data_1KSH
#
_model_server_result.job_id            CgM8lhPel5Y3ri0DKeFv6w 
_model_server_result.datetime_utc      '2024-11-05 13:42:01' 
_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          1ksh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":201}' 
#
_entry.id    1KSH 
#
_exptl.entry_id    1KSH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_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            1KSH 
_cell.length_a            44.454 
_cell.length_b            65.395 
_cell.length_c            104.409 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1KSH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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                      5 
_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
covale ? covale1 A C SER 136 A SER 134 1_555 A N CME 137 A CME 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C CME 137 A CME 135 1_555 A N ASN 138 A ASN 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 B C GLN 87 B GLN 85 1_555 B N CME 88 B CME 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale4 B C CME 88 B CME 86 1_555 B N LEU 89 B LEU 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
metalc ? metalc1 A OG1 THR 32 A THR 30 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc2 A OG1 THR 49 A THR 47 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc3 E O1B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? 
metalc ? metalc4 C MG MG . A MG 202 1_555 D O1 PO4 . A PO4 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc5 C MG MG . A MG 202 1_555 F O HOH . A HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc6 C MG MG . A MG 202 1_555 F O HOH . A HOH 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
#
_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 104 n n 
PB O2B GDP sing 105 n n 
PB O3B GDP sing 106 n n 
PB O3A GDP sing 107 n n 
O2B HOB2 GDP sing 108 n n 
O3B HOB3 GDP sing 109 n n 
O3A PA GDP sing 110 n n 
PA O1A GDP doub 111 n n 
PA O2A GDP sing 112 n n 
PA O5' GDP sing 113 n n 
O2A HOA2 GDP sing 114 n n 
O5' C5' GDP sing 115 n n 
C5' C4' GDP sing 116 n n 
C5' H5' GDP sing 117 n n 
C5' "H5''" GDP sing 118 n n 
C4' O4' GDP sing 119 n n 
C4' C3' GDP sing 120 n n 
C4' H4' GDP sing 121 n n 
O4' C1' GDP sing 122 n n 
C3' O3' GDP sing 123 n n 
C3' C2' GDP sing 124 n n 
C3' H3' GDP sing 125 n n 
O3' HO3' GDP sing 126 n n 
C2' O2' GDP sing 127 n n 
C2' C1' GDP sing 128 n n 
C2' H2' GDP sing 129 n n 
O2' HO2' GDP sing 130 n n 
C1' N9 GDP sing 131 n n 
C1' H1' GDP sing 132 n n 
N9 C8 GDP sing 133 n y 
N9 C4 GDP sing 134 n y 
C8 N7 GDP doub 135 n y 
C8 H8 GDP sing 136 n n 
N7 C5 GDP sing 137 n y 
C5 C6 GDP sing 138 n n 
C5 C4 GDP doub 139 n y 
C6 O6 GDP doub 140 n n 
C6 N1 GDP sing 141 n n 
N1 C2 GDP sing 142 n n 
N1 HN1 GDP sing 143 n n 
C2 N2 GDP sing 144 n n 
C2 N3 GDP doub 145 n n 
N2 HN21 GDP sing 146 n n 
N2 HN22 GDP sing 147 n n 
N3 C4 GDP sing 148 n n 
#
_atom_sites.entry_id                     1KSH 
_atom_sites.fract_transf_matrix[1][1]    0.022495 
_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]    0.015292 
_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]    0.009578 
_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 MG A 1 202 2 MG MG . 
D 4 PO4 A 1 203 3 PO4 PO4 . 
E 5 GDP A 1 201 1 GDP GDP . 
F 6 HOH A 1 204 1 HOH WAT . 
F 6 HOH A 2 205 2 HOH WAT . 
F 6 HOH A 3 206 3 HOH WAT . 
F 6 HOH A 4 207 10 HOH WAT . 
F 6 HOH A 5 208 11 HOH WAT . 
F 6 HOH A 6 209 12 HOH WAT . 
F 6 HOH A 7 210 13 HOH WAT . 
F 6 HOH A 8 211 18 HOH WAT . 
F 6 HOH A 9 212 19 HOH WAT . 
F 6 HOH A 10 213 20 HOH WAT . 
F 6 HOH A 11 214 21 HOH WAT . 
F 6 HOH A 12 215 22 HOH WAT . 
F 6 HOH A 13 216 23 HOH WAT . 
F 6 HOH A 14 217 24 HOH WAT . 
F 6 HOH A 15 218 25 HOH WAT . 
F 6 HOH A 16 219 26 HOH WAT . 
F 6 HOH A 17 220 27 HOH WAT . 
F 6 HOH A 18 221 29 HOH WAT . 
F 6 HOH A 19 222 30 HOH WAT . 
F 6 HOH A 20 223 31 HOH WAT . 
F 6 HOH A 21 224 32 HOH WAT . 
F 6 HOH A 22 225 35 HOH WAT . 
F 6 HOH A 23 226 36 HOH WAT . 
