data_8SXZ
#
_model_server_result.job_id            URiyL9vEx4V_gz1EBR033w 
_model_server_result.datetime_utc      '2024-10-19 03:37:03' 
_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          8sxz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":801}' 
#
_entry.id    8SXZ 
#
_exptl.entry_id    8SXZ 
_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            8SXZ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SXZ 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,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    ? 
_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                     8SXZ 
_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 . . . G 2 188.745 235.649 390.871 1 3.96 ? PB GDP 801 c 1 
HETATM 2 O O1B GDP . . . G 2 189.546 236.546 389.978 1 3.95 ? O1B GDP 801 c 1 
HETATM 3 O O2B GDP . . . G 2 188.969 234.199 390.58 1 3.81 ? O2B GDP 801 c 1 
HETATM 4 O O3B GDP . . . G 2 188.944 235.901 392.341 1 4.05 ? O3B GDP 801 c 1 
HETATM 5 O O3A GDP . . . G 2 187.196 235.901 390.58 1 4.71 ? O3A GDP 801 c 1 
HETATM 6 P PA GDP . . . G 2 186.404 234.594 390.156 1 5.53 ? PA GDP 801 c 1 
HETATM 7 O O1A GDP . . . G 2 186.956 234.219 388.835 1 5.97 ? O1A GDP 801 c 1 
HETATM 8 O O2A GDP . . . G 2 186.542 233.593 391.241 1 5.88 ? O2A GDP 801 c 1 
HETATM 9 O O5' GDP . . . G 2 184.901 235.086 389.953 1 5.52 ? O5' GDP 801 c 1 
HETATM 10 C C5' GDP . . . G 2 184.536 236.263 390.649 1 5.56 ? C5' GDP 801 c 1 
HETATM 11 C C4' GDP . . . G 2 183.044 236.471 390.525 1 5.44 ? C4' GDP 801 c 1 
HETATM 12 O O4' GDP . . . G 2 182.806 237.218 389.35 1 5.47 ? O4' GDP 801 c 1 
HETATM 13 C C3' GDP . . . G 2 182.261 235.196 390.362 1 5.5 ? C3' GDP 801 c 1 
HETATM 14 O O3' GDP . . . G 2 181.115 235.257 391.177 1 5.58 ? O3' GDP 801 c 1 
HETATM 15 C C2' GDP . . . G 2 181.8 235.156 388.944 1 5.39 ? C2' GDP 801 c 1 
HETATM 16 O O2' GDP . . . G 2 180.511 234.555 388.829 1 5.4 ? O2' GDP 801 c 1 
HETATM 17 C C1' GDP . . . G 2 181.759 236.616 388.591 1 5.05 ? C1' GDP 801 c 1 
HETATM 18 N N9 GDP . . . G 2 181.981 236.806 387.148 1 4.21 ? N9 GDP 801 c 1 
HETATM 19 C C8 GDP . . . G 2 183.179 236.842 386.569 1 3.97 ? C8 GDP 801 c 1 
HETATM 20 N N7 GDP . . . G 2 183.07 237.031 385.245 1 3.97 ? N7 GDP 801 c 1 
HETATM 21 C C5 GDP . . . G 2 181.773 237.118 384.967 1 4.22 ? C5 GDP 801 c 1 
HETATM 22 C C6 GDP . . . G 2 180.974 237.32 383.756 1 4.1 ? C6 GDP 801 c 1 
HETATM 23 O O6 GDP . . . G 2 181.537 237.451 382.662 1 4.06 ? O6 GDP 801 c 1 
HETATM 24 N N1 GDP . . . G 2 179.654 237.356 383.865 1 3.89 ? N1 GDP 801 c 1 
HETATM 25 C C2 GDP . . . G 2 179.051 237.216 385.039 1 3.74 ? C2 GDP 801 c 1 
HETATM 26 N N2 GDP . . . G 2 177.706 237.268 385.046 1 3.84 ? N2 GDP 801 c 1 
HETATM 27 N N3 GDP . . . G 2 179.721 237.027 386.199 1 4 ? N3 GDP 801 c 1 
HETATM 28 C C4 GDP . . . G 2 181.053 236.973 386.218 1 4.09 ? C4 GDP 801 c 1 
HETATM 29 H H5' GDP . . . G 2 184.803 236.167 391.7 1 6.67 ? H5' GDP 801 c 1 
HETATM 30 H "H5''" GDP . . . G 2 185.091 237.121 390.258 1 6.67 ? "H5''" GDP 801 c 1 
HETATM 31 H H4' GDP . . . G 2 182.681 237.002 391.405 1 6.53 ? H4' GDP 801 c 1 
HETATM 32 H H3' GDP . . . G 2 182.839 234.306 390.601 1 6.6 ? H3' GDP 801 c 1 
HETATM 33 H HO3' GDP . . . G 2 180.331 235.271 390.609 1 6.7 ? HO3' GDP 801 c 1 
HETATM 34 H H2' GDP . . . G 2 182.538 234.654 388.318 1 6.47 ? H2' GDP 801 c 1 
HETATM 35 H HO2' GDP . . . G 2 180.081 234.856 388.01 1 6.48 ? HO2' GDP 801 c 1 
HETATM 36 H H1' GDP . . . G 2 180.798 237.026 388.887 1 6.06 ? H1' GDP 801 c 1 
HETATM 37 H H8 GDP . . . G 2 184.112 236.73 387.097 1 4.76 ? H8 GDP 801 c 1 
HETATM 38 H HN1 GDP . . . G 2 179.081 237.495 383.035 1 4.67 ? HN1 GDP 801 c 1 
HETATM 39 H HN21 GDP . . . G 2 177.215 237.407 384.166 1 4.61 ? HN21 GDP 801 c 1 
HETATM 40 H HN22 GDP . . . G 2 177.178 237.174 385.908 1 4.61 ? HN22 GDP 801 c 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    62 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           40 
#