data_6YVP
#
_model_server_result.job_id            U7_EIK6qbmduJXWvGkkEIw 
_model_server_result.datetime_utc      '2024-11-18 21:46:38' 
_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          6yvp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    6YVP 
#
_exptl.entry_id    6YVP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              347.221 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" 
_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          103.034 
_cell.angle_gamma         90 
_cell.entry_id            6YVP 
_cell.length_a            71.649 
_cell.length_b            36.531 
_cell.length_c            86.887 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YVP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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,C,E 1 1,2 
B,D,F 2 1,3 
#
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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -19.595557 0 84.648478 
#
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 H14 N5 O7 P' 
_chem_comp.formula_weight    347.221 
_chem_comp.id                DGP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
P OP1 DGP doub 83 n n 
P OP2 DGP sing 84 n n 
P OP3 DGP sing 85 n n 
P O5' DGP sing 86 n n 
OP2 HOP2 DGP sing 87 n n 
OP3 HOP3 DGP sing 88 n n 
O5' C5' DGP sing 89 n n 
C5' C4' DGP sing 90 n n 
C5' H5' DGP sing 91 n n 
C5' "H5''" DGP sing 92 n n 
C4' O4' DGP sing 93 n n 
C4' C3' DGP sing 94 n n 
C4' H4' DGP sing 95 n n 
O4' C1' DGP sing 96 n n 
C3' O3' DGP sing 97 n n 
C3' C2' DGP sing 98 n n 
C3' H3' DGP sing 99 n n 
O3' HO3' DGP sing 100 n n 
C2' C1' DGP sing 101 n n 
C2' H2' DGP sing 102 n n 
C2' "H2''" DGP sing 103 n n 
C1' N9 DGP sing 104 n n 
C1' H1' DGP sing 105 n n 
N9 C8 DGP sing 106 n y 
N9 C4 DGP sing 107 n y 
C8 N7 DGP doub 108 n y 
C8 H8 DGP sing 109 n n 
N7 C5 DGP sing 110 n y 
C5 C6 DGP sing 111 n n 
C5 C4 DGP doub 112 n y 
C6 O6 DGP doub 113 n n 
C6 N1 DGP sing 114 n n 
N1 C2 DGP sing 115 n n 
N1 HN1 DGP sing 116 n n 
C2 N2 DGP sing 117 n n 
C2 N3 DGP doub 118 n n 
N2 HN21 DGP sing 119 n n 
N2 HN22 DGP sing 120 n n 
N3 C4 DGP sing 121 n n 
#
_atom_sites.entry_id                     6YVP 
_atom_sites.fract_transf_matrix[1][1]    0.013957 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003231 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.027374 
_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]    0.011814 
_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 DGP AAA 1 201 201 DGP DGP . 
D 2 DGP BBB 1 201 201 DGP DGP . 
E 3 HOH AAA 1 301 2 HOH HOH . 
E 3 HOH AAA 2 302 27 HOH HOH . 
E 3 HOH AAA 3 303 9 HOH HOH . 
E 3 HOH AAA 4 304 98 HOH HOH . 
E 3 HOH AAA 5 305 118 HOH HOH . 
E 3 HOH AAA 6 306 5 HOH HOH . 
E 3 HOH AAA 7 307 1 HOH HOH . 
E 3 HOH AAA 8 308 8 HOH HOH . 
E 3 HOH AAA 9 309 58 HOH HOH . 
E 3 HOH AAA 10 310 23 HOH HOH . 
E 3 HOH AAA 11 311 6 HOH HOH . 
E 3 HOH AAA 12 312 4 HOH HOH . 
E 3 HOH AAA 13 313 24 HOH HOH . 
E 3 HOH AAA 14 314 65 HOH HOH . 
E 3 HOH AAA 15 315 7 HOH HOH . 
E 3 HOH AAA 16 316 66 HOH HOH . 
E 3 HOH AAA 17 317 57 HOH HOH . 
E 3 HOH AAA 18 318 103 HOH HOH . 
E 3 HOH AAA 19 319 19 HOH HOH . 
E 3 HOH AAA 20 320 111 HOH HOH . 
E 3 HOH AAA 21 321 84 HOH HOH . 
E 3 HOH AAA 22 322 20 HOH HOH . 
E 3 HOH AAA 23 323 94 HOH HOH . 
E 3 HOH AAA 24 324 99 HOH HOH . 
E 3 HOH AAA 25 325 100 HOH HOH . 
E 3 HOH AAA 26 326 97 HOH HOH . 
E 3 HOH AAA 27 327 92 HOH HOH . 
E 3 HOH AAA 28 328 95 HOH HOH . 
