data_8F0M
#
_model_server_result.job_id            iF_Hu-BjMHfx6IFL_TyUQg 
_model_server_result.datetime_utc      '2025-07-30 23:08:48' 
_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          8f0m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":202}' 
#
_entry.id    8F0M 
#
_exptl.entry_id    8F0M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    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            8F0M 
_cell.length_a            151.386 
_cell.length_b            44.733 
_cell.length_c            88.162 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8F0M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 2 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,B,E,F,G,H,K,L 1 1 
C,D,I,J,M,N 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             F 
_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 A O GLY 1 A GLY -1 1_555 I MG MG . C MG 201 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc2 A OG SER 19 A SER 17 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc3 E MG MG . A MG 201 1_555 F O2B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc4 E MG MG . A MG 201 1_555 K O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc5 E MG MG . A MG 201 1_555 K O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc6 E MG MG . A MG 201 1_555 K O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc7 E MG MG . A MG 201 1_555 K O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc8 C OG SER 19 C SER 17 1_555 I MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc9 I MG MG . C MG 201 1_555 J O3G GSP . C GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
metalc ? metalc10 I MG MG . C MG 201 1_555 J O1B GSP . C GSP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc11 I MG MG . C MG 201 1_555 M O HOH . C HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc12 I MG MG . C MG 201 1_555 M O HOH . C HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
#
_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                     8F0M 
_atom_sites.fract_transf_matrix[1][1]    0.006606 
_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]    0.022355 
_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]    0.011343 
_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 3 MG A 1 201 201 MG MG . 
F 4 GDP A 1 202 202 GDP GDP . 
G 5 GLC A 1 203 202 GLC GLC . 
H 5 GLC B 1 201 201 GLC GLC . 
I 3 MG C 1 201 201 MG MG . 
J 6 GSP C 1 202 202 GSP GSP . 
K 7 HOH A 1 301 98 HOH HOH . 
K 7 HOH A 2 302 37 HOH HOH . 
K 7 HOH A 3 303 97 HOH HOH . 
K 7 HOH A 4 304 83 HOH HOH . 
K 7 HOH A 5 305 1 HOH HOH . 
K 7 HOH A 6 306 26 HOH HOH . 
K 7 HOH A 7 307 43 HOH HOH . 
K 7 HOH A 8 308 36 HOH HOH . 
K 7 HOH A 9 309 7 HOH HOH . 
K 7 HOH A 10 310 40 HOH HOH . 
K 7 HOH A 11 311 30 HOH HOH . 
K 7 HOH A 12 312 3 HOH HOH . 
K 7 HOH A 13 313 58 HOH HOH . 
K 7 HOH A 14 314 57 HOH HOH . 
K 7 HOH A 15 315 48 HOH HOH . 
K 7 HOH A 16 316 94 HOH HOH . 
K 7 HOH A 17 317 89 HOH HOH . 
K 7 HOH A 18 318 19 HOH HOH . 
K 7 HOH A 19 319 50 HOH HOH . 
K 7 HOH A 20 320 49 HOH HOH . 
K 7 HOH A 21 321 4 HOH HOH . 
K 7 HOH A 22 322 41 HOH HOH . 
K 7 HOH A 23 323 62 HOH HOH . 
K 7 HOH A 24 324 92 HOH HOH . 
K 7 HOH A 25 325 84 HOH HOH . 
K 7 HOH A 26 326 20 HOH HOH . 
K 7 HOH A 27 327 71 HOH HOH . 
K 7 HOH A 28 328 12 HOH HOH . 
K 7 HOH A 29 329 77 HOH HOH . 
K 7 HOH A 30 330 21 HOH HOH . 
K 7 HOH A 31 331 102 HOH HOH . 
K 7 HOH A 32 332 64 HOH HOH . 
L 7 HOH B 1 301 23 HOH HOH . 
L 7 HOH B 2 302 39 HOH HOH . 
L 7 HOH B 3 303 72 HOH HOH . 
