data_6XET
#
_model_server_result.job_id            caFFMPHYwRgxeeqIRfBXTg 
_model_server_result.datetime_utc      '2024-11-22 22:12:57' 
_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          6xet 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":501}' 
#
_entry.id    6XET 
#
_exptl.entry_id    6XET 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          6 
_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            6XET 
_cell.length_a            66.097 
_cell.length_b            126.938 
_cell.length_c            250.461 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XET 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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,I,J,K,L,M,N,O,P,Q,R,S,T 
_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                      6 
_struct_asym.id                             H 
_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 K O3G GTP . C GTP 501 1_555 L MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
metalc ? metalc2 K O2B GTP . C GTP 501 1_555 L MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc3 L MG MG . C MG 502 1_555 R O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc4 L MG MG . C MG 502 1_555 R O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc5 L MG MG . C MG 502 1_555 R O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc6 L MG MG . C MG 502 1_555 R O HOH . C HOH 624 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
#
_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                     6XET 
_atom_sites.fract_transf_matrix[1][1]    0.015129 
_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]    0.007878 
_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]    0.003993 
_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
F 4 GTP A 1 501 501 GTP GTP . 
G 5 SO4 A 1 502 2 SO4 SO4 . 
H 6 GDP B 1 501 501 GDP GDP . 
I 7 TU2 B 1 502 1 TU2 TU2 . 
J 5 SO4 B 1 503 1 SO4 SO4 . 
K 4 GTP C 1 501 501 GTP GTP . 
L 8 MG C 1 502 503 MG MG . 
M 4 GTP D 1 501 501 GTP GTP . 
N 7 TU2 D 1 502 2 TU2 TU2 . 
O 5 SO4 D 1 503 3 SO4 SO4 . 
P 9 HOH A 1 601 149 HOH HOH . 
P 9 HOH A 2 602 160 HOH HOH . 
P 9 HOH A 3 603 6 HOH HOH . 
P 9 HOH A 4 604 134 HOH HOH . 
P 9 HOH A 5 605 163 HOH HOH . 
P 9 HOH A 6 606 247 HOH HOH . 
P 9 HOH A 7 607 157 HOH HOH . 
P 9 HOH A 8 608 147 HOH HOH . 
P 9 HOH A 9 609 248 HOH HOH . 
P 9 HOH A 10 610 238 HOH HOH . 
P 9 HOH A 11 611 250 HOH HOH . 
P 9 HOH A 12 612 165 HOH HOH . 
P 9 HOH A 13 613 140 HOH HOH . 
P 9 HOH A 14 614 249 HOH HOH . 
P 9 HOH A 15 615 135 HOH HOH . 
P 9 HOH A 16 616 151 HOH HOH . 
P 9 HOH A 17 617 146 HOH HOH . 
P 9 HOH A 18 618 141 HOH HOH . 
P 9 HOH A 19 619 162 HOH HOH . 
P 9 HOH A 20 620 143 HOH HOH . 
P 9 HOH A 21 621 164 HOH HOH . 
P 9 HOH A 22 622 289 HOH HOH . 
P 9 HOH A 23 623 251 HOH HOH . 
P 9 HOH A 24 624 246 HOH HOH . 
P 9 HOH A 25 625 241 HOH HOH . 
P 9 HOH A 26 626 137 HOH HOH . 
P 9 HOH A 27 627 159 HOH HOH . 
P 9 HOH A 28 628 158 HOH HOH . 
P 9 HOH A 29 629 183 HOH HOH . 
P 9 HOH A 30 630 243 HOH HOH . 
P 9 HOH A 31 631 239 HOH HOH . 
P 9 HOH A 32 632 227 HOH HOH . 
P 9 HOH A 33 633 242 HOH HOH . 
P 9 HOH A 34 634 303 HOH HOH . 
Q 9 HOH B 1 601 176 HOH HOH . 
Q 9 HOH B 2 602 188 HOH HOH . 
Q 9 HOH B 3 603 173 HOH HOH . 
Q 9 HOH B 4 604 168 HOH HOH . 
Q 9 HOH B 5 605 171 HOH HOH . 
Q 9 HOH B 6 606 254 HOH HOH . 
Q 9 HOH B 7 607 181 HOH HOH . 
Q 9 HOH B 8 608 290 HOH HOH . 
Q 9 HOH B 9 609 275 HOH HOH . 
Q 9 HOH B 10 610 260 HOH HOH . 
Q 9 HOH B 11 611 5 HOH HOH . 
Q 9 HOH B 12 612 259 HOH HOH . 
Q 9 HOH B 13 613 245 HOH HOH . 
Q 9 HOH B 14 614 180 HOH HOH . 
Q 9 HOH B 15 615 179 HOH HOH . 
