data_3SS8
#
_model_server_result.job_id            b8Z3MgwsF0pygJPPwG_bCQ 
_model_server_result.datetime_utc      '2024-12-04 17:09:11' 
_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          3ss8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":300}' 
#
_entry.id    3SS8 
#
_exptl.entry_id    3SS8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          2 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            3SS8 
_cell.length_a            48.346 
_cell.length_b            75.401 
_cell.length_c            156.494 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3SS8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_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,C,D,E,F,K 1 1 
B,G,H,I,J,L 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
? 2 C N N 
? 2 G N 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 OD1 ASN 13 A ASN 11 1_555 D K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? 
metalc ? metalc2 A OG1 THR 17 A THR 15 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc3 A O GLY 31 A GLY 29 1_555 D K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? 
metalc ? metalc4 A O TRP 33 A TRP 31 1_555 D K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? 
metalc ? metalc5 A OG1 THR 37 A THR 35 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc6 K O HOH . A HOH 271 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc7 K O HOH . A HOH 272 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc8 C O2B GDP . A GDP 300 1_555 D K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? 
metalc ? metalc9 C O2A GDP . A GDP 300 1_555 D K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? 
metalc ? metalc10 C O3A GDP . A GDP 300 1_555 D K K . A K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.435 ? 
metalc ? metalc11 C O3B GDP . A GDP 300 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.893 ? 
metalc ? metalc12 B OD1 ASN 13 B ASN 11 1_555 H K K . B K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.142 ? 
metalc ? metalc13 B OG1 THR 17 B THR 15 1_555 I MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc14 B O GLY 31 B GLY 29 1_555 H K K . B K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? 
metalc ? metalc15 B O TRP 33 B TRP 31 1_555 H K K . B K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? 
metalc ? metalc16 B OG1 THR 37 B THR 35 1_555 I MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc17 L O HOH . B HOH 271 1_555 I MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? 
metalc ? metalc18 L O HOH . B HOH 272 1_555 I MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc19 G O2B GDP . B GDP 300 1_555 H K K . B K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc20 G O2A GDP . B GDP 300 1_555 H K K . B K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? 
metalc ? metalc21 G O3A GDP . B GDP 300 1_555 H K K . B K 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.444 ? 
metalc ? metalc22 G O3B GDP . B GDP 300 1_555 I MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
#
_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 87 n n 
PB O2B GDP sing 88 n n 
PB O3B GDP sing 89 n n 
PB O3A GDP sing 90 n n 
O2B HOB2 GDP sing 91 n n 
O3B HOB3 GDP sing 92 n n 
O3A PA GDP sing 93 n n 
PA O1A GDP doub 94 n n 
PA O2A GDP sing 95 n n 
PA O5' GDP sing 96 n n 
O2A HOA2 GDP sing 97 n n 
O5' C5' GDP sing 98 n n 
C5' C4' GDP sing 99 n n 
C5' H5' GDP sing 100 n n 
C5' "H5''" GDP sing 101 n n 
C4' O4' GDP sing 102 n n 
C4' C3' GDP sing 103 n n 
C4' H4' GDP sing 104 n n 
O4' C1' GDP sing 105 n n 
C3' O3' GDP sing 106 n n 
C3' C2' GDP sing 107 n n 
C3' H3' GDP sing 108 n n 
O3' HO3' GDP sing 109 n n 
C2' O2' GDP sing 110 n n 
C2' C1' GDP sing 111 n n 
C2' H2' GDP sing 112 n n 
O2' HO2' GDP sing 113 n n 
C1' N9 GDP sing 114 n n 
C1' H1' GDP sing 115 n n 
N9 C8 GDP sing 116 n y 
N9 C4 GDP sing 117 n y 
C8 N7 GDP doub 118 n y 
C8 H8 GDP sing 119 n n 
N7 C5 GDP sing 120 n y 
C5 C6 GDP sing 121 n n 
C5 C4 GDP doub 122 n y 
C6 O6 GDP doub 123 n n 
C6 N1 GDP sing 124 n n 
N1 C2 GDP sing 125 n n 
N1 HN1 GDP sing 126 n n 
C2 N2 GDP sing 127 n n 
C2 N3 GDP doub 128 n n 
N2 HN21 GDP sing 129 n n 
N2 HN22 GDP sing 130 n n 
N3 C4 GDP sing 131 n n 
#
_atom_sites.entry_id                     3SS8 
_atom_sites.fract_transf_matrix[1][1]    0.020684 
_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]    0.013262 
_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]    0.00639 
_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 GDP A 1 300 300 GDP GDP . 
