data_9C6R
#
_model_server_result.job_id            -kN-3nTyXQyknmj66CYRjQ 
_model_server_result.datetime_utc      '2025-01-10 07:15:11' 
_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          9c6r 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":1202}' 
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_entry.id    9C6R 
#
_exptl.entry_id    9C6R 
_exptl.method      'ELECTRON MICROSCOPY' 
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_entity.details                     ? 
_entity.formula_weight              443.201 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "GUANOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
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_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            9C6R 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 9C6R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
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_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    16-meric 
_pdbx_struct_assembly.oligomeric_count      16 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
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_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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
? 5 S N N 
? 5 V N N 
? 5 Y N N 
? 5 BA N N 
? 5 EA N N 
? 5 HA N N 
? 5 KA N N 
? 5 NA N N 
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_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     ? 
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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                     9C6R 
_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
Q 3 GTP A 1 601 601 GTP GTP . 
R 4 YGY B 1 1201 1201 YGY YGY . 
S 5 GDP B 1 1202 1202 GDP GDP . 
T 3 GTP F 1 601 601 GTP GTP . 
U 4 YGY G 1 1201 1201 YGY YGY . 
V 5 GDP G 1 1202 1202 GDP GDP . 
W 3 GTP K 1 601 601 GTP GTP . 
X 4 YGY L 1 1201 1201 YGY YGY . 
Y 5 GDP L 1 1202 1202 GDP GDP . 
Z 4 YGY P 1 1201 1201 YGY YGY . 
AA 3 GTP P 1 1202 601 GTP GTP . 
BA 5 GDP Q 1 501 1202 GDP GDP . 
CA 3 GTP U 1 601 601 GTP GTP . 
DA 4 YGY V 1 1201 1201 YGY YGY . 
EA 5 GDP V 1 1202 1202 GDP GDP . 
FA 3 GTP Z 1 601 601 GTP GTP . 
GA 4 YGY a 1 1201 1201 YGY YGY . 
HA 5 GDP a 1 1202 1202 GDP GDP . 
IA 3 GTP e 1 601 601 GTP GTP . 
JA 4 YGY f 1 1201 1201 YGY YGY . 
KA 5 GDP f 1 1202 1202 GDP GDP . 
LA 3 GTP j 1 601 601 GTP GTP . 
MA 4 YGY k 1 1201 1201 YGY YGY . 
NA 5 GDP k 1 1202 1202 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 . . . S 5 287.118 387.408 270.778 1 44.62 ? PB GDP 1202 B 1 
HETATM 2 O O1B GDP . . . S 5 287.353 388.484 269.745 1 44.62 ? O1B GDP 1202 B 1 
HETATM 3 O O2B GDP . . . S 5 286.578 386.171 270.108 1 44.62 ? O2B GDP 1202 B 1 
HETATM 4 O O3B GDP . . . S 5 286.107 387.894 271.784 1 44.62 ? O3B GDP 1202 B 1 
HETATM 5 O O3A GDP . . . S 5 288.504 387.046 271.521 1 44.62 ? O3A GDP 1202 B 1 
HETATM 6 P PA GDP . . . S 5 289.461 388.193 272.118 1 44.62 ? PA GDP 1202 B 1 
HETATM 7 O O1A GDP . . . S 5 290.728 388.245 271.319 1 44.62 ? O1A GDP 1202 B 1 
HETATM 8 O O2A GDP . . . S 5 288.788 389.543 272.109 1 44.62 ? O2A GDP 1202 B 1 
HETATM 9 O O5' GDP . . . S 5 289.785 387.723 273.62 1 44.62 ? O5' GDP 1202 B 1 
HETATM 10 C C5' GDP . . . S 5 289.61 388.639 274.697 1 44.62 ? C5' GDP 1202 B 1 
HETATM 11 C C4' GDP . . . S 5 290.125 388.051 276.003 1 44.62 ? C4' GDP 1202 B 1 
HETATM 12 O O4' GDP . . . S 5 291.435 388.555 276.214 1 44.62 ? O4' GDP 1202 B 1 
HETATM 13 C C3' GDP . . . S 5 289.31 388.472 277.205 1 44.62 ? C3' GDP 1202 B 1 
HETATM 14 O O3' GDP . . . S 5 289.155 387.348 278.064 1 44.62 ? O3' GDP 1202 B 1 
HETATM 15 C C2' GDP . . . S 5 290.123 389.506 277.944 1 44.62 ? C2' GDP 1202 B 1 
HETATM 16 O O2' GDP . . . S 5 290.167 389.164 279.328 1 44.62 ? O2' GDP 1202 B 1 
HETATM 17 C C1' GDP . . . S 5 291.512 389.392 277.365 1 44.62 ? C1' GDP 1202 B 1 
HETATM 18 N N9 GDP . . . S 5 292.036 390.69 276.891 1 44.62 ? N9 GDP 1202 B 1 
HETATM 19 C C8 GDP . . . S 5 291.497 391.442 275.918 1 44.62 ? C8 GDP 1202 B 1 
HETATM 20 N N7 GDP . . . S 5 292.239 392.554 275.699 1 44.62 ? N7 GDP 1202 B 1 
HETATM 21 C C5 GDP . . . S 5 293.285 392.507 276.54 1 44.62 ? C5 GDP 1202 B 1 
HETATM 22 C C6 GDP . . . S 5 294.45 393.361 276.834 1 44.62 ? C6 GDP 1202 B 1 
HETATM 23 O O6 GDP . . . S 5 294.632 394.428 276.215 1 44.62 ? O6 GDP 1202 B 1 
HETATM 24 N N1 GDP . . . S 5 295.304 392.96 277.778 1 44.62 ? N1 GDP 1202 B 1 
HETATM 25 C C2 GDP . . . S 5 295.132 391.818 278.461 1 44.62 ? C2 GDP 1202 B 1 
HETATM 26 N N2 GDP . . . S 5 296.039 391.482 279.405 1 44.62 ? N2 GDP 1202 B 1 
HETATM 27 N N3 GDP . . . S 5 294.088 390.985 278.246 1 44.62 ? N3 GDP 1202 B 1 
HETATM 28 C C4 GDP . . . S 5 293.15 391.277 277.32 1 44.62 ? C4 GDP 1202 B 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    153 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           28 
#