Q 9 HOH B 16 616 182 HOH HOH . 
Q 9 HOH B 17 617 178 HOH HOH . 
Q 9 HOH B 18 618 292 HOH HOH . 
Q 9 HOH B 19 619 177 HOH HOH . 
Q 9 HOH B 20 620 252 HOH HOH . 
Q 9 HOH B 21 621 167 HOH HOH . 
Q 9 HOH B 22 622 166 HOH HOH . 
Q 9 HOH B 23 623 184 HOH HOH . 
Q 9 HOH B 24 624 261 HOH HOH . 
Q 9 HOH B 25 625 276 HOH HOH . 
Q 9 HOH B 26 626 258 HOH HOH . 
Q 9 HOH B 27 627 262 HOH HOH . 
Q 9 HOH B 28 628 4 HOH HOH . 
Q 9 HOH B 29 629 185 HOH HOH . 
Q 9 HOH B 30 630 187 HOH HOH . 
Q 9 HOH B 31 631 169 HOH HOH . 
Q 9 HOH B 32 632 170 HOH HOH . 
Q 9 HOH B 33 633 186 HOH HOH . 
Q 9 HOH B 34 634 175 HOH HOH . 
Q 9 HOH B 35 635 263 HOH HOH . 
Q 9 HOH B 36 636 244 HOH HOH . 
Q 9 HOH B 37 637 161 HOH HOH . 
R 9 HOH C 1 601 194 HOH HOH . 
R 9 HOH C 2 602 201 HOH HOH . 
R 9 HOH C 3 603 132 HOH HOH . 
R 9 HOH C 4 604 306 HOH HOH . 
R 9 HOH C 5 605 223 HOH HOH . 
R 9 HOH C 6 606 131 HOH HOH . 
R 9 HOH C 7 607 130 HOH HOH . 
R 9 HOH C 8 608 202 HOH HOH . 
R 9 HOH C 9 609 267 HOH HOH . 
R 9 HOH C 10 610 287 HOH HOH . 
R 9 HOH C 11 611 204 HOH HOH . 
R 9 HOH C 12 612 197 HOH HOH . 
R 9 HOH C 13 613 279 HOH HOH . 
R 9 HOH C 14 614 266 HOH HOH . 
R 9 HOH C 15 615 264 HOH HOH . 
R 9 HOH C 16 616 281 HOH HOH . 
R 9 HOH C 17 617 269 HOH HOH . 
R 9 HOH C 18 618 228 HOH HOH . 
R 9 HOH C 19 619 190 HOH HOH . 
R 9 HOH C 20 620 236 HOH HOH . 
R 9 HOH C 21 621 280 HOH HOH . 
R 9 HOH C 22 622 206 HOH HOH . 
R 9 HOH C 23 623 270 HOH HOH . 
R 9 HOH C 24 624 133 HOH HOH . 
R 9 HOH C 25 625 203 HOH HOH . 
R 9 HOH C 26 626 268 HOH HOH . 
R 9 HOH C 27 627 229 HOH HOH . 
R 9 HOH C 28 628 265 HOH HOH . 
R 9 HOH C 29 629 199 HOH HOH . 
R 9 HOH C 30 630 291 HOH HOH . 
R 9 HOH C 31 631 193 HOH HOH . 
R 9 HOH C 32 632 195 HOH HOH . 
R 9 HOH C 33 633 278 HOH HOH . 
R 9 HOH C 34 634 192 HOH HOH . 
R 9 HOH C 35 635 174 HOH HOH . 
R 9 HOH C 36 636 293 HOH HOH . 
R 9 HOH C 37 637 200 HOH HOH . 
S 9 HOH D 1 601 304 HOH HOH . 
S 9 HOH D 2 602 224 HOH HOH . 
S 9 HOH D 3 603 213 HOH HOH . 
S 9 HOH D 4 604 209 HOH HOH . 
S 9 HOH D 5 605 294 HOH HOH . 
S 9 HOH D 6 606 211 HOH HOH . 
S 9 HOH D 7 607 3 HOH HOH . 
S 9 HOH D 8 608 215 HOH HOH . 
S 9 HOH D 9 609 205 HOH HOH . 
S 9 HOH D 10 610 212 HOH HOH . 
S 9 HOH D 11 611 1 HOH HOH . 
S 9 HOH D 12 612 222 HOH HOH . 
S 9 HOH D 13 613 219 HOH HOH . 
S 9 HOH D 14 614 208 HOH HOH . 
S 9 HOH D 15 615 214 HOH HOH . 
S 9 HOH D 16 616 196 HOH HOH . 
S 9 HOH D 17 617 283 HOH HOH . 
S 9 HOH D 18 618 210 HOH HOH . 