E 3 HOH AAA 29 329 59 HOH HOH . 
E 3 HOH AAA 30 330 112 HOH HOH . 
E 3 HOH AAA 31 331 90 HOH HOH . 
E 3 HOH AAA 32 332 88 HOH HOH . 
E 3 HOH AAA 33 333 63 HOH HOH . 
E 3 HOH AAA 34 334 87 HOH HOH . 
E 3 HOH AAA 35 335 18 HOH HOH . 
E 3 HOH AAA 36 336 104 HOH HOH . 
E 3 HOH AAA 37 337 60 HOH HOH . 
E 3 HOH AAA 38 338 22 HOH HOH . 
E 3 HOH AAA 39 339 106 HOH HOH . 
E 3 HOH AAA 40 340 93 HOH HOH . 
E 3 HOH AAA 41 341 101 HOH HOH . 
E 3 HOH AAA 42 342 105 HOH HOH . 
E 3 HOH AAA 43 343 89 HOH HOH . 
E 3 HOH AAA 44 344 21 HOH HOH . 
E 3 HOH AAA 45 345 62 HOH HOH . 
E 3 HOH AAA 46 346 68 HOH HOH . 
E 3 HOH AAA 47 347 86 HOH HOH . 
E 3 HOH AAA 48 348 64 HOH HOH . 
E 3 HOH AAA 49 349 96 HOH HOH . 
E 3 HOH AAA 50 350 91 HOH HOH . 
E 3 HOH AAA 51 351 61 HOH HOH . 
E 3 HOH AAA 52 352 56 HOH HOH . 
E 3 HOH AAA 53 353 67 HOH HOH . 
E 3 HOH AAA 54 354 107 HOH HOH . 
E 3 HOH AAA 55 355 117 HOH HOH . 
E 3 HOH AAA 56 356 36 HOH HOH . 
E 3 HOH AAA 57 357 83 HOH HOH . 
F 3 HOH BBB 1 301 14 HOH HOH . 
F 3 HOH BBB 2 302 71 HOH HOH . 
F 3 HOH BBB 3 303 12 HOH HOH . 
F 3 HOH BBB 4 304 52 HOH HOH . 
F 3 HOH BBB 5 305 13 HOH HOH . 
F 3 HOH BBB 6 306 48 HOH HOH . 
F 3 HOH BBB 7 307 79 HOH HOH . 
F 3 HOH BBB 8 308 82 HOH HOH . 
F 3 HOH BBB 9 309 16 HOH HOH . 
F 3 HOH BBB 10 310 109 HOH HOH . 
F 3 HOH BBB 11 311 10 HOH HOH . 
F 3 HOH BBB 12 312 114 HOH HOH . 
F 3 HOH BBB 13 313 43 HOH HOH . 
F 3 HOH BBB 14 314 11 HOH HOH . 
F 3 HOH BBB 15 315 17 HOH HOH . 
F 3 HOH BBB 16 316 15 HOH HOH . 
F 3 HOH BBB 17 317 28 HOH HOH . 
F 3 HOH BBB 18 318 33 HOH HOH . 
F 3 HOH BBB 19 319 41 HOH HOH . 
F 3 HOH BBB 20 320 32 HOH HOH . 
F 3 HOH BBB 21 321 47 HOH HOH . 
F 3 HOH BBB 22 322 69 HOH HOH . 
F 3 HOH BBB 23 323 73 HOH HOH . 
F 3 HOH BBB 24 324 49 HOH HOH . 
F 3 HOH BBB 25 325 51 HOH HOH . 
F 3 HOH BBB 26 326 116 HOH HOH . 
F 3 HOH BBB 27 327 26 HOH HOH . 
F 3 HOH BBB 28 328 115 HOH HOH . 
F 3 HOH BBB 29 329 76 HOH HOH . 
F 3 HOH BBB 30 330 72 HOH HOH . 
F 3 HOH BBB 31 331 70 HOH HOH . 
F 3 HOH BBB 32 332 75 HOH HOH . 
F 3 HOH BBB 33 333 53 HOH HOH . 
F 3 HOH BBB 34 334 46 HOH HOH . 
F 3 HOH BBB 35 335 45 HOH HOH . 
F 3 HOH BBB 36 336 113 HOH HOH . 
F 3 HOH BBB 37 337 77 HOH HOH . 
F 3 HOH BBB 38 338 29 HOH HOH . 
F 3 HOH BBB 39 339 34 HOH HOH . 
F 3 HOH BBB 40 340 42 HOH HOH . 
F 3 HOH BBB 41 341 39 HOH HOH . 
