data_6HJO
#
_model_server_result.job_id            afQhHCUU_niPwz4dWobjIA 
_model_server_result.datetime_utc      '2024-11-16 06:45:14' 
_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          6hjo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":200}' 
#
_entry.id    6HJO 
#
_exptl.entry_id    6HJO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    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            6HJO 
_cell.length_a            53.98 
_cell.length_b            89.18 
_cell.length_c            118.52 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6HJO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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    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
? 2 C N N 
? 2 D 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 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                     6HJO 
_atom_sites.fract_transf_matrix[1][1]    0.018525 
_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]    0.011213 
_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]    0.008437 
_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 GDP A 1 200 200 GDP GDP . 
D 2 GDP B 1 200 200 GDP GDP . 
E 3 HOH A 1 301 69 HOH HOH . 
E 3 HOH A 2 302 6 HOH HOH . 
E 3 HOH A 3 303 5 HOH HOH . 
E 3 HOH A 4 304 7 HOH HOH . 
E 3 HOH A 5 305 21 HOH HOH . 
E 3 HOH A 6 306 1 HOH HOH . 
E 3 HOH A 7 307 51 HOH HOH . 
E 3 HOH A 8 308 3 HOH HOH . 
E 3 HOH A 9 309 70 HOH HOH . 
E 3 HOH A 10 310 29 HOH HOH . 
E 3 HOH A 11 311 10 HOH HOH . 
E 3 HOH A 12 312 14 HOH HOH . 
E 3 HOH A 13 313 9 HOH HOH . 
E 3 HOH A 14 314 15 HOH HOH . 
E 3 HOH A 15 315 35 HOH HOH . 
E 3 HOH A 16 316 4 HOH HOH . 
E 3 HOH A 17 317 56 HOH HOH . 
E 3 HOH A 18 318 54 HOH HOH . 
E 3 HOH A 19 319 20 HOH HOH . 
E 3 HOH A 20 320 48 HOH HOH . 
E 3 HOH A 21 321 16 HOH HOH . 
E 3 HOH A 22 322 46 HOH HOH . 
E 3 HOH A 23 323 32 HOH HOH . 
E 3 HOH A 24 324 62 HOH HOH . 
E 3 HOH A 25 325 25 HOH HOH . 
E 3 HOH A 26 326 11 HOH HOH . 
E 3 HOH A 27 327 67 HOH HOH . 
E 3 HOH A 28 328 68 HOH HOH . 
E 3 HOH A 29 329 55 HOH HOH . 
E 3 HOH A 30 330 42 HOH HOH . 
E 3 HOH A 31 331 65 HOH HOH . 
E 3 HOH A 32 332 38 HOH HOH . 
E 3 HOH A 33 333 49 HOH HOH . 
E 3 HOH A 34 334 57 HOH HOH . 
E 3 HOH A 35 335 27 HOH HOH . 
E 3 HOH A 36 336 36 HOH HOH . 
E 3 HOH A 37 337 64 HOH HOH . 
E 3 HOH A 38 338 24 HOH HOH . 
E 3 HOH A 39 339 31 HOH HOH . 
E 3 HOH A 40 340 72 HOH HOH . 
E 3 HOH A 41 341 47 HOH HOH . 
F 3 HOH B 1 301 17 HOH HOH . 
F 3 HOH B 2 302 53 HOH HOH . 
F 3 HOH B 3 303 12 HOH HOH . 
F 3 HOH B 4 304 8 HOH HOH . 
F 3 HOH B 5 305 43 HOH HOH . 
F 3 HOH B 6 306 52 HOH HOH . 
F 3 HOH B 7 307 30 HOH HOH . 
F 3 HOH B 8 308 2 HOH HOH . 
F 3 HOH B 9 309 33 HOH HOH . 
F 3 HOH B 10 310 13 HOH HOH . 
F 3 HOH B 11 311 58 HOH HOH . 
F 3 HOH B 12 312 59 HOH HOH . 
F 3 HOH B 13 313 18 HOH HOH . 
F 3 HOH B 14 314 28 HOH HOH . 
F 3 HOH B 15 315 60 HOH HOH . 
F 3 HOH B 16 316 74 HOH HOH . 
F 3 HOH B 17 317 26 HOH HOH . 
F 3 HOH B 18 318 45 HOH HOH . 
F 3 HOH B 19 319 23 HOH HOH . 
F 3 HOH B 20 320 22 HOH HOH . 
F 3 HOH B 21 321 71 HOH HOH . 
F 3 HOH B 22 322 19 HOH HOH . 
F 3 HOH B 23 323 41 HOH HOH . 