F 6 HOH A 24 227 39 HOH WAT . 
F 6 HOH A 25 228 40 HOH WAT . 
F 6 HOH A 26 229 41 HOH WAT . 
F 6 HOH A 27 230 42 HOH WAT . 
F 6 HOH A 28 231 43 HOH WAT . 
F 6 HOH A 29 232 44 HOH WAT . 
F 6 HOH A 30 233 45 HOH WAT . 
F 6 HOH A 31 234 46 HOH WAT . 
F 6 HOH A 32 235 47 HOH WAT . 
F 6 HOH A 33 236 52 HOH WAT . 
F 6 HOH A 34 237 54 HOH WAT . 
F 6 HOH A 35 238 55 HOH WAT . 
F 6 HOH A 36 239 58 HOH WAT . 
F 6 HOH A 37 240 59 HOH WAT . 
F 6 HOH A 38 241 60 HOH WAT . 
F 6 HOH A 39 242 61 HOH WAT . 
F 6 HOH A 40 243 62 HOH WAT . 
F 6 HOH A 41 244 63 HOH WAT . 
F 6 HOH A 42 245 64 HOH WAT . 
F 6 HOH A 43 246 66 HOH WAT . 
F 6 HOH A 44 247 67 HOH WAT . 
F 6 HOH A 45 248 69 HOH WAT . 
F 6 HOH A 46 249 70 HOH WAT . 
F 6 HOH A 47 250 74 HOH WAT . 
F 6 HOH A 48 251 75 HOH WAT . 
F 6 HOH A 49 252 76 HOH WAT . 
F 6 HOH A 50 253 77 HOH WAT . 
F 6 HOH A 51 254 78 HOH WAT . 
F 6 HOH A 52 255 81 HOH WAT . 
F 6 HOH A 53 256 84 HOH WAT . 
F 6 HOH A 54 257 87 HOH WAT . 
F 6 HOH A 55 258 90 HOH WAT . 
F 6 HOH A 56 259 91 HOH WAT . 
F 6 HOH A 57 260 92 HOH WAT . 
F 6 HOH A 58 261 93 HOH WAT . 
F 6 HOH A 59 262 100 HOH WAT . 
F 6 HOH A 60 263 102 HOH WAT . 
F 6 HOH A 61 264 103 HOH WAT . 
F 6 HOH A 62 265 104 HOH WAT . 
F 6 HOH A 63 266 106 HOH WAT . 
F 6 HOH A 64 267 111 HOH WAT . 
F 6 HOH A 65 268 114 HOH WAT . 
F 6 HOH A 66 269 116 HOH WAT . 
F 6 HOH A 67 270 117 HOH WAT . 
F 6 HOH A 68 271 118 HOH WAT . 
F 6 HOH A 69 272 119 HOH WAT . 
F 6 HOH A 70 273 121 HOH WAT . 
F 6 HOH A 71 274 123 HOH WAT . 
F 6 HOH A 72 275 124 HOH WAT . 
F 6 HOH A 73 276 125 HOH WAT . 
G 6 HOH B 1 151 4 HOH WAT . 
G 6 HOH B 2 152 5 HOH WAT . 
G 6 HOH B 3 153 6 HOH WAT . 
G 6 HOH B 4 154 7 HOH WAT . 
G 6 HOH B 5 155 8 HOH WAT . 
G 6 HOH B 6 156 9 HOH WAT . 
G 6 HOH B 7 157 14 HOH WAT . 
G 6 HOH B 8 158 15 HOH WAT . 
G 6 HOH B 9 159 16 HOH WAT . 
G 6 HOH B 10 160 17 HOH WAT . 
G 6 HOH B 11 161 28 HOH WAT . 
G 6 HOH B 12 162 33 HOH WAT . 
G 6 HOH B 13 163 34 HOH WAT . 
G 6 HOH B 14 164 37 HOH WAT . 
G 6 HOH B 15 165 38 HOH WAT . 
G 6 HOH B 16 166 48 HOH WAT . 
G 6 HOH B 17 167 49 HOH WAT . 
G 6 HOH B 18 168 50 HOH WAT . 
G 6 HOH B 19 169 51 HOH WAT . 
G 6 HOH B 20 170 53 HOH WAT . 
G 6 HOH B 21 171 56 HOH WAT . 
G 6 HOH B 22 172 57 HOH WAT . 
G 6 HOH B 23 173 68 HOH WAT . 
G 6 HOH B 24 174 71 HOH WAT . 
G 6 HOH B 25 175 72 HOH WAT . 
G 6 HOH B 26 176 73 HOH WAT . 
G 6 HOH B 27 177 79 HOH WAT . 
G 6 HOH B 28 178 82 HOH WAT . 
G 6 HOH B 29 179 83 HOH WAT . 
G 6 HOH B 30 180 85 HOH WAT . 
G 6 HOH B 31 181 86 HOH WAT . 
G 6 HOH B 32 182 88 HOH WAT . 
G 6 HOH B 33 183 89 HOH WAT . 
