data_4DID
#
_model_server_result.job_id            c3NrCyc3ZicW6aEX9avZUg 
_model_server_result.datetime_utc      '2024-11-22 17:07:32' 
_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          4did 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":200}' 
#
_entry.id    4DID 
#
_exptl.entry_id    4DID 
_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    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            4DID 
_cell.length_a            106.88 
_cell.length_b            106.88 
_cell.length_c            87.57 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DID 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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 
_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                      3 
_struct_asym.id                             C 
_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 A OG1 THR 27 A THR 17 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc2 A O THR 45 A THR 35 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc3 C O2B GDP . A GDP 200 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc4 D MG MG . A MG 201 1_555 E O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc5 D MG MG . A MG 201 1_555 E O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc6 D MG MG . A MG 201 1_555 E O HOH . A HOH 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
#
_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                     4DID 
_atom_sites.fract_transf_matrix[1][1]    0.009356 
_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]    0.009356 
_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]    0.011419 
_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 3 GDP A 1 200 200 GDP GDP . 
D 4 MG A 1 201 201 MG MG . 
E 5 HOH A 1 301 1 HOH HOH . 
E 5 HOH A 2 302 2 HOH HOH . 
E 5 HOH A 3 303 3 HOH HOH . 
E 5 HOH A 4 304 4 HOH HOH . 
E 5 HOH A 5 305 5 HOH HOH . 
E 5 HOH A 6 306 7 HOH HOH . 
E 5 HOH A 7 307 9 HOH HOH . 
E 5 HOH A 8 308 11 HOH HOH . 
E 5 HOH A 9 309 12 HOH HOH . 
E 5 HOH A 10 310 14 HOH HOH . 
E 5 HOH A 11 311 15 HOH HOH . 
E 5 HOH A 12 312 16 HOH HOH . 
E 5 HOH A 13 313 20 HOH HOH . 
E 5 HOH A 14 314 21 HOH HOH . 
E 5 HOH A 15 315 22 HOH HOH . 
E 5 HOH A 16 316 23 HOH HOH . 
E 5 HOH A 17 317 25 HOH HOH . 
E 5 HOH A 18 318 26 HOH HOH . 
E 5 HOH A 19 319 28 HOH HOH . 
E 5 HOH A 20 320 29 HOH HOH . 
E 5 HOH A 21 321 31 HOH HOH . 
E 5 HOH A 22 322 32 HOH HOH . 
E 5 HOH A 23 323 33 HOH HOH . 
E 5 HOH A 24 324 34 HOH HOH . 
E 5 HOH A 25 325 36 HOH HOH . 
E 5 HOH A 26 326 37 HOH HOH . 
E 5 HOH A 27 327 38 HOH HOH . 
E 5 HOH A 28 328 39 HOH HOH . 
E 5 HOH A 29 329 40 HOH HOH . 
E 5 HOH A 30 330 42 HOH HOH . 
E 5 HOH A 31 331 43 HOH HOH . 
E 5 HOH A 32 332 45 HOH HOH . 
E 5 HOH A 33 333 46 HOH HOH . 
E 5 HOH A 34 334 47 HOH HOH . 
E 5 HOH A 35 335 48 HOH HOH . 
E 5 HOH A 36 336 53 HOH HOH . 
E 5 HOH A 37 337 54 HOH HOH . 
E 5 HOH A 38 338 57 HOH HOH . 
E 5 HOH A 39 339 58 HOH HOH . 
E 5 HOH A 40 340 63 HOH HOH . 
E 5 HOH A 41 341 64 HOH HOH . 
E 5 HOH A 42 342 66 HOH HOH . 
E 5 HOH A 43 343 70 HOH HOH . 
F 5 HOH B 1 201 6 HOH HOH . 
F 5 HOH B 2 202 8 HOH HOH . 
F 5 HOH B 3 203 10 HOH HOH . 
F 5 HOH B 4 204 13 HOH HOH . 
F 5 HOH B 5 205 17 HOH HOH . 
F 5 HOH B 6 206 18 HOH HOH . 
F 5 HOH B 7 207 19 HOH HOH . 
F 5 HOH B 8 208 24 HOH HOH . 
F 5 HOH B 9 209 27 HOH HOH . 
F 5 HOH B 10 210 30 HOH HOH . 
F 5 HOH B 11 211 35 HOH HOH . 
F 5 HOH B 12 212 41 HOH HOH . 
F 5 HOH B 13 213 44 HOH HOH . 
F 5 HOH B 14 214 49 HOH HOH . 
F 5 HOH B 15 215 50 HOH HOH . 
F 5 HOH B 16 216 51 HOH HOH . 