F 3 HOH BBB 42 342 44 HOH HOH . 
F 3 HOH BBB 43 343 55 HOH HOH . 
F 3 HOH BBB 44 344 78 HOH HOH . 
F 3 HOH BBB 45 345 102 HOH HOH . 
F 3 HOH BBB 46 346 50 HOH HOH . 
F 3 HOH BBB 47 347 37 HOH HOH . 
F 3 HOH BBB 48 348 81 HOH HOH . 
F 3 HOH BBB 49 349 25 HOH HOH . 
F 3 HOH BBB 50 350 85 HOH HOH . 
F 3 HOH BBB 51 351 38 HOH HOH . 
F 3 HOH BBB 52 352 80 HOH HOH . 
F 3 HOH BBB 53 353 54 HOH HOH . 
F 3 HOH BBB 54 354 40 HOH HOH . 
F 3 HOH BBB 55 355 74 HOH HOH . 
F 3 HOH BBB 56 356 110 HOH HOH . 
F 3 HOH BBB 57 357 3 HOH HOH . 
F 3 HOH BBB 58 358 108 HOH HOH . 
F 3 HOH BBB 59 359 30 HOH HOH . 
F 3 HOH BBB 60 360 35 HOH HOH . 
F 3 HOH BBB 61 361 31 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 P DGP . . . C 2 -0.388 0.824 11.056 1 66.41 ? P DGP 201 AAA 1 
HETATM 2 O OP1 DGP . . . C 2 -0.674 1.274 9.637 1 66.92 ? OP1 DGP 201 AAA 1 
HETATM 3 O OP2 DGP . . . C 2 -0.87 -0.584 11.334 1 62.69 ? OP2 DGP 201 AAA 1 
HETATM 4 O OP3 DGP . . . C 2 -0.81 1.839 12.099 1 66.3 ? OP3 DGP 201 AAA 1 
HETATM 5 O O5' DGP . . . C 2 1.231 0.73 11.195 1 61.8 ? O5' DGP 201 AAA 1 
HETATM 6 C C5' DGP . . . C 2 1.968 0.954 12.415 1 58.93 ? C5' DGP 201 AAA 1 
HETATM 7 C C4' DGP . . . C 2 3.473 0.652 12.26 1 56.79 ? C4' DGP 201 AAA 1 
HETATM 8 O O4' DGP . . . C 2 4.2 1.179 13.383 1 52.68 ? O4' DGP 201 AAA 1 
HETATM 9 C C3' DGP . . . C 2 3.832 -0.844 12.186 1 56.31 ? C3' DGP 201 AAA 1 
HETATM 10 O O3' DGP . . . C 2 4.463 -1.218 10.951 1 58.25 ? O3' DGP 201 AAA 1 
HETATM 11 C C2' DGP . . . C 2 4.812 -1.115 13.307 1 53.05 ? C2' DGP 201 AAA 1 
HETATM 12 C C1' DGP . . . C 2 5.251 0.273 13.727 1 51.7 ? C1' DGP 201 AAA 1 
HETATM 13 N N9 DGP . . . C 2 5.575 0.288 15.169 1 49.8 ? N9 DGP 201 AAA 1 
HETATM 14 C C8 DGP . . . C 2 4.793 -0.02 16.222 1 47.94 ? C8 DGP 201 AAA 1 
HETATM 15 N N7 DGP . . . C 2 5.5 0.112 17.376 1 48.57 ? N7 DGP 201 AAA 1 
HETATM 16 C C5 DGP . . . C 2 6.761 0.508 17.063 1 49.27 ? C5 DGP 201 AAA 1 
HETATM 17 C C6 DGP . . . C 2 8.042 0.85 17.764 1 48.45 ? C6 DGP 201 AAA 1 
HETATM 18 O O6 DGP . . . C 2 8.165 0.813 19.013 1 43.19 ? O6 DGP 201 AAA 1 
HETATM 19 N N1 DGP . . . C 2 9.094 1.215 16.996 1 50.97 ? N1 DGP 201 AAA 1 
HETATM 20 C C2 DGP . . . C 2 9.027 1.286 15.641 1 48.92 ? C2 DGP 201 AAA 1 
HETATM 21 N N2 DGP . . . C 2 10.109 1.653 14.915 1 47.52 ? N2 DGP 201 AAA 1 
HETATM 22 N N3 DGP . . . C 2 7.905 0.985 14.958 1 48.07 ? N3 DGP 201 AAA 1 
HETATM 23 C C4 DGP . . . C 2 6.78 0.609 15.597 1 48.76 ? C4 DGP 201 AAA 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           226 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           23 
#