data_8FC9
#
_model_server_result.job_id            ZmEWVyucdNiEE3DDbiL9vw 
_model_server_result.datetime_utc      '2024-10-11 06:22:05' 
_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          8fc9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":302}' 
#
_entry.id    8FC9 
#
_exptl.entry_id    8FC9 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          4 
_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            8FC9 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8FC9 
_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_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 
_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
? 4 J N N 
? 4 L N N 
? 4 N N N 
? 4 P 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 B OG1 THR 19 E THR 19 1_555 I MG MG . E MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc2 B O THR 37 E THR 37 1_555 I MG MG . E MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc3 I MG MG . E MG 301 1_555 J O1B GDP . E GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? 
metalc ? metalc4 C OG1 THR 19 F THR 19 1_555 K MG MG . F MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc5 C O THR 37 F THR 37 1_555 K MG MG . F MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc6 K MG MG . F MG 301 1_555 L O1B GDP . F GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? 
metalc ? metalc7 D OG1 THR 19 G THR 19 1_555 M MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc8 D O THR 37 G THR 37 1_555 M MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc9 M MG MG . G MG 301 1_555 N O1B GDP . G GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? 
metalc ? metalc10 E OG1 THR 19 H THR 19 1_555 O MG MG . H MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc11 E O THR 37 H THR 37 1_555 O MG MG . H MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc12 O MG MG . H MG 301 1_555 P O1B GDP . H GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? 
#
_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                     8FC9 
_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
I 3 MG E 1 301 301 MG MG . 
J 4 GDP E 1 302 302 GDP GDP . 
K 3 MG F 1 301 301 MG MG . 
L 4 GDP F 1 302 302 GDP GDP . 
M 3 MG G 1 301 301 MG MG . 
N 4 GDP G 1 302 302 GDP GDP . 
O 3 MG H 1 301 301 MG MG . 
P 4 GDP H 1 302 302 GDP GDP . 
#
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 . . . L 4 167.489 67.602 120.418 1 162.49 ? PB GDP 302 F 1 
HETATM 2 O O1B GDP . . . L 4 166.914 68.779 119.667 1 162.49 ? O1B GDP 302 F 1 
HETATM 3 O O2B GDP . . . L 4 167.124 67.704 121.877 1 162.49 ? O2B GDP 302 F 1 
HETATM 4 O O3B GDP . . . L 4 168.992 67.604 120.282 1 162.49 ? O3B GDP 302 F 1 
HETATM 5 O O3A GDP . . . L 4 166.908 66.23 119.808 1 162.49 ? O3A GDP 302 F 1 
HETATM 6 P PA GDP . . . L 4 167.097 65.93 118.24 1 162.49 ? PA GDP 302 F 1 
HETATM 7 O O1A GDP . . . L 4 165.837 66.285 117.487 1 162.49 ? O1A GDP 302 F 1 
HETATM 8 O O2A GDP . . . L 4 168.267 66.712 117.696 1 162.49 ? O2A GDP 302 F 1 
HETATM 9 O O5' GDP . . . L 4 167.373 64.342 118.167 1 162.49 ? O5' GDP 302 F 1 
HETATM 10 C C5' GDP . . . L 4 168.618 63.892 117.634 1 162.49 ? C5' GDP 302 F 1 
HETATM 11 C C4' GDP . . . L 4 168.538 62.487 117.041 1 162.49 ? C4' GDP 302 F 1 
HETATM 12 O O4' GDP . . . L 4 167.559 61.679 117.697 1 162.49 ? O4' GDP 302 F 1 
HETATM 13 C C3' GDP . . . L 4 168.139 62.518 115.572 1 162.49 ? C3' GDP 302 F 1 
HETATM 14 O O3' GDP . . . L 4 169.288 62.471 114.714 1 162.49 ? O3' GDP 302 F 1 
HETATM 15 C C2' GDP . . . L 4 167.216 61.326 115.372 1 162.49 ? C2' GDP 302 F 1 
HETATM 16 O O2' GDP . . . L 4 167.74 60.29 114.541 1 162.49 ? O2' GDP 302 F 1 
HETATM 17 C C1' GDP . . . L 4 167.059 60.724 116.751 1 162.49 ? C1' GDP 302 F 1 
HETATM 18 N N9 GDP . . . L 4 165.632 60.398 116.952 1 162.49 ? N9 GDP 302 F 1 
HETATM 19 C C8 GDP . . . L 4 164.708 61.233 117.457 1 162.49 ? C8 GDP 302 F 1 
HETATM 20 N N7 GDP . . . L 4 163.495 60.623 117.501 1 162.49 ? N7 GDP 302 F 1 
HETATM 21 C C5 GDP . . . L 4 163.642 59.377 117.013 1 162.49 ? C5 GDP 302 F 1 
HETATM 22 C C6 GDP . . . L 4 162.763 58.208 116.778 1 162.49 ? C6 GDP 302 F 1 
HETATM 23 O O6 GDP . . . L 4 161.548 58.259 117.066 1 162.49 ? O6 GDP 302 F 1 
HETATM 24 N N1 GDP . . . L 4 163.305 57.1 116.253 1 162.49 ? N1 GDP 302 F 1 
HETATM 25 C C2 GDP . . . L 4 164.612 57.024 115.936 1 162.49 ? C2 GDP 302 F 1 
HETATM 26 N N2 GDP . . . L 4 165.082 55.867 115.408 1 162.49 ? N2 GDP 302 F 1 
HETATM 27 N N3 GDP . . . L 4 165.477 58.056 116.123 1 162.49 ? N3 GDP 302 F 1 
HETATM 28 C C4 GDP . . . L 4 165.056 59.233 116.646 1 162.49 ? C4 GDP 302 F 1 
HETATM 29 H H5' GDP . . . L 4 169.373 63.907 118.422 1 162.48 ? H5' GDP 302 F 1 
HETATM 30 H "H5''" GDP . . . L 4 168.94 64.587 116.856 1 162.48 ? "H5''" GDP 302 F 1 
HETATM 31 H H4' GDP . . . L 4 169.528 62.017 117.126 1 162.48 ? H4' GDP 302 F 1 
HETATM 32 H H3' GDP . . . L 4 167.568 63.443 115.401 1 162.48 ? H3' GDP 302 F 1 
HETATM 33 H HO3' GDP . . . L 4 169.029 62.695 113.808 1 162.48 ? HO3' GDP 302 F 1 
HETATM 34 H H2' GDP . . . L 4 166.239 61.673 115.001 1 162.48 ? H2' GDP 302 F 1 
HETATM 35 H HO2' GDP . . . L 4 167.847 60.596 113.641 1 162.48 ? HO2' GDP 302 F 1 
HETATM 36 H H1' GDP . . . L 4 167.663 59.807 116.791 1 162.48 ? H1' GDP 302 F 1 
HETATM 37 H H8 GDP . . . L 4 164.909 62.245 117.783 1 162.48 ? H8 GDP 302 F 1 
HETATM 38 H HN1 GDP . . . L 4 162.697 56.274 116.086 1 162.48 ? HN1 GDP 302 F 1 
HETATM 39 H HN21 GDP . . . L 4 164.458 55.086 115.26 1 162.48 ? HN21 GDP 302 F 1 
HETATM 40 H HN22 GDP . . . L 4 166.058 55.782 115.161 1 162.48 ? HN22 GDP 302 F 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           40 
#