I 3 26.62 -0.778 251.578 1 31.12 ? C6 GDP 204 B 1 
HETATM 23 O O6 GDP . . . I 3 27.065 -0.687 250.468 1 34.33 ? O6 GDP 204 B 1 
HETATM 24 N N1 GDP . . . I 3 26.681 -2.03 252.2 1 30.99 ? N1 GDP 204 B 1 
HETATM 25 C C2 GDP . . . I 3 26.18 -2.206 253.507 1 33.03 ? C2 GDP 204 B 1 
HETATM 26 N N2 GDP . . . I 3 26.229 -3.459 254.152 1 35.62 ? N2 GDP 204 B 1 
HETATM 27 N N3 GDP . . . I 3 25.606 -1.095 254.21 1 31.72 ? N3 GDP 204 B 1 
HETATM 28 C C4 GDP . . . I 3 25.551 0.196 253.58 1 39.04 ? C4 GDP 204 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          19 
_model_server_stats.element_count           28 
#