data_8CGY
#
_model_server_result.job_id            2p9L5BUryLs4JPFcUmXoYA 
_model_server_result.datetime_utc      '2024-10-10 18:18:08' 
_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          8cgy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    8CGY 
#
_exptl.entry_id    8CGY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          3 
_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            8CGY 
_cell.length_a            207.1 
_cell.length_b            207.1 
_cell.length_c            92.5 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8CGY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        90 
_symmetry.space_group_name_Hall    'P 4ab 2ab' 
_symmetry.space_group_name_H-M     'P 4 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -207.1 0 
3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -103.55 -103.55 0 
4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 103.55 -103.55 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 G N N 
#
_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 132 n n 
PB O2B GDP sing 133 n n 
PB O3B GDP sing 134 n n 
PB O3A GDP sing 135 n n 
O2B HOB2 GDP sing 136 n n 
O3B HOB3 GDP sing 137 n n 
O3A PA GDP sing 138 n n 
PA O1A GDP doub 139 n n 
PA O2A GDP sing 140 n n 
PA O5' GDP sing 141 n n 
O2A HOA2 GDP sing 142 n n 
O5' C5' GDP sing 143 n n 
C5' C4' GDP sing 144 n n 
C5' H5' GDP sing 145 n n 
C5' "H5''" GDP sing 146 n n 
C4' O4' GDP sing 147 n n 
C4' C3' GDP sing 148 n n 
C4' H4' GDP sing 149 n n 
O4' C1' GDP sing 150 n n 
C3' O3' GDP sing 151 n n 
C3' C2' GDP sing 152 n n 
C3' H3' GDP sing 153 n n 
O3' HO3' GDP sing 154 n n 
C2' O2' GDP sing 155 n n 
C2' C1' GDP sing 156 n n 
C2' H2' GDP sing 157 n n 
O2' HO2' GDP sing 158 n n 
C1' N9 GDP sing 159 n n 
C1' H1' GDP sing 160 n n 
N9 C8 GDP sing 161 n y 
N9 C4 GDP sing 162 n y 
C8 N7 GDP doub 163 n y 
C8 H8 GDP sing 164 n n 
N7 C5 GDP sing 165 n y 
C5 C6 GDP sing 166 n n 
C5 C4 GDP doub 167 n y 
C6 O6 GDP doub 168 n n 
C6 N1 GDP sing 169 n n 
N1 C2 GDP sing 170 n n 
N1 HN1 GDP sing 171 n n 
C2 N2 GDP sing 172 n n 
C2 N3 GDP doub 173 n n 
N2 HN21 GDP sing 174 n n 
N2 HN22 GDP sing 175 n n 
N3 C4 GDP sing 176 n n 
#
_atom_sites.entry_id                     8CGY 
_atom_sites.fract_transf_matrix[1][1]    0.004829 
_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]    0.004829 
_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]    0.010811 
_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 ATP A 1 601 501 ATP ATP . 
D 3 GDP A 1 602 502 GDP GDP . 
E 4 PO4 A 1 603 2 PO4 PO4 . 
F 2 ATP B 1 601 501 ATP ATP . 
G 3 GDP B 1 602 502 GDP GDP . 
H 4 PO4 B 1 603 1 PO4 PO4 . 
I 5 HOH A 1 701 1 HOH HOH . 