D 3 K A 1 301 301 K K . 
E 4 MG A 1 302 302 MG MG . 
F 5 ALF A 1 303 303 ALF ALF . 
G 2 GDP B 1 300 300 GDP GDP . 
H 3 K B 1 301 301 K K . 
I 4 MG B 1 302 302 MG MG . 
J 5 ALF B 1 303 303 ALF ALF . 
K 6 HOH A 1 271 1 HOH HOH . 
K 6 HOH A 2 272 2 HOH HOH . 
K 6 HOH A 3 273 5 HOH HOH . 
K 6 HOH A 4 274 12 HOH HOH . 
K 6 HOH A 5 275 13 HOH HOH . 
K 6 HOH A 6 276 14 HOH HOH . 
K 6 HOH A 7 277 15 HOH HOH . 
K 6 HOH A 8 278 23 HOH HOH . 
K 6 HOH A 9 279 24 HOH HOH . 
K 6 HOH A 10 280 25 HOH HOH . 
K 6 HOH A 11 281 28 HOH HOH . 
K 6 HOH A 12 282 29 HOH HOH . 
K 6 HOH A 13 283 30 HOH HOH . 
K 6 HOH A 14 284 32 HOH HOH . 
K 6 HOH A 15 285 34 HOH HOH . 
K 6 HOH A 16 286 36 HOH HOH . 
K 6 HOH A 17 287 38 HOH HOH . 
K 6 HOH A 18 288 39 HOH HOH . 
K 6 HOH A 19 289 40 HOH HOH . 
K 6 HOH A 20 290 41 HOH HOH . 
K 6 HOH A 21 291 42 HOH HOH . 
K 6 HOH A 22 292 43 HOH HOH . 
K 6 HOH A 23 293 45 HOH HOH . 
K 6 HOH A 24 294 46 HOH HOH . 
K 6 HOH A 25 295 48 HOH HOH . 
K 6 HOH A 26 296 50 HOH HOH . 
K 6 HOH A 27 297 51 HOH HOH . 
K 6 HOH A 28 298 52 HOH HOH . 
K 6 HOH A 29 299 53 HOH HOH . 
K 6 HOH A 30 304 54 HOH HOH . 
K 6 HOH A 31 305 55 HOH HOH . 
K 6 HOH A 32 306 56 HOH HOH . 
K 6 HOH A 33 307 60 HOH HOH . 
K 6 HOH A 34 308 61 HOH HOH . 
K 6 HOH A 35 309 62 HOH HOH . 
K 6 HOH A 36 310 63 HOH HOH . 
K 6 HOH A 37 311 64 HOH HOH . 
K 6 HOH A 38 312 65 HOH HOH . 
K 6 HOH A 39 313 66 HOH HOH . 
K 6 HOH A 40 314 67 HOH HOH . 
K 6 HOH A 41 315 68 HOH HOH . 
L 6 HOH B 1 271 3 HOH HOH . 
L 6 HOH B 2 272 4 HOH HOH . 
L 6 HOH B 3 273 6 HOH HOH . 
L 6 HOH B 4 274 7 HOH HOH . 
L 6 HOH B 5 275 8 HOH HOH . 
L 6 HOH B 6 276 9 HOH HOH . 
L 6 HOH B 7 277 10 HOH HOH . 
L 6 HOH B 8 278 11 HOH HOH . 
L 6 HOH B 9 279 16 HOH HOH . 
L 6 HOH B 10 280 17 HOH HOH . 
L 6 HOH B 11 281 18 HOH HOH . 
L 6 HOH B 12 282 19 HOH HOH . 
L 6 HOH B 13 283 20 HOH HOH . 
L 6 HOH B 14 284 21 HOH HOH . 
L 6 HOH B 15 285 22 HOH HOH . 
L 6 HOH B 16 286 26 HOH HOH . 
L 6 HOH B 17 287 27 HOH HOH . 
L 6 HOH B 18 288 31 HOH HOH . 
L 6 HOH B 19 289 33 HOH HOH . 
L 6 HOH B 20 290 35 HOH HOH . 
L 6 HOH B 21 291 37 HOH HOH . 
L 6 HOH B 22 292 44 HOH HOH . 