L 7 HOH B 4 304 68 HOH HOH . 
L 7 HOH B 5 305 63 HOH HOH . 
L 7 HOH B 6 306 74 HOH HOH . 
L 7 HOH B 7 307 70 HOH HOH . 
L 7 HOH B 8 308 75 HOH HOH . 
L 7 HOH B 9 309 22 HOH HOH . 
L 7 HOH B 10 310 88 HOH HOH . 
L 7 HOH B 11 311 17 HOH HOH . 
L 7 HOH B 12 312 10 HOH HOH . 
L 7 HOH B 13 313 53 HOH HOH . 
L 7 HOH B 14 314 47 HOH HOH . 
L 7 HOH B 15 315 25 HOH HOH . 
L 7 HOH B 16 316 69 HOH HOH . 
L 7 HOH B 17 317 29 HOH HOH . 
L 7 HOH B 18 318 8 HOH HOH . 
L 7 HOH B 19 319 9 HOH HOH . 
L 7 HOH B 20 320 34 HOH HOH . 
L 7 HOH B 21 321 76 HOH HOH . 
L 7 HOH B 22 322 80 HOH HOH . 
L 7 HOH B 23 323 67 HOH HOH . 
L 7 HOH B 24 324 24 HOH HOH . 
L 7 HOH B 25 325 28 HOH HOH . 
L 7 HOH B 26 326 85 HOH HOH . 
M 7 HOH C 1 301 35 HOH HOH . 
M 7 HOH C 2 302 55 HOH HOH . 
M 7 HOH C 3 303 38 HOH HOH . 
M 7 HOH C 4 304 15 HOH HOH . 
M 7 HOH C 5 305 13 HOH HOH . 
M 7 HOH C 6 306 42 HOH HOH . 
M 7 HOH C 7 307 91 HOH HOH . 
M 7 HOH C 8 308 27 HOH HOH . 
M 7 HOH C 9 309 99 HOH HOH . 
M 7 HOH C 10 310 5 HOH HOH . 
M 7 HOH C 11 311 61 HOH HOH . 
M 7 HOH C 12 312 14 HOH HOH . 
M 7 HOH C 13 313 6 HOH HOH . 
M 7 HOH C 14 314 60 HOH HOH . 
M 7 HOH C 15 315 73 HOH HOH . 
M 7 HOH C 16 316 95 HOH HOH . 
M 7 HOH C 17 317 65 HOH HOH . 
M 7 HOH C 18 318 96 HOH HOH . 
M 7 HOH C 19 319 101 HOH HOH . 
M 7 HOH C 20 320 46 HOH HOH . 
M 7 HOH C 21 321 51 HOH HOH . 
M 7 HOH C 22 322 45 HOH HOH . 
M 7 HOH C 23 323 56 HOH HOH . 
M 7 HOH C 24 324 31 HOH HOH . 
M 7 HOH C 25 325 33 HOH HOH . 
M 7 HOH C 26 326 44 HOH HOH . 
M 7 HOH C 27 327 86 HOH HOH . 
M 7 HOH C 28 328 87 HOH HOH . 
N 7 HOH D 1 101 11 HOH HOH . 
N 7 HOH D 2 102 32 HOH HOH . 
N 7 HOH D 3 103 59 HOH HOH . 
N 7 HOH D 4 104 54 HOH HOH . 
N 7 HOH D 5 105 82 HOH HOH . 
N 7 HOH D 6 106 52 HOH HOH . 
N 7 HOH D 7 107 2 HOH HOH . 
N 7 HOH D 8 108 93 HOH HOH . 
N 7 HOH D 9 109 18 HOH HOH . 
N 7 HOH D 10 110 79 HOH HOH . 
N 7 HOH D 11 111 16 HOH HOH . 
N 7 HOH D 12 112 81 HOH HOH . 
N 7 HOH D 13 113 100 HOH HOH . 
N 7 HOH D 14 114 78 HOH HOH . 
