data_8SZ8
#
_model_server_result.job_id            59hNKDC6VAHkCYgpm25O9g 
_model_server_result.datetime_utc      '2024-11-23 03:36:34' 
_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          8sz8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":801}' 
#
_entry.id    8SZ8 
#
_exptl.entry_id    8SZ8 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    4 
_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            8SZ8 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SZ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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 OG SER 49 b SER 45 1_555 F MG MG . b MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
metalc ? metalc2 A OG1 THR 69 b THR 65 1_555 F MG MG . b MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? 
metalc ? metalc3 E O1B GDP . b GDP 801 1_555 F MG MG . b MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? 
metalc ? metalc4 E O3B GDP . b GDP 801 1_555 F MG MG . b MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc5 B OG SER 49 c SER 45 1_555 H MG MG . c MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? 
metalc ? metalc6 B OG1 THR 69 c THR 65 1_555 H MG MG . c MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc7 G O2B GDP . c GDP 801 1_555 H MG MG . c MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc8 C OG SER 49 f SER 45 1_555 J MG MG . f MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? 
metalc ? metalc9 C OG1 THR 69 f THR 65 1_555 J MG MG . f MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc10 I O3B GDP . f GDP 801 1_555 J MG MG . f MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? 
metalc ? metalc11 D OG SER 49 g SER 45 1_555 L MG MG . g MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc12 D OG1 THR 69 g THR 65 1_555 L MG MG . g MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? 
metalc ? metalc13 K O2B GDP . g GDP 801 1_555 L MG MG . g MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? 
#
_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                     8SZ8 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
E 2 GDP b 1 801 1 GDP GDP . 
F 3 MG b 1 802 1 MG MG . 
G 2 GDP c 1 801 1 GDP GDP . 
H 3 MG c 1 802 3 MG MG . 
I 2 GDP f 1 801 1 GDP GDP . 
J 3 MG f 1 802 2 MG MG . 
K 2 GDP g 1 801 1 GDP GDP . 
L 3 MG g 1 802 4 MG MG . 
#
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 2 185.043 260.4 386.03 1 6.53 ? PB GDP 801 b 1 
HETATM 2 O O1B GDP . . . E 2 185.891 260.147 384.817 1 6.68 ? O1B GDP 801 b 1 
HETATM 3 O O2B GDP . . . E 2 185.73 260.157 387.337 1 6.56 ? O2B GDP 801 b 1 
HETATM 4 O O3B GDP . . . E 2 184.453 261.772 385.958 1 7.03 ? O3B GDP 801 b 1 
HETATM 5 O O3A GDP . . . E 2 183.807 259.399 385.902 1 6.24 ? O3A GDP 801 b 1 
HETATM 6 P PA GDP . . . E 2 182.449 260.148 385.584 1 6.71 ? PA GDP 801 b 1 
HETATM 7 O O1A GDP . . . E 2 182.664 260.989 384.387 1 7.11 ? O1A GDP 801 b 1 
HETATM 8 O O2A GDP . . . E 2 182.113 260.889 386.819 1 7.23 ? O2A GDP 801 b 1 
HETATM 9 O O5' GDP . . . E 2 181.351 259.012 385.364 1 6.75 ? O5' GDP 801 b 1 
HETATM 10 C C5' GDP . . . E 2 181.495 258.256 384.183 1 6.5 ? C5' GDP 801 b 1 
HETATM 11 C C4' GDP . . . E 2 180.275 257.402 383.985 1 5.72 ? C4' GDP 801 b 1 
HETATM 12 O O4' GDP . . . E 2 179.871 256.822 385.206 1 5.36 ? O4' GDP 801 b 1 
HETATM 13 C C3' GDP . . . E 2 179.083 258.208 383.556 1 6.14 ? C3' GDP 801 b 1 
HETATM 14 O O3' GDP . . . E 2 178.712 257.796 382.26 1 6.44 ? O3' GDP 801 b 1 
HETATM 15 C C2' GDP . . . E 2 177.966 257.867 384.492 1 5.89 ? C2' GDP 801 b 1 
HETATM 16 O O2' GDP . . . E 2 176.739 257.683 383.789 1 6.19 ? O2' GDP 801 b 1 
HETATM 17 C C1' GDP . . . E 2 178.467 256.6 385.119 1 5.18 ? C1' GDP 801 b 1 
HETATM 18 N N9 GDP . . . E 2 177.875 256.388 386.446 1 4.82 ? N9 GDP 801 b 1 
HETATM 19 C C8 GDP . . . E 2 178.318 256.949 387.565 1 4.45 ? C8 GDP 801 b 1 
HETATM 20 N N7 GDP . . . E 2 177.582 256.569 388.618 1 4.62 ? N7 GDP 801 b 1 
HETATM 21 C C5 GDP . . . E 2 176.653 255.735 388.166 1 4.66 ? C5 GDP 801 b 1 
HETATM 22 C C6 GDP . . . E 2 175.556 254.972 388.76 1 4.45 ? C6 GDP 801 b 1 
HETATM 23 O O6 GDP . . . E 2 175.351 255.039 389.977 1 4.95 ? O6 GDP 801 b 1 
HETATM 24 N N1 GDP . . . E 2 174.801 254.219 387.978 1 4.83 ? N1 GDP 801 b 1 
HETATM 25 C C2 GDP . . . E 2 175.024 254.148 386.671 1 4.81 ? C2 GDP 801 b 1 
HETATM 26 N N2 GDP . . . E 2 174.202 253.356 385.953 1 4.51 ? N2 GDP 801 b 1 
HETATM 27 N N3 GDP . . . E 2 176.019 254.826 386.052 1 4.51 ? N3 GDP 801 b 1 
HETATM 28 C C4 GDP . . . E 2 176.843 255.615 386.737 1 4.85 ? C4 GDP 801 b 1 
HETATM 29 H H5' GDP . . . E 2 181.603 258.936 383.343 1 7.8 ? H5' GDP 801 b 1 
HETATM 30 H "H5''" GDP . . . E 2 182.397 257.637 384.226 1 7.8 ? "H5''" GDP 801 b 1 
HETATM 31 H H4' GDP . . . E 2 180.5 256.638 383.239 1 6.86 ? H4' GDP 801 b 1 
HETATM 32 H H3' GDP . . . E 2 179.269 259.279 383.578 1 7.37 ? H3' GDP 801 b 1 
HETATM 33 H HO3' GDP . . . E 2 177.767 257.585 382.259 1 7.73 ? HO3' GDP 801 b 1 
HETATM 34 H H2' GDP . . . E 2 177.871 258.63 385.263 1 7.07 ? H2' GDP 801 b 1 
HETATM 35 H HO2' GDP . . . E 2 175.995 257.871 384.385 1 7.43 ? HO2' GDP 801 b 1 
HETATM 36 H H1' GDP . . . E 2 178.249 255.762 384.463 1 6.22 ? H1' GDP 801 b 1 
HETATM 37 H H8 GDP . . . E 2 179.154 257.626 387.613 1 5.34 ? H8 GDP 801 b 1 
HETATM 38 H HN1 GDP . . . E 2 174.032 253.681 388.375 1 5.8 ? HN1 GDP 801 b 1 
HETATM 39 H HN21 GDP . . . E 2 173.458 252.855 386.434 1 5.41 ? HN21 GDP 801 b 1 
HETATM 40 H HN22 GDP . . . E 2 174.311 253.25 384.947 1 5.41 ? HN22 GDP 801 b 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    49 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           40 
#