F 3 HOH B 24 324 39 HOH HOH . 
F 3 HOH B 25 325 61 HOH HOH . 
F 3 HOH B 26 326 44 HOH HOH . 
F 3 HOH B 27 327 40 HOH HOH . 
F 3 HOH B 28 328 50 HOH HOH . 
F 3 HOH B 29 329 34 HOH HOH . 
F 3 HOH B 30 330 66 HOH HOH . 
F 3 HOH B 31 331 37 HOH HOH . 
F 3 HOH B 32 332 63 HOH HOH . 
F 3 HOH B 33 333 73 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 2 -24.402 -7.005 -5.772 1 28.75 ? PB GDP 200 B 1 
HETATM 2 O O1B GDP . . . D 2 -24.436 -5.584 -6.224 1 28.14 ? O1B GDP 200 B 1 
HETATM 3 O O2B GDP . . . D 2 -25.746 -7.674 -5.789 1 27.85 ? O2B GDP 200 B 1 
HETATM 4 O O3B GDP . . . D 2 -23.731 -7.176 -4.426 1 23.71 ? O3B GDP 200 B 1 
HETATM 5 O O3A GDP . . . D 2 -23.513 -7.743 -6.867 1 28.9 ? O3A GDP 200 B 1 
HETATM 6 P PA GDP . . . D 2 -22.229 -8.682 -6.89 1 30.41 ? PA GDP 200 B 1 
HETATM 7 O O1A GDP . . . D 2 -21.025 -7.907 -6.369 1 29.27 ? O1A GDP 200 B 1 
HETATM 8 O O2A GDP . . . D 2 -22.501 -9.908 -6.126 1 26.5 ? O2A GDP 200 B 1 
HETATM 9 O O5' GDP . . . D 2 -22.067 -8.959 -8.463 1 30.43 ? O5' GDP 200 B 1 
HETATM 10 C C5' GDP . . . D 2 -22.935 -9.854 -9.197 1 29.34 ? C5' GDP 200 B 1 
HETATM 11 C C4' GDP . . . D 2 -22.13 -10.56 -10.261 1 29.59 ? C4' GDP 200 B 1 
HETATM 12 O O4' GDP . . . D 2 -21.498 -9.584 -11.123 1 29.66 ? O4' GDP 200 B 1 
HETATM 13 C C3' GDP . . . D 2 -21.01 -11.476 -9.758 1 31.04 ? C3' GDP 200 B 1 
HETATM 14 O O3' GDP . . . D 2 -20.934 -12.649 -10.554 1 32.79 ? O3' GDP 200 B 1 
HETATM 15 C C2' GDP . . . D 2 -19.763 -10.602 -9.914 1 28.73 ? C2' GDP 200 B 1 
HETATM 16 O O2' GDP . . . D 2 -18.524 -11.288 -10.044 1 31.39 ? O2' GDP 200 B 1 
HETATM 17 C C1' GDP . . . D 2 -20.109 -9.847 -11.191 1 29.77 ? C1' GDP 200 B 1 
HETATM 18 N N9 GDP . . . D 2 -19.399 -8.571 -11.327 1 27.2 ? N9 GDP 200 B 1 
HETATM 19 C C8 GDP . . . D 2 -19.295 -7.555 -10.409 1 24.09 ? C8 GDP 200 B 1 
HETATM 20 N N7 GDP . . . D 2 -18.597 -6.534 -10.84 1 24.96 ? N7 GDP 200 B 1 
HETATM 21 C C5 GDP . . . D 2 -18.212 -6.9 -12.121 1 27.56 ? C5 GDP 200 B 1 
HETATM 22 C C6 GDP . . . D 2 -17.425 -6.211 -13.106 1 28.09 ? C6 GDP 200 B 1 
HETATM 23 O O6 GDP . . . D 2 -16.87 -5.124 -12.973 1 27.3 ? O6 GDP 200 B 1 
HETATM 24 N N1 GDP . . . D 2 -17.296 -6.94 -14.277 1 25.37 ? N1 GDP 200 B 1 
HETATM 25 C C2 GDP . . . D 2 -17.825 -8.196 -14.489 1 28.05 ? C2 GDP 200 B 1 
HETATM 26 N N2 GDP . . . D 2 -17.623 -8.748 -15.687 1 28.6 ? N2 GDP 200 B 1 
HETATM 27 N N3 GDP . . . D 2 -18.534 -8.858 -13.576 1 25.07 ? N3 GDP 200 B 1 
HETATM 28 C C4 GDP . . . D 2 -18.701 -8.156 -12.433 1 26.19 ? C4 GDP 200 B 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           28 
#