S 9 HOH D 19 619 305 HOH HOH . 
S 9 HOH D 20 620 237 HOH HOH . 
S 9 HOH D 21 621 220 HOH HOH . 
S 9 HOH D 22 622 295 HOH HOH . 
S 9 HOH D 23 623 232 HOH HOH . 
S 9 HOH D 24 624 284 HOH HOH . 
S 9 HOH D 25 625 297 HOH HOH . 
S 9 HOH D 26 626 282 HOH HOH . 
S 9 HOH D 27 627 298 HOH HOH . 
S 9 HOH D 28 628 307 HOH HOH . 
S 9 HOH D 29 629 286 HOH HOH . 
T 9 HOH E 1 201 302 HOH HOH . 
T 9 HOH E 2 202 145 HOH HOH . 
T 9 HOH E 3 203 207 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 . . . H 6 4.332 21.425 33.563 1 44.52 ? PB GDP 501 B 1 
HETATM 2 O O1B GDP . . . H 6 5.677 22.1 33.622 1 50.47 ? O1B GDP 501 B 1 
HETATM 3 O O2B GDP . . . H 6 3.234 22.156 34.285 1 40.32 ? O2B GDP 501 B 1 
HETATM 4 O O3B GDP . . . H 6 4.464 20.027 34.133 1 47.69 ? O3B GDP 501 B 1 
HETATM 5 O O3A GDP . . . H 6 3.971 21.444 32.001 1 48.79 ? O3A GDP 501 B 1 
HETATM 6 P PA GDP . . . H 6 2.63 20.819 31.396 1 46.61 ? PA GDP 501 B 1 
HETATM 7 O O1A GDP . . . H 6 1.626 21.837 30.938 1 57.79 ? O1A GDP 501 B 1 
HETATM 8 O O2A GDP . . . H 6 1.951 19.871 32.353 1 53.36 ? O2A GDP 501 B 1 
HETATM 9 O O5' GDP . . . H 6 3.394 20.1 30.159 1 41.05 ? O5' GDP 501 B 1 
HETATM 10 C C5' GDP . . . H 6 3.014 20.265 28.796 1 40.31 ? C5' GDP 501 B 1 
HETATM 11 C C4' GDP . . . H 6 2.566 18.93 28.242 1 40.43 ? C4' GDP 501 B 1 
HETATM 12 O O4' GDP . . . H 6 1.371 18.664 28.951 1 39.57 ? O4' GDP 501 B 1 
HETATM 13 C C3' GDP . . . H 6 2.18 18.982 26.77 1 43.17 ? C3' GDP 501 B 1 
HETATM 14 O O3' GDP . . . H 6 2.531 17.746 26.159 1 44.1 ? O3' GDP 501 B 1 
HETATM 15 C C2' GDP . . . H 6 0.671 19.078 26.742 1 46.11 ? C2' GDP 501 B 1 
HETATM 16 O O2' GDP . . . H 6 0.161 18.226 25.728 1 57.98 ? O2' GDP 501 B 1 
HETATM 17 C C1' GDP . . . H 6 0.29 18.446 28.057 1 44.23 ? C1' GDP 501 B 1 
HETATM 18 N N9 GDP . . . H 6 -0.915 18.97 28.736 1 41.36 ? N9 GDP 501 B 1 
HETATM 19 C C8 GDP . . . H 6 -0.999 20.114 29.423 1 39.84 ? C8 GDP 501 B 1 
HETATM 20 N N7 GDP . . . H 6 -2.244 20.267 29.943 1 39.68 ? N7 GDP 501 B 1 
HETATM 21 C C5 GDP . . . H 6 -2.968 19.195 29.613 1 40.12 ? C5 GDP 501 B 1 
HETATM 22 C C6 GDP . . . H 6 -4.347 18.728 29.856 1 44.17 ? C6 GDP 501 B 1 
HETATM 23 O O6 GDP . . . H 6 -5.149 19.411 30.528 1 43.57 ? O6 GDP 501 B 1 
HETATM 24 N N1 GDP . . . H 6 -4.697 17.551 29.32 1 48.78 ? N1 GDP 501 B 1 
HETATM 25 C C2 GDP . . . H 6 -3.845 16.799 28.585 1 47.46 ? C2 GDP 501 B 1 
HETATM 26 N N2 GDP . . . H 6 -4.261 15.618 28.073 1 46.83 ? N2 GDP 501 B 1 
HETATM 27 N N3 GDP . . . H 6 -2.568 17.167 28.334 1 48.68 ? N3 GDP 501 B 1 
HETATM 28 C C4 GDP . . . H 6 -2.086 18.337 28.815 1 44.17 ? C4 GDP 501 B 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           28 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           28 
#