L 6 HOH B 23 293 47 HOH HOH . 
L 6 HOH B 24 294 49 HOH HOH . 
L 6 HOH B 25 295 57 HOH HOH . 
L 6 HOH B 26 296 58 HOH HOH . 
L 6 HOH B 27 297 59 HOH HOH . 
L 6 HOH B 28 298 69 HOH HOH . 
L 6 HOH B 29 299 70 HOH HOH . 
L 6 HOH B 30 304 71 HOH HOH . 
L 6 HOH B 31 305 72 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 2 6.069 16.929 -34.279 1 18.49 ? PB GDP 300 A 1 
HETATM 2 O O1B GDP . . . C 2 5.038 17.502 -33.356 1 19.8 ? O1B GDP 300 A 1 
HETATM 3 O O2B GDP . . . C 2 5.71 15.434 -34.748 1 16.61 ? O2B GDP 300 A 1 
HETATM 4 O O3B GDP . . . C 2 7.527 16.825 -33.588 1 18.63 ? O3B GDP 300 A 1 
HETATM 5 O O3A GDP . . . C 2 6.227 17.799 -35.619 1 19.47 ? O3A GDP 300 A 1 
HETATM 6 P PA GDP . . . C 2 7.69 18.149 -36.274 1 19.3 ? PA GDP 300 A 1 
HETATM 7 O O1A GDP . . . C 2 8.609 18.835 -35.332 1 19.37 ? O1A GDP 300 A 1 
HETATM 8 O O2A GDP . . . C 2 8.279 16.73 -36.802 1 19.39 ? O2A GDP 300 A 1 
HETATM 9 O O5' GDP . . . C 2 7.375 19.012 -37.553 1 20.23 ? O5' GDP 300 A 1 
HETATM 10 C C5' GDP . . . C 2 6.214 18.727 -38.356 1 20.3 ? C5' GDP 300 A 1 
HETATM 11 C C4' GDP . . . C 2 6.294 19.42 -39.716 1 20.71 ? C4' GDP 300 A 1 
HETATM 12 O O4' GDP . . . C 2 5.855 20.74 -39.411 1 20.51 ? O4' GDP 300 A 1 
HETATM 13 C C3' GDP . . . C 2 7.718 19.537 -40.283 1 20.95 ? C3' GDP 300 A 1 
HETATM 14 O O3' GDP . . . C 2 7.643 19.396 -41.696 1 20.66 ? O3' GDP 300 A 1 
HETATM 15 C C2' GDP . . . C 2 8.172 20.948 -39.886 1 21.21 ? C2' GDP 300 A 1 
HETATM 16 O O2' GDP . . . C 2 9.025 21.478 -40.891 1 22.54 ? O2' GDP 300 A 1 
HETATM 17 C C1' GDP . . . C 2 6.848 21.703 -39.869 1 21.35 ? C1' GDP 300 A 1 
HETATM 18 N N9 GDP . . . C 2 6.635 22.788 -38.894 1 21.35 ? N9 GDP 300 A 1 
HETATM 19 C C8 GDP . . . C 2 6.833 22.781 -37.575 1 21.37 ? C8 GDP 300 A 1 
HETATM 20 N N7 GDP . . . C 2 6.494 23.97 -37.078 1 21 ? N7 GDP 300 A 1 
HETATM 21 C C5 GDP . . . C 2 6.076 24.744 -38.075 1 21.79 ? C5 GDP 300 A 1 
HETATM 22 C C6 GDP . . . C 2 5.609 26.059 -38.157 1 22.28 ? C6 GDP 300 A 1 
HETATM 23 O O6 GDP . . . C 2 5.508 26.768 -37.159 1 23.39 ? O6 GDP 300 A 1 
HETATM 24 N N1 GDP . . . C 2 5.234 26.569 -39.409 1 22.43 ? N1 GDP 300 A 1 
HETATM 25 C C2 GDP . . . C 2 5.345 25.746 -40.542 1 22.11 ? C2 GDP 300 A 1 
HETATM 26 N N2 GDP . . . C 2 5.006 26.196 -41.739 1 23.25 ? N2 GDP 300 A 1 
HETATM 27 N N3 GDP . . . C 2 5.799 24.49 -40.431 1 21.9 ? N3 GDP 300 A 1 
HETATM 28 C C4 GDP . . . C 2 6.16 23.981 -39.236 1 22.09 ? C4 GDP 300 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           28 
#