I 5 HOH A 2 702 2 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 . . . D 3 -44.491 -71.182 31.967 1 155.37 ? PB GDP 602 A 1 
HETATM 2 O O1B GDP . . . D 3 -45.382 -71.241 30.733 1 129.99 -1 O1B GDP 602 A 1 
HETATM 3 O O2B GDP . . . D 3 -43.838 -72.525 32.174 1 99.68 ? O2B GDP 602 A 1 
HETATM 4 O O3B GDP . . . D 3 -45.314 -70.849 33.189 1 111.35 -1 O3B GDP 602 A 1 
HETATM 5 O O3A GDP . . . D 3 -43.304 -70.022 31.742 1 117.03 ? O3A GDP 602 A 1 
HETATM 6 P PA GDP . . . D 3 -43.525 -68.351 31.633 1 89.77 ? PA GDP 602 A 1 
HETATM 7 O O1A GDP . . . D 3 -44.362 -67.992 30.43 1 121.54 -1 O1A GDP 602 A 1 
HETATM 8 O O2A GDP . . . D 3 -44.19 -67.827 32.894 1 80.77 ? O2A GDP 602 A 1 
HETATM 9 O O5' GDP . . . D 3 -42.015 -67.691 31.425 1 104.6 ? O5' GDP 602 A 1 
HETATM 10 C C5' GDP . . . D 3 -41.745 -66.341 31.668 1 75.03 ? C5' GDP 602 A 1 
HETATM 11 C C4' GDP . . . D 3 -42.207 -65.443 30.573 1 59.9 ? C4' GDP 602 A 1 
HETATM 12 O O4' GDP . . . D 3 -41.509 -63.932 30.913 1 73 ? O4' GDP 602 A 1 
HETATM 13 C C3' GDP . . . D 3 -41.818 -65.768 29.383 1 74.22 ? C3' GDP 602 A 1 
HETATM 14 O O3' GDP . . . D 3 -42.921 -65.482 28.427 1 64.51 ? O3' GDP 602 A 1 
HETATM 15 C C2' GDP . . . D 3 -40.586 -64.875 29.04 1 72.66 ? C2' GDP 602 A 1 
HETATM 16 O O2' GDP . . . D 3 -40.521 -64.558 27.766 1 73.44 ? O2' GDP 602 A 1 
HETATM 17 C C1' GDP . . . D 3 -40.854 -63.542 29.854 1 69.32 ? C1' GDP 602 A 1 
HETATM 18 N N9 GDP . . . D 3 -39.643 -62.84 30.238 1 59.36 ? N9 GDP 602 A 1 
HETATM 19 C C8 GDP . . . D 3 -38.405 -63.096 29.856 1 59.12 ? C8 GDP 602 A 1 
HETATM 20 N N7 GDP . . . D 3 -37.584 -62.225 30.425 1 53.61 ? N7 GDP 602 A 1 
HETATM 21 C C5 GDP . . . D 3 -38.307 -61.396 31.176 1 42.44 ? C5 GDP 602 A 1 
HETATM 22 C C6 GDP . . . D 3 -37.944 -60.218 32.051 1 44.54 ? C6 GDP 602 A 1 
HETATM 23 O O6 GDP . . . D 3 -36.808 -59.9 32.143 1 50.59 ? O6 GDP 602 A 1 
HETATM 24 N N1 GDP . . . D 3 -38.983 -59.509 32.755 1 55.17 ? N1 GDP 602 A 1 
HETATM 25 C C2 GDP . . . D 3 -40.362 -59.927 32.621 1 38.52 ? C2 GDP 602 A 1 
HETATM 26 N N2 GDP . . . D 3 -41.428 -59.232 33.318 1 64.27 ? N2 GDP 602 A 1 
HETATM 27 N N3 GDP . . . D 3 -40.698 -61.066 31.773 1 44.82 ? N3 GDP 602 A 1 
HETATM 28 C C4 GDP . . . D 3 -39.621 -61.789 31.054 1 60.14 ? C4 GDP 602 A 1 
HETATM 29 H H5' GDP . . . D 3 -40.674 -66.22 31.781 1 90.13 ? H5' GDP 602 A 1 
HETATM 30 H "H5''" GDP . . . D 3 -42.246 -66.05 32.584 1 90.13 ? "H5''" GDP 602 A 1 
HETATM 31 H H4' GDP . . . D 3 -43.289 -65.443 30.511 1 71.97 ? H4' GDP 602 A 1 
HETATM 32 H H3' GDP . . . D 3 -41.516 -66.803 29.365 1 89.16 ? H3' GDP 602 A 1 
HETATM 33 H HO3' GDP . . . D 3 -43.147 -64.561 28.452 1 77.5 ? HO3' GDP 602 A 1 
HETATM 34 H H2' GDP . . . D 3 -39.684 -65.399 29.334 1 87.29 ? H2' GDP 602 A 1 
HETATM 35 H HO2' GDP . . . D 3 -41.32 -64.145 27.498 1 88.22 ? HO2' GDP 602 A 1 
HETATM 36 H H1' GDP . . . D 3 -41.446 -62.873 29.231 1 83.28 ? H1' GDP 602 A 1 
HETATM 37 H H8 GDP . . . D 3 -38.108 -63.892 29.183 1 71.03 ? H8 GDP 602 A 1 
HETATM 38 H HN1 GDP . . . D 3 -38.748 -58.719 33.344 1 66.29 ? HN1 GDP 602 A 1 
HETATM 39 H HN21 GDP . . . D 3 -42.374 -59.538 33.21 1 77.22 ? HN21 GDP 602 A 1 
HETATM 40 H HN22 GDP . . . D 3 -41.215 -58.439 33.911 1 77.22 ? HN22 GDP 602 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          24 
_model_server_stats.element_count           40 
#