G 6 HOH B 34 184 94 HOH WAT . 
G 6 HOH B 35 185 95 HOH WAT . 
G 6 HOH B 36 186 96 HOH WAT . 
G 6 HOH B 37 187 97 HOH WAT . 
G 6 HOH B 38 188 98 HOH WAT . 
G 6 HOH B 39 189 99 HOH WAT . 
G 6 HOH B 40 190 101 HOH WAT . 
G 6 HOH B 41 191 105 HOH WAT . 
G 6 HOH B 42 192 108 HOH WAT . 
G 6 HOH B 43 193 109 HOH WAT . 
G 6 HOH B 44 194 110 HOH WAT . 
G 6 HOH B 45 195 112 HOH WAT . 
G 6 HOH B 46 196 113 HOH WAT . 
G 6 HOH B 47 197 115 HOH WAT . 
G 6 HOH B 48 198 120 HOH WAT . 
G 6 HOH B 49 199 122 HOH WAT . 
G 6 HOH B 50 200 126 HOH WAT . 
G 6 HOH B 51 201 127 HOH WAT . 
#
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 5 14.54 3.802 40.106 1 28.84 ? PB GDP 201 A 1 
HETATM 2 O O1B GDP . . . E 5 15.946 3.718 40.531 1 26.15 ? O1B GDP 201 A 1 
HETATM 3 O O2B GDP . . . E 5 13.834 5.123 40.433 1 33.1 ? O2B GDP 201 A 1 
HETATM 4 O O3B GDP . . . E 5 14.148 3.642 38.642 1 28.99 ? O3B GDP 201 A 1 
HETATM 5 O O3A GDP . . . E 5 13.625 2.864 40.98 1 30.62 ? O3A GDP 201 A 1 
HETATM 6 P PA GDP . . . E 5 13.874 1.956 42.117 1 30.89 ? PA GDP 201 A 1 
HETATM 7 O O1A GDP . . . E 5 14.828 0.827 41.765 1 30.03 ? O1A GDP 201 A 1 
HETATM 8 O O2A GDP . . . E 5 14.528 2.708 43.262 1 27 ? O2A GDP 201 A 1 
HETATM 9 O O5' GDP . . . E 5 12.499 1.406 42.433 1 30.91 ? O5' GDP 201 A 1 
HETATM 10 C C5' GDP . . . E 5 11.431 2.265 42.82 1 32.63 ? C5' GDP 201 A 1 
HETATM 11 C C4' GDP . . . E 5 10.371 1.454 43.658 1 34.41 ? C4' GDP 201 A 1 
HETATM 12 O O4' GDP . . . E 5 9.854 0.422 42.857 1 34.53 ? O4' GDP 201 A 1 
HETATM 13 C C3' GDP . . . E 5 10.977 0.8 44.922 1 36.45 ? C3' GDP 201 A 1 
HETATM 14 O O3' GDP . . . E 5 9.898 0.905 45.875 1 40.92 ? O3' GDP 201 A 1 
HETATM 15 C C2' GDP . . . E 5 11.218 -0.637 44.475 1 37.91 ? C2' GDP 201 A 1 
HETATM 16 O O2' GDP . . . E 5 11.245 -1.639 45.514 1 38.5 ? O2' GDP 201 A 1 
HETATM 17 C C1' GDP . . . E 5 10.083 -0.857 43.471 1 35.97 ? C1' GDP 201 A 1 
HETATM 18 N N9 GDP . . . E 5 10.474 -1.776 42.376 1 39.18 ? N9 GDP 201 A 1 
HETATM 19 C C8 GDP . . . E 5 11.566 -1.736 41.506 1 39.53 ? C8 GDP 201 A 1 
HETATM 20 N N7 GDP . . . E 5 11.562 -2.753 40.636 1 39.21 ? N7 GDP 201 A 1 
HETATM 21 C C5 GDP . . . E 5 10.375 -3.532 40.938 1 38.32 ? C5 GDP 201 A 1 
HETATM 22 C C6 GDP . . . E 5 9.706 -4.802 40.392 1 37.19 ? C6 GDP 201 A 1 
HETATM 23 O O6 GDP . . . E 5 10.184 -5.416 39.45 1 34.61 ? O6 GDP 201 A 1 
HETATM 24 N N1 GDP . . . E 5 8.538 -5.307 40.919 1 39.12 ? N1 GDP 201 A 1 
HETATM 25 C C2 GDP . . . E 5 7.871 -4.705 41.999 1 39.42 ? C2 GDP 201 A 1 
HETATM 26 N N2 GDP . . . E 5 6.74 -5.208 42.505 1 39.68 ? N2 GDP 201 A 1 
HETATM 27 N N3 GDP . . . E 5 8.478 -3.539 42.506 1 39.56 ? N3 GDP 201 A 1 
HETATM 28 C C4 GDP . . . E 5 9.745 -2.941 41.968 1 40.11 ? C4 GDP 201 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           28 
#