F 5 HOH B 17 217 52 HOH HOH . 
F 5 HOH B 18 218 55 HOH HOH . 
F 5 HOH B 19 219 56 HOH HOH . 
F 5 HOH B 20 220 59 HOH HOH . 
F 5 HOH B 21 221 60 HOH HOH . 
F 5 HOH B 22 222 61 HOH HOH . 
F 5 HOH B 23 223 62 HOH HOH . 
F 5 HOH B 24 224 65 HOH HOH . 
F 5 HOH B 25 225 67 HOH HOH . 
F 5 HOH B 26 226 68 HOH HOH . 
F 5 HOH B 27 227 69 HOH HOH . 
F 5 HOH B 28 228 71 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 3 28.545 -12.542 7.167 1 45.17 ? PB GDP 200 A 1 
HETATM 2 O O1B GDP . . . C 3 30.034 -12.673 6.945 1 47.62 ? O1B GDP 200 A 1 
HETATM 3 O O2B GDP . . . C 3 28.058 -13.757 7.931 1 45.26 ? O2B GDP 200 A 1 
HETATM 4 O O3B GDP . . . C 3 27.855 -12.44 5.815 1 49.16 ? O3B GDP 200 A 1 
HETATM 5 O O3A GDP . . . C 3 28.135 -11.219 7.973 1 41.56 ? O3A GDP 200 A 1 
HETATM 6 P PA GDP . . . C 3 27.912 -11.104 9.573 1 43.96 ? PA GDP 200 A 1 
HETATM 7 O O1A GDP . . . C 3 29.051 -11.786 10.311 1 39.68 ? O1A GDP 200 A 1 
HETATM 8 O O2A GDP . . . C 3 26.547 -11.631 10.002 1 42.88 ? O2A GDP 200 A 1 
HETATM 9 O O5' GDP . . . C 3 27.932 -9.496 9.736 1 49.58 ? O5' GDP 200 A 1 
HETATM 10 C C5' GDP . . . C 3 29.146 -8.774 9.446 1 47.95 ? C5' GDP 200 A 1 
HETATM 11 C C4' GDP . . . C 3 29.14 -7.382 10.081 1 46.52 ? C4' GDP 200 A 1 
HETATM 12 O O4' GDP . . . C 3 27.985 -6.636 9.652 1 48 ? O4' GDP 200 A 1 
HETATM 13 C C3' GDP . . . C 3 29.061 -7.501 11.592 1 50.13 ? C3' GDP 200 A 1 
HETATM 14 O O3' GDP . . . C 3 29.939 -6.533 12.187 1 49.51 ? O3' GDP 200 A 1 
HETATM 15 C C2' GDP . . . C 3 27.607 -7.186 11.906 1 49.56 ? C2' GDP 200 A 1 
HETATM 16 O O2' GDP . . . C 3 27.407 -6.601 13.191 1 44.71 ? O2' GDP 200 A 1 
HETATM 17 C C1' GDP . . . C 3 27.213 -6.227 10.79 1 46.38 ? C1' GDP 200 A 1 
HETATM 18 N N9 GDP . . . C 3 25.787 -6.357 10.447 1 52.18 ? N9 GDP 200 A 1 
HETATM 19 C C8 GDP . . . C 3 25.148 -7.484 10.048 1 48.02 ? C8 GDP 200 A 1 
HETATM 20 N N7 GDP . . . C 3 23.832 -7.213 9.792 1 46.7 ? N7 GDP 200 A 1 
HETATM 21 C C5 GDP . . . C 3 23.631 -5.904 10.026 1 50.22 ? C5 GDP 200 A 1 
HETATM 22 C C6 GDP . . . C 3 22.488 -4.977 9.954 1 51.18 ? C6 GDP 200 A 1 
HETATM 23 O O6 GDP . . . C 3 21.354 -5.391 9.596 1 54.79 ? O6 GDP 200 A 1 
HETATM 24 N N1 GDP . . . C 3 22.709 -3.695 10.278 1 48.71 ? N1 GDP 200 A 1 
HETATM 25 C C2 GDP . . . C 3 23.916 -3.229 10.663 1 51.4 ? C2 GDP 200 A 1 
HETATM 26 N N2 GDP . . . C 3 24.052 -1.916 10.975 1 48.52 ? N2 GDP 200 A 1 
HETATM 27 N N3 GDP . . . C 3 25.008 -4.025 10.757 1 50.37 ? N3 GDP 200 A 1 
HETATM 28 C C4 GDP . . . C 3 24.922 -5.34 10.452 1 52.08 ? C4 GDP 200 A 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#