N 7 HOH D 15 115 90 HOH HOH . 
N 7 HOH D 16 116 66 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 . . . F 4 16.389 33.183 13.172 1 33.45 ? PB GDP 202 A 1 
HETATM 2 O O1B GDP . . . F 4 17.603 34.056 13.38 1 29.14 ? O1B GDP 202 A 1 
HETATM 3 O O2B GDP . . . F 4 15.179 33.802 13.829 1 41.13 ? O2B GDP 202 A 1 
HETATM 4 O O3B GDP . . . F 4 16.63 31.82 13.773 1 30.67 ? O3B GDP 202 A 1 
HETATM 5 O O3A GDP . . . F 4 16.113 32.988 11.602 1 37.81 ? O3A GDP 202 A 1 
HETATM 6 P PA GDP . . . F 4 15.508 34.162 10.683 1 31.14 ? PA GDP 202 A 1 
HETATM 7 O O1A GDP . . . F 4 14 34.137 10.743 1 36.57 ? O1A GDP 202 A 1 
HETATM 8 O O2A GDP . . . F 4 16.043 35.519 11.071 1 39.64 ? O2A GDP 202 A 1 
HETATM 9 O O5' GDP . . . F 4 16.021 33.723 9.222 1 39.41 ? O5' GDP 202 A 1 
HETATM 10 C C5' GDP . . . F 4 17.278 34.186 8.731 1 30.53 ? C5' GDP 202 A 1 
HETATM 11 C C4' GDP . . . F 4 17.244 34.159 7.211 1 39.07 ? C4' GDP 202 A 1 
HETATM 12 O O4' GDP . . . F 4 16.82 32.868 6.768 1 32.5 ? O4' GDP 202 A 1 
HETATM 13 C C3' GDP . . . F 4 16.23 35.168 6.702 1 45.13 ? C3' GDP 202 A 1 
HETATM 14 O O3' GDP . . . F 4 16.815 35.96 5.664 1 50.45 ? O3' GDP 202 A 1 
HETATM 15 C C2' GDP . . . F 4 15.094 34.341 6.139 1 34.43 ? C2' GDP 202 A 1 
HETATM 16 O O2' GDP . . . F 4 14.563 34.94 4.955 1 50.15 ? O2' GDP 202 A 1 
HETATM 17 C C1' GDP . . . F 4 15.731 32.992 5.849 1 36.31 ? C1' GDP 202 A 1 
HETATM 18 N N9 GDP . . . F 4 14.758 31.893 6.059 1 37.57 ? N9 GDP 202 A 1 
HETATM 19 C C8 GDP . . . F 4 14.032 31.674 7.171 1 32.94 ? C8 GDP 202 A 1 
HETATM 20 N N7 GDP . . . F 4 13.247 30.576 7.031 1 34.96 ? N7 GDP 202 A 1 
HETATM 21 C C5 GDP . . . F 4 13.476 30.067 5.806 1 34.5 ? C5 GDP 202 A 1 
HETATM 22 C C6 GDP . . . F 4 12.984 28.914 5.015 1 41.61 ? C6 GDP 202 A 1 
HETATM 23 O O6 GDP . . . F 4 12.134 28.127 5.483 1 40.81 ? O6 GDP 202 A 1 
HETATM 24 N N1 GDP . . . F 4 13.479 28.741 3.782 1 45.45 ? N1 GDP 202 A 1 
HETATM 25 C C2 GDP . . . F 4 14.396 29.572 3.251 1 44.76 ? C2 GDP 202 A 1 
HETATM 26 N N2 GDP . . . F 4 14.845 29.326 1.997 1 49.14 ? N2 GDP 202 A 1 
HETATM 27 N N3 GDP . . . F 4 14.891 30.646 3.918 1 38.6 ? N3 GDP 202 A 1 
HETATM 28 C C4 GDP . . . F 4 14.476 30.937 5.173 1 39 ? C4 GDP 